http://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=LaHeyer 2026-05-17T19:09:36Z User contributions MediaWiki 1.28.2 http://gcat.davidson.edu/GcatWiki/index.php?title=Bio-Math_Connections_January_-_May_2010&diff=11211 2010-01-22T21:15:30Z

<p>LaHeyer: </p> <hr /> <div>Write in which project you will present, your name, and which campus you represent. For example:<br /> <br /> * MOWestern/Davidson 2009 project:: Malcolm Campbell:: Davidson<br /> * Cambridge 2009 project:: Michael Rydberg, Nitya Rao, Erin Feeney:: Davidson</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Missouri_Western/Davidson_iGEM2009&diff=7682 2009-04-03T19:48:10Z

<p>LaHeyer: </p> <hr /> <div>This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.<br /> <br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] &lt;br&gt;<br /> [http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-along Freezer Stocks]&lt;br&gt;<br /> <br /> <br /> We need to learn more about these topics:<br /> &lt;center&gt;'''Biology-based'''&lt;/center&gt;<br /> #[[What is msDNA?]]<br /> #[[How is msDNA normally produced?]]<br /> #[[How is msDNA stored in E. coli?]] <br /> #[[How many copies are carried per cell?]] <br /> #[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]]<br /> #[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]]<br /> #[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]<br /> #[[Can we solve a 3-SAT problem with supressor logic?]]<br /> #[[What role can physical modeling of protein structure play in our project?]]<br /> <br /> <br /> <br /> &lt;center&gt;'''Math-based'''&lt;/center&gt;<br /> #What interesting challenges or problems does origami offer?<br /> #Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?<br /> #What has been done before and how can we improve upon that?<br /> #We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).<br /> #Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?<br /> #How has 3SAT been addressed with a DNA computer? Can we use those methods?<br /> #Can we get bacteria to solve a problem large enough to challenge a person?<br /> #Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?<br /> <br /> <br /> &lt;center&gt;'''Behavior-based'''&lt;/center&gt;<br /> #[[What constructs are we testing?]]<br /> #[[What school districts do we have access to?]]<br /> #[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]<br /> #[[Do you need any more input from the veterans before the survey is ready?]]</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Halorhabdus_utahensis_Genome&diff=7106 2008-11-04T16:22:22Z

<p>LaHeyer: /* Pathway Tutorials */</p> <hr /> <div>This page will be used by Davidson College students in the [http://www.bio.davidson.edu/Courses/Bio343/LabMethods.html Genomics Laboratory course].<br /> __NOTOC__<br /> == Links to Multiple Databases ==<br /> *[http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&amp;page=taxonDetail&amp;taxon_oid=2500575004 JGI IMG EDU] &lt;br&gt; public access &lt;br&gt; *[[Media:JGIAnnotation.xls|JGI Annotation Excel Spreadsheet]]<br /> *[http://www.tigr.org/tigr-scripts/prok_manatee/shared/login.cgi Manatee at JCVI] &lt;br&gt; use the davidson number sent by email as username and password (database is nthu01 - this is case sensitive) &lt;br&gt; *[[Media:ManateeAnnotation.xls|Manatee Annotation Excel Spreadsheet]]<br /> *[http://rast.nmpdr.org/ SEED view via RAST] &lt;br&gt; use the username and password combination sent to you by SEED &lt;br&gt; *[[Media:RastAnnotation.xls|RAST Annotation Excel Spreadsheet]]&lt;br&gt; *[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=18261238 RAST Publication in PubMed]<br /> *[http://www.genome.jp/kegg/kaas/ KEGG]&lt;br&gt; We can submit our genes to KEGG to have it mapped out, but SEED and Manatee may already do this. Do we want to ask them to upload it into their database? &lt;br&gt;<br /> *[http://wishart.biology.ualberta.ca/basys/cache/135af8726ad6f61ec4c5f1e9c4d139ac/index.html BASYs]&lt;br&gt;&lt;br&gt;<br /> *[http://gcat.davidson.edu/Registry/compare/ Pairwise comparisons of All Three Annotations]<br /> <br /> <br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI_5contigs.txt JGI Full genome, 5 separate contigs &amp; 3.1 Mbp, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.txt JGI gene DNA sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.xls JGI gene annotations, Excel] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_proteins.txt JGI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_merged.txt CJVI Full genome, 5 contigs fused, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_ORFs.txt CJVI gene sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_proteins.txt CJVI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/GeneLengths.xls 3-way comparison, Excel] &lt;br&gt;<br /> [[Venn_diagrams]] Venn diagram of 3-way comparison<br /> <br /> &lt;br&gt;<br /> <br /> == RNA Genes ==<br /> <br /> *[[tRNA Genes Check List]]&lt;br&gt;<br /> *[[rRNA operon]]&lt;br&gt;<br /> *[[2 misc. RNA genes]] (short summary list)&lt;br&gt;<br /> *[[Missing tRNA-trp gene found]]&lt;br&gt;<br /> <br /> == Other Resources ==<br /> *[[Consensus Shine Dalgarno]] Excel File for ''H. utahensis'' &lt;br&gt;<br /> *[[References]]&lt;br&gt;<br /> *[[Gene Annotation Template]]&lt;br&gt;<br /> *[[General Questions]]&lt;br&gt;<br /> *[[Page for Annotated Genes]]&lt;br&gt;<br /> *[http://www.bio.davidson.edu/courses/genomics/2008/Win/ec/ Search EC number in RAST, JGI or Manatee] &lt;br&gt;<br /> *[http://gcat.davidson.edu/Wideloache/Webfiles/ecNumBlast.html Blast an EC number against the H. utahensis genome]&lt;br&gt;<br /> <br /> == Research Questions ==<br /> #How do the three systems compare for finding ORFs and RNA genes?<br /> #Is there a pattern of missed genes for any of the 3 sites? <br /> #Do the three systems differ in their ability to find good start codons and Shine-Dalgarno sequences? [We need a standard set of genes for comparison. Only highly conserved or a range of genes?]<br /> # Were Shine-Dalgarno sequences calculated for our species or default values used? If default, what sequence?<br /> #Can we fill any holes in their automated annotation? Is there a mechanism for users to add in genes?<br /> #How do the 3 sites compare for ease of use?<br /> #What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working?<br /> #How does each of the 3 sites compare for pathway detection and visualization? <br /> #Do they find the origin of replication? Can we find it? <br /> <br /> * How do the 3 systems compare when one gene is called hypothetical and the other calls it a functional protein? How can they vary and who is getting it closer to correct (however you define that, possibly by date of matched entry: Pallavi and Mary)<br /> * Why did one system call a gene when the other two did not? (Matt and Lara)<br /> * How do the 3 sites compare for ease of use? What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working? (Samantha and Nick)<br /> * Where is the origin of replication and did the 3 systems attempt to identify this?<br /> * Did the 3 systems utilize Shine-Dalgarno sequences to help them call start codons? Did they utilize our species's consensus Shine-Dalgarno? (Peter)<br /> * We need to fill in the [[Venn diagrams]] for our 3-way comparison. Let's compare the size of ORFs and generate a [[Gene Length Histograms|graph comparing the distributions]] for all 3. (Max and Will - they also take requests). <br /> <br /> &lt;hr&gt;<br /> =Our Favorites=<br /> == My favorite genes==<br /> Pallavi - Monooxygenase vs. Peroxiredoxin<br /> <br /> Mary - JGI gene 2500588521 (922976...924046) [[Media:My favorite gene.ppt]]<br /> <br /> Max - [http://app.sliderocket.com/app/FullPlayer.aspx?id=f2058b94-845f-4a11-94eb-142f251a7fea JGI gene 2500587636 (2-1849)]<br /> <br /> Samantha - JGI gene 2500575882 (80504-80878) [[Media:Earl.ppt]]<br /> <br /> Nick - JGI gene 2300587691 (69942...72866) [[Media:Gene presentation.ppt]]<br /> <br /> Will - JGI gene 2500590430 (2847205..2854335)<br /> <br /> Jay - JGI gene 2500588397 (806410..807321) [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Fav_Gene/FavoriteGenePresentation.pptx Co/Zn/Cd PowerPoint]<br /> <br /> Matt - Transcriptional Regulator nrdR (3109722..3110204 + 7274..7765)<br /> <br /> Peter - tRNA intron endonuclease [[Media:TRNAtrpintronendonuclease.ppt]]<br /> <br /> Laura - 16S Small ribosomal subunit, JGI gene 2500590728 (2397347..2398825)<br /> <br /> == My Favorite Pathways==<br /> Pallavi - Carbohydrate Metabolism<br /> <br /> Jay - Membrane Transport<br /> <br /> Will - Signal Transduction<br /> <br /> Max -energy<br /> <br /> ''Suggestions by Kjeld''&lt;br&gt;<br /> '''[[Cellulase]]''' by Pallavi&lt;br&gt;<br /> I think it would be very interesting to look for genes involved in cellulose degradation: endocellulases, exocellolases (=cellobiohydrolases) and b-glucosidases.<br /> Many cellulose degrades produce a range of each type. A cellolulyic system able to function at 4.6 M of NaCl is an interesting one. We either did not observed (or look for cellulose degradation). However, these systems are normally inducible and you need to test several substrates and inducers. It would be nice to have a compilation of putative “cellulase” genes.<br /> There are several good recent reviews on cellulases (also mentioning E.C. numbers and enzyme families) that your students could consult.<br /> <br /> '''[[Chitinase]]''' by Matt&lt;br&gt;<br /> Apparently you detected a chitinase but according to our records it does not gorw on N-acetyl-glucosamine which is somewhat strange. It grows on glucose though. <br /> <br /> '''[[Lipases]]''' by Mary&lt;br&gt;<br /> Lipases (/esterases) would also be interesting to look for – some lipases have important industrial applications.<br /> <br /> '''[[Amylases]]''' by Samantha&lt;br&gt;<br /> We did not observed growth on starch. Did you find any “amylase-coding genes”?<br /> <br /> '''[[Xylose (glucose) isomerase)]]''' by Nick&lt;br&gt;<br /> An enzyme of great commercial value. <br /> <br /> '''[[Amino acids]]''' lead by Laura and assisted by Max, Jay, Nick and Samantha&lt;br&gt;<br /> According to our records AX-2 is able to grow in a “defined medium”. This is at variance with your “holes” for synthesis of amino acids. However, there could have been some “carry over” of amino acids when inoculating a culture grown in complex medium (e.g. containing yeast extract). However, we are normally aware of this problem and do repeated culturing to dilute out potential growth factors present in yeast extract.<br /> <br /> '''[[Proteases]]''' by Peter&lt;br&gt;<br /> We did not detect protease activity – albeit only checking a few substrates.<br /> <br /> '''[[Protein Export]]''' by Malcolm &lt;br&gt;<br /> We need to know how these proteins might reach outside the cell which is where the food would be and thus the digestive enzymes or importers need to reach the outside world or the cell membrane.<br /> <br /> = Student-created tutorials: =<br /> == Tutorials for Annotating Genomes ==<br /> <br /> # Will DeLoache - [http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/BioPerlTutorial/BioPerl.htm BioPerl Installation] &lt;br&gt;<br /> # Max Win - [http://www.bio.davidson.edu/courses/genomics/2008/Win/perl.html Introduction to Perl for non-programmers.(with step by step explanations,simple exercises and solutions)]&lt;br&gt;<br /> # Pallavi - Conserved Domains Database (CDD) [[Media:CDDtutorial.doc]] &lt;br&gt;<br /> # Mary - Protein Data Bank (PDB) [[Media:PDB Tutorial.doc]] &lt;br&gt;<br /> # Laura Voss - Pfam Database [http://www.bio.davidson.edu/Courses/Bio343/Pfam_tutorial.doc Pfam Tutorial] &lt;br&gt;<br /> # Samantha Simpson - [http://www.bio.davidson.edu/courses/genomics/2008/Simpson/Tutorial.html NCBI BLAST]&lt;br&gt;<br /> # Peter Bakke - [[Media:ShineDalgarnoTutorial.doc]]&lt;br&gt;<br /> # Jay McNair - [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Origin_Tutorial/OriginTutorial.doc Origin of Replication Tutorial]&lt;br&gt;<br /> # Nick Carney - Navigating the JGI Database [[Media:NavigatingJGItutorial.doc]]&lt;br&gt;<br /> # Matt Lotz - SEED Viewer - [[Media:SEEDTutorial.doc]] &lt;br&gt;<br /> == Pathway Tutorials==<br /> [http://www.pathguide.org/ Pathguide] - a possible source of tutorials and extensive information<br /> <br /> [http://www.bigre.ulb.ac.be/Users/didier/pathfinding/ Shortest Path Tool]<br /> <br /> *Pallavi: I will compare RAST and KEGG in pathway annotations and use Glycolysis/Gluconeogenesis as my example<br /> <br /> &lt;hr&gt;<br /> <br /> =Glossary words (A - Z):=<br /> [[#A| A ]] [[#B| B ]] [[#C| C ]] [[#D| D ]] [[#E| E ]] [[#F| F ]] [[#G| G ]] [[#H| H ]] [[#I| I ]] [[#J| J ]] [[#K| K ]] [[#L| L ]] [[#M| M ]] [[#N| N ]] [[#O| O ]] [[#P| P ]] [[#Q| Q ]] [[#R| R ]] [[#S| S ]] [[#T| T ]] [[#U| U ]] [[#V| V ]] [[#W| W ]] [[#X| X ]] [[#Y| Y ]] [[#Z| Z ]] <br /> <br /> == A ==<br /> '''Accession Number''' - a unique identifier given to DNA and protein sequences to allow for tracking of sequence information within a single database [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics)] (Will).<br /> <br /> '''Antisense (RNA or DNA)'''-a piece of DNA or RNA that binds to a complementary sequence of DNA or RNA. These segments of genetic material can be used to identify the existence of a disease gene and they can also be used to bind to specific DNA or mRNA sequences to inhibit their function ([http://biotech.fyicenter.com/glossary/Bioinformatics_Glossary.html 5] Pallavi).<br /> <br /> '''&lt;i&gt;Arabidopsis thaliana&lt;/i&gt;''' - the scientific name for the thale cress plant; it was the first plant to have its genome sequenced, and is a model organism for understanding plant biology and genetics ([http://en.wikipedia.org/wiki/Thale_cress Wikipedia.org], Jay)<br /> <br /> == B ==<br /> '''BAC''' - &lt;i&gt;b&lt;/i&gt;acterial &lt;i&gt;a&lt;/i&gt;rticifical &lt;i&gt;c&lt;/i&gt;hromosome, a DNA construct used for transforming or cloning segments of DNA and often used to sequence the genetic code of organisms ([http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome Wikipedia.org], Jay)<br /> <br /> '''bioinformatics''' - the multi-disciplinary approach of using biology, computer science and mathematics to solve or better understand biological problems [http://en.wikipedia.org/wiki/Bioinformatics] (Matt)<br /> <br /> '''BLAST''' - (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. [http://blast.ncbi.nlm.nih.gov/Blast.cgi] (Mary)<br /> <br /> '''bioperl'''- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications such as accessing sequence data from local and remote databases, transforming formats of database, manipulating individual sequences, searching for similar sequences, searching for genes and other structures on genomic DNA, or developing a machine readable sequence annotations. [http://en.wikipedia.org/wiki/BioPerl] (Wikipedia, Max Win)<br /> <br /> == C ==<br /> '''carbon fixation''' - using carbon dioxide to create organic materials [http://en.wikipedia.org/wiki/Carbon_fixation] (Samantha)&lt;BR&gt;<br /> <br /> '''CDD''' (Conserved Domains Database)- a database used to identify the conserved domains present in a protein query sequence [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml] (Mary)<br /> <br /> '''chaperonin''' - a protein complex that assists some newly formed polypeptide chains by folding them into their final, functional, three-dimensional form [http://en.wikipedia.org/wiki/Chaperonins] (Matt)<br /> <br /> '''chemotaxis''' - the process in which cells will seek out or flee from a high concentration of certain chemicals and is found in both uni- and multicellular organisms. This process is used to avoid toxins or find food in unicelllular organisms or tasks such as reproduction in multicellular organisms [http://en.wikipedia.org/wiki/Chemotaxis] (Nick)<br /> <br /> '''chemotaxonomy''' - the attempt to classify and identify organisms according to demonstrable differences and similarities in their biochemical compositions [http://en.wikipedia.org/wiki/Chemotaxonomy] (Mary)<br /> <br /> '''ClustalW''' - A web-based or command line tool that performs multiple sequence alignments to determine evolutionary relationships between three or more sequences [http://en.wikipedia.org/wiki/Clustal] (Will).<br /> <br /> '''COG''' (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs ([http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml COG] Pallavi) &lt;br&gt;<br /> <br /> '''concatemer''' - long continuous DNA molecule that contains the same DNA sequence repeated in series [http://en.wikipedia.org/wiki/Concatemer](Samantha)&lt;BR&gt;<br /> <br /> '''contigs''' (contiguous DNA)- overlapping DNA segments that as a collection from a longer and gapless segment of DNA. (Discovery Genomics, Proteomics and Bioinformatics [http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''coverage''' - refers to the number of times, on average, any piece of DNA in a sequenced genome has been individually sequenced (Lecture, Jay)<br /> <br /> '''CPAN (Comprehensive Perl Archive Network)''' - an archive of over 12,200 modules of software written in Perl, as well as documentation for it. It contains a module called CPAN (or CPAN.pm) which is used as an installer for Perl modules such as BioPerl [http://en.wikipedia.org/wiki/CPAN](Will).<br /> <br /> '''Cytogenetics'''-the study of normal and abnormal chromosomes. This involves studying the causes of chromosomal abnormalities and looking at the structure of chromosomes ([http://www.vivo.colostate.edu/hbooks/genetics/medgen/chromo/index.html 7] Pallavi).<br /> <br /> == D ==<br /> '''''de novo'' synthesis''' - the synthesis of complex molecules from simple molecules (e.g. sugars and nucleotides), rather than from recycled molecules; from the latin &quot;of the new&quot; [http://en.wikipedia.org/wiki/De_novo_synthesis] (Matt)<br /> <br /> '''dehydrogenase''' - a type of enzyme that oxidizes a substrate by transferring one or more protons and a pair of electrons to an acceptor. [http://en.wikipedia.org/wiki/Dehydrogenase] (Peter)<br /> <br /> '''diatom''' - a major group of eukaryotic algae, and one of the most common types of phytoplankton. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica called a frustule. These frustules show a wide diversity in form, but usually consist of two asymmetrical sides with a split between them. [http://en.wikipedia.org/wiki/Diatom] (Mary)<br /> <br /> '''domain (protein)''' - the structural and functional groups of a protein, which can exist independently of the protein itself. Domains typically perform a specific function, such as binding to promoters or substrates, and many proteins can have one or several domains in common. Evolutionarily-linked proteins are more likely to have domains in common. Domains are used to organize proteins into families. ([http://en.wikipedia.org/wiki/Domain_(protein) Wikipedia article], Laura)<br /> <br /> '''dot plot'''-graphical display comparing sequence conservation between two genomes with dots indicating strings of identical bases. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> == E ==<br /> <br /> '''EC number''' (Enzyme Commission Number)- a numerical classification scheme for enzymes, based on the chemical reactions they catalyze [http://en.wikipedia.org/wiki/EC_number] (Mary)<br /> <br /> '''E-value''' (Expect value)- When performing a BLAST search, you will obtain an E-value for each sequence that is retrieved. And E-value can be thought of as the probability that two sequences are similar to each other by chance. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''Extremophile''' - an organism that thrives in and may even require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth [http://en.wikipedia.org/wiki/Extremophile] (Will).<br /> <br /> == F ==<br /> <br /> '''FASTA format''' - a format used to convey either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented by single-letter codes. The sequence name and other descriptors often precede the amino acid sequence. [http://en.wikipedia.org/wiki/FASTA_format] (Nick)&lt;br&gt;<br /> <br /> '''family (protein)''' - a group of evolutionarily-related proteins, often with one or several domains in common. Families are organized by domain overlap, structural/functional similarity, and sequence similarity. ([http://en.wikipedia.org/wiki/Protein_family Wikipedia article] and lecture, Laura)<br /> <br /> '''finished genome''' - a genome that has been sequenced at least partly by hand, resulting at least 99.99% sequence accuracy (Lecture, Jay)&lt;br&gt;<br /> <br /> '''fusion mRNA'''-mRNA that results from the transcription of a gene after a chromosomal translocation event. This results in an mRNA sequence that comes from two different genes (Rowley and Blumenthal 2008 ''Science'' Pallavi)<br /> <br /> == G ==<br /> <br /> '''GC Content''' - the percentage of bases within a certain sequence of DNA (e.g. a gene or a genome) that are either guanine or cytosine; a higher GC content is characteristic of a coding region of a gene; differences in GC content between a gene and a genome can be used as evidence for horizontal gene transfer [http://en.wikipedia.org/wiki/GC-content] (Matt)&lt;br&gt;<br /> <br /> '''GC-skew''' – uneven distribution of guanine and cytosine bases between the two strands of DNA where GC base pairs occur. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''gene amplification''' - production of multiple copies of a gene in order to amplify the amount of protein that the gene encodes for [http://www.medterms.com/script/main/art.asp?articlekey=13537] [http://www.answers.com/topic/gene-amplification] (Matt)<br /> <br /> '''gene fusion'''-occurs when DNA segments of two different genes come together. Can result in hybrid proteins ([http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html 9] Pallavi)<br /> <br /> '''gene knockout''' - a process in which a gene is deactivated within a test organism in order to better understand the function of the gene in that organism [http://en.wikipedia.org/wiki/Gene_knockout] (Matt)<br /> <br /> '''gene oncology'''- a collaborative effort of investigators to unify and standardize terms associated with the role a gene or protein plays in an organism. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''glaucophyte''' - freshwater algae that have not been studied well [http://en.wikipedia.org/wiki/Glaucophyte](Samantha)&lt;br&gt;<br /> <br /> == H ==<br /> <br /> '''haemolysin or hemolysin''' - a chemical produced by a bacteria that causes lysis of red blood cells [http://en.wikipedia.org/wiki/Hemolysis_(microbiology)] (Nick)<br /> <br /> '''halophile''' - an organism, most often of the Archaea domain, that lives in environments containing high concentrations of salt [http://en.wikipedia.org/wiki/Halophile] (Matt)<br /> <br /> '''haplotype'''-collection of alleles that travel together (Lecture, Pallavi)<br /> <br /> '''haptophyte''' - phylum of algae [http://en.wikipedia.org/wiki/Haptophyte](Samantha)<br /> <br /> '''heterokont''' - major line of eukaryotes consisting of about 10,500 known species, most of which are algae [http://en.wikipedia.org/wiki/Heterokont](Samantha)<br /> <br /> '''Hidden Markov Model''' - a statistical model used in protein recognition databases such as Pfam. A Hidden Markov Model keeps track of several variables and possible variations thereof, such as the possible amino acid sequences that make up a protein domain (since there can be some variance in an amino acid sequence) or the variations in the component sounds that make up a word, and uses those points to match a given sequence to the word, domain, or other complex sequence it most closely matches. An HMM in speech recognition software, for example, can identify that a certain set of sounds make up a certain word, even with the variations in pronunciation and accent that different people will give those sounds. ([http://en.wikipedia.org/wiki/Hidden_Markov_Model Wikipedia] and lecture, Laura) <br /> <br /> '''HMM Logo''' - a graphical representation of an HMM, detailing the possible amino acid sequences, the relative frequencies and probabilities of each amino acid in the sequence, the relative contribution each amino acid has to the overall protein family, and the charge or nature of the amino acids themselves. ([http://www.sanger.ac.uk/Software/analysis/logomat-m/help.shtml How to read HMM Logos, on Pfam], Laura)<br /> <br /> '''homeobox''' - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades [http://en.wikipedia.org/wiki/Homeobox](Samantha)<br /> <br /> '''homodimer''' - a protein made of paired identical polypeptides ([http://www.answers.com/topic/homodimer Answers.com], Jay)<br /> <br /> '''horizontal gene transfer'''-DNA transmission between species and incorporation of the DNA into the recipient's genome ([http://www.csrees.usda.gov/nea/biotech/res/biotechnology_res_glossary.html horizontal gene transfer] Pallavi)<br /> <br /> '''''Hox'' gene'''-a gene that contains a homeobox region that is involved in morphogenesis along the cranio-caudal body axis ([http://www.uprightape.net/UA_Glossary.html 4] Pallavi)<br /> <br /> '''hydrolase''' - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often take part in subsequent reactions [http://en.wikipedia.org/wiki/Hydrolase] (Nick)<br /> <br /> == I ==<br /> <br /> '''ideogram''' - in genomics, usually describes a stylized representation of a chromosome with banding patterns (Campbell-Heyer Genomics textbook, Jay)<br /> <br /> '''identities''' - in a BLAST output, the number and fraction of total residues which are identical in a given alignment [www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''indole'''-a chemical compound that is produced from the break down of tryptophan ([http://medical-dictionary.thefreedictionary.com/indole indole] Pallavi)<br /> <br /> '''inclusion body''' - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [http://en.wikipedia.org/wiki/Inclusion_body] (Nick)<br /> <br /> '''intron''' - a region of DNA in a gene that is not part of the final coding sequence for the protein. [http://en.wikipedia.org/wiki/Intron] (Peter)<br /> <br /> '''isoelectric point''' - the pH at which a molecule is neutral [http://en.wikipedia.org/wiki/Isoelectric_point] (Nick)<br /> <br /> '''isozymes''' - members of a gene family with very similar cellular roles (Cambpell-Heyer Genomics textbook, Jay)<br /> <br /> == J ==<br /> <br /> == K ==<br /> '''KEGG (Kyoto Encyclopedia of Genes and Genomes)''' - a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The Pathway database records networks of molecular interactions in the cells, and variants of them specific to particular organisms [http://en.wikipedia.org/wiki/KEGG](Will).<br /> <br /> '''kinase''' - a type of enzyme that transfers a phosphate group from a high-energy donor molecule to a target molecule in a process called phosphorylation. [http://en.wikipedia.org/wiki/Kinase] (Peter)<br /> <br /> == L ==<br /> <br /> == M ==<br /> '''Manatee''' - a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. This on-going, open source initiative was developed with two missions. One, to allow biologists the ability to functionally annotate their genomes using a powerful, stand-alone web application with a robustly designed relational annotation database. And secondly, to invite outside developers the opportunity to contribute their own ideas and requirements to enhance Manatee's ability to accomplish biological goals [http://manatee.sourceforge.net/](Will). &lt;br&gt;<br /> <br /> '''microsatellites'''-stretches of repetitive, short DNA segments that can be used to track the inheritance of certain traits within families ([http://www.clanlindsay.com/genetic_dna_glossary.htm 3] Pallavi)<br /> <br /> '''minisatellites'''-segments of DNA that can be used for individual identification (ex. DNA fingerprinting) or in determining relationships between people (ex. paternity cases) ([http://www.clanlindsay.com/genetic_dna_glossary.htm 2] Pallavi).<br /> <br /> '''motif''' - a sequence of amino acids or nucleotides that performs a particular role and is often conserved in other species or molecules. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''mycoplasma''' - genus of bacteria that lack a cell wall [http://en.wikipedia.org/wiki/Mycoplasma] (Nick)<br /> <br /> == N ==<br /> <br /> '''NORFs''' (nonannotated open reading frame) - on open reading frame that was considered not to be a real gene when the genome was annotated.( Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''nucleomorph''' - reduced eukaryotic nuclei found in plastids [http://en.wikipedia.org/wiki/Nucleomorph](Samantha)<br /> <br /> == O ==<br /> '''object-oriented programming''' - a programming paradigm in which collections of data, associated with operations on that data, are modularly defined and then built upon (CSC 121 Lecture, Will). <br /> <br /> '''open reading frame (ORF)'''-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) [http://www.fao.org/DOCREP/003/X3910E/X3910E18.htm ORF] (Pallavi)<br /> <br /> '''operon''' - a segment of DNA involving an operator, promoter, and one or more genes that operate as a single unit during transcription [http://en.wikipedia.org/wiki/Operon] (Nick)<br /> <br /> '''optical mapping'''-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome [http://www.geocities.com/bioinformaticsweb/genomicglossary.html optical mapping] (Pallavi)<br /> <br /> '''ortholog'''-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)<br /> <br /> '''oxidoreductase''' - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [http://en.wikipedia.org/wiki/Oxidoreductase] (Nick)<br /> <br /> == P ==<br /> <br /> '''paralog'''-identical DNA sequences within a species (Lecture, Pallavi)<br /> <br /> '''p-arm''' - the shorter arm of a chromosome's two arms separated by the centromere (compare to q-arm, the longer arm) ([http://www.medterms.com/script/main/art.asp?articlekey=4715 MedTerms Dictionary], Jay)<br /> <br /> '''Perl''' - Developed by Larry Wall in 1987, Perl is a [http://en.wikipedia.org/wiki/High-level_programming_language high-level programming language] used frequently by biologists and bioinformaticists [http://en.wikipedia.org/wiki/Perl] (Will). <br /> <br /> '''periplasmic space''' - the space between the inner cytoplasmic membrane and external outer membrane in bacteria or archaea. [http://en.wikipedia.org/wiki/Periplasmic_space] (Peter)<br /> <br /> '''Pfam''' - a database for protein domain families that matches amino acid sequences or nucleotide sequences to the related group of proteins to which they most likely belong. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura)<br /> <br /> '''plasmid''' - an extra-chromosomal DNA molecule that is capable of replicating independently of the chromosomal DNA. Commonly found in bacteria and archaea. [http://en.wikipedia.org/wiki/Plasmid](Peter)<br /> <br /> '''plastid''' - major organelles in plants or algae [http://en.wikipedia.org/wiki/Plastid](Samantha)<br /> <br /> '''pleomorphism''' - the occurrence of two or more structural forms during a life cycle [http://en.wikipedia.org/wiki/Pleomorphism] (Mary)<br /> <br /> '''phylogenetic tree''' - a diagram showing the evolutionary relationships between biological species that are thought to share a common ancestor [http://en.wikipedia.org/wiki/Phylogenetic_tree] (Nick)<br /> <br /> '''phylotypes''' – a term intended to resolve the challenge of “species” when classifying prokaryotes using DNA sequence comparisons. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''positives''' - in a BLAST output, the number and fraction of residues for which the alignment scores have positive rather than negative values [http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''proteome''' - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions [http://en.wikipedia.org/wiki/Proteome](Samantha)<br /> <br /> '''PSORT''' - a prediction server that judges where a mature protein could be in the cell, based on its transmembrane domains, its predicted mature amino acid composition, and its signal sequences. ([http://psort.ims.u-tokyo.ac.jp/form.html PSORT], Laura)<br /> <br /> '''psuedogenes'''-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)<br /> <br /> '''purine''' - a category of nitrogenous base consisting of a pyrimidine ring fused to an imidazole ring. Notable purine bases are adenine and guanine. [http://en.wikipedia.org/wiki/Purine] (Peter)<br /> <br /> '''pyrimidine''' - a category of nitrogenous base consisting of a heterocyclic aromatic ring containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Notable pyrimidine bases are cytosine, thymine, and uracil. [http://en.wikipedia.org/wiki/Pyrimidine] (Peter)<br /> <br /> == Q ==<br /> <br /> '''q-arm''' - the longer arm of a chromosome's two arms separated by the centromere (compare to p-arm, the shorter arm) ([http://www.medterms.com/script/main/art.asp?articlekey=5152 MedTerms Dictionary], Jay)&lt;br&gt;<br /> <br /> '''query sequence''' - the sequence (whether amino acid or nucleotide) entered into a database’s search function and checked against the database entries. ([http://en.wikipedia.org/wiki/BLAST BLAST on Wikipedia], Laura)<br /> <br /> == R ==<br /> <br /> '''RAST''' - (Rapid Annotation using Subsystem Technology)- a fully-automated service for annotating bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree. ([http://rast.nmpdr.org/], Max Win)<br /> <br /> '''rDNA'''-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. ([http://en.wikipedia.org/wiki/Ribosomal_DNA rDNA] Pallavi)<br /> <br /> '''residue (protein)''' - the remaining portion of an amino acid after a water molecule has been removed and it has been incorporated into a protein. Functional residues, referred to in Pfam, are the residues that perform some specific identifiable function or are part of a domain, and can be conserved across evolutionarily-related proteins. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura) &lt;br&gt;<br /> <br /> '''retropseudogenes'''-these are genes that have been reverse-transcribed from mRNA and the resulting DNA sequence is incorporated back into the genome. They are non-functional segments of DNA and can be distinguished from pseudogenes in that they do not have intron sequences. ([http://genome.cshlp.org/cgi/content/full/10/5/672 1] Pallavi)<br /> <br /> '''retrotransposons''' - RNA transcribed back into DNA and added into the genome [http://en.wikipedia.org/wiki/Retrotransposon](Samantha)<br /> <br /> '''ribonuclease''' - a nuclease that catalyzes the degradation of RNA into smaller components [http://en.wikipedia.org/wiki/Ribonuclease] (Mary)<br /> <br /> == S ==<br /> '''Serovar'''-a subdivision of a species based on the characteristics of their cell surface antigens ([http://www.biology-online.org/dictionary/Serovar serovar] Pallavi)<br /> <br /> '''scaffold''' - a section of a sequenced genome composed of contigs that are in the right order but not necessarily connected ([http://www.medterms.com/script/main/art.asp?articlekey=25223 MedTerms Dictionary], Jay)<br /> <br /> '''&quot;Shadow enhancers&quot;'''-secondary enhancers that are thought to be important for natural selection to occur in regulatory DNA segments. They evolve much faster than primary enhancers, which suggests that they are under fewer functional constraints (Wray and Babbit 2008 ''Science'' Pallavi)<br /> <br /> '''Shine-Dalgarno sequence''' - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and [http://en.wikipedia.org/wiki/Shine-dalgarno Wikipedia article], Laura)&lt;br&gt;<br /> Note: The Shine-Dalgarno consensus sequence for our genome is ccGGAGGt.<br /> <br /> '''SignalP''' - a prediction server that judges whether or not a query protein is a signal peptide. SignalP measures each amino acid against the amino acid sequences of probable signal peptide matches and predicts the cleavage site of the signal peptide. ([http://www.cbs.dtu.dk/services/SignalP-3.0/output.php SignalP Output explained], Laura)<br /> <br /> '''signal peptide''' - a short peptide chain that directs the post-translational transport of a protein [http://en.wikipedia.org/wiki/Signal_peptide] (Matt)<br /> <br /> '''Smith-Waterman alignment''' - A well-known algorithm for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure [http://en.wikipedia.org/wiki/Smith_waterman](Will).<br /> <br /> '''SNP (Single Nucleotide Polymorphism)''' - a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual) [http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism](Will).<br /> <br /> '''symporter''' - an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane. [http://en.wikipedia.org/wiki/Symporter] (Peter)<br /> <br /> '''synteny''' - a neologism from the Greek for &quot;on the same ribbon&quot;. Genes that are syntenic in one species are on the same chromosome; genes that are syntenic across species retain the same order on respective chromosomes as a result of descent from a common ancestor ([http://www.answers.com/synteny Answers.com], Jay)<br /> <br /> '''synthetase''' - a type of enzyme that creates a new covalent bond and requires direct input of energy from a high-energy phosphate. [http://books.google.com/books?id=bB8XnCykRmIC&amp;pg=PA522&amp;lpg=PA522&amp;dq=%22synthetase+is+an+enzyme%22&amp;source=web&amp;ots=wkws4ksMsg&amp;sig=zWLkDIk7T78hcf9S84nWs3u5Apw&amp;hl=en&amp;sa=X&amp;oi=book_result&amp;resnum=9&amp;ct=result] (Peter)<br /> <br /> == T ==<br /> '''transferase''' - an enzyme that catalyzes the transfer of a functional group from one molecule (the donor) to another (the acceptor) [http://en.wikipedia.org/wiki/Transferase] (Matt)<br /> <br /> '''transmembrane helix''' - a single transmembrane alpha helix of a transmembrane protein, usually about twenty amino acids in length. They are usually predicted by hydrophobicity. [http://en.wikipedia.org/wiki/Transmembrane_domain](Mary)<br /> <br /> '''transposons / transposable elements''' - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. [http://en.wikipedia.org/wiki/Transposon](Samantha)<br /> <br /> '''Transposon Mutagenesis'''-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene ([http://cancerweb.ncl.ac.uk/cgi-bin/omd?transposon+mutagenesis transposon mutagenesis] Pallavi)<br /> <br /> '''Trans-splicing'''-fragmented exon sequences fuse to form a mature species of mRNA. This process results in fusion mRNA ([http://www.representinggenes.org/Glossary.html 8] Pallavi).<br /> <br /> '''tRNA splicing endonuclease''' - an enzyme that cleaves intervening sequences of precursor tRNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?splicing+endonuclease] (Peter)&lt;br&gt;<br /> <br /> == U ==<br /> <br /> == V ==<br /> '''Vertical gene transfer'''-the transmission or absorption of genetic material that is associated with sexual reproduction and, thus, acknowledges species-specific boundaries ([http://www.gmo-compass.org/eng/glossary/#G 6] Pallavi)<br /> <br /> == W ==<br /> <br /> '''whole genome shotgun sequencing''' - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. [http://en.wikipedia.org/wiki/Whole_genome_shotgun](Samantha)<br /> &lt;br&gt;<br /> <br /> == X ==<br /> '''xenolog''' - homologs that are created by horizontal gene transfer between two different species [http://en.wikipedia.org/wiki/Xenolog#Xenology] (Matt)&lt;br&gt;<br /> <br /> == Y ==<br /> <br /> == Z ==<br /> <br /> &lt;BR&gt;</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Halorhabdus_utahensis_Genome&diff=7105 2008-11-04T16:21:39Z

<p>LaHeyer: /* Pathway Tutorials */</p> <hr /> <div>This page will be used by Davidson College students in the [http://www.bio.davidson.edu/Courses/Bio343/LabMethods.html Genomics Laboratory course].<br /> __NOTOC__<br /> == Links to Multiple Databases ==<br /> *[http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&amp;page=taxonDetail&amp;taxon_oid=2500575004 JGI IMG EDU] &lt;br&gt; public access &lt;br&gt; *[[Media:JGIAnnotation.xls|JGI Annotation Excel Spreadsheet]]<br /> *[http://www.tigr.org/tigr-scripts/prok_manatee/shared/login.cgi Manatee at JCVI] &lt;br&gt; use the davidson number sent by email as username and password (database is nthu01 - this is case sensitive) &lt;br&gt; *[[Media:ManateeAnnotation.xls|Manatee Annotation Excel Spreadsheet]]<br /> *[http://rast.nmpdr.org/ SEED view via RAST] &lt;br&gt; use the username and password combination sent to you by SEED &lt;br&gt; *[[Media:RastAnnotation.xls|RAST Annotation Excel Spreadsheet]]&lt;br&gt; *[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=18261238 RAST Publication in PubMed]<br /> *[http://www.genome.jp/kegg/kaas/ KEGG]&lt;br&gt; We can submit our genes to KEGG to have it mapped out, but SEED and Manatee may already do this. Do we want to ask them to upload it into their database? &lt;br&gt;<br /> *[http://wishart.biology.ualberta.ca/basys/cache/135af8726ad6f61ec4c5f1e9c4d139ac/index.html BASYs]&lt;br&gt;&lt;br&gt;<br /> *[http://gcat.davidson.edu/Registry/compare/ Pairwise comparisons of All Three Annotations]<br /> <br /> <br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI_5contigs.txt JGI Full genome, 5 separate contigs &amp; 3.1 Mbp, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.txt JGI gene DNA sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.xls JGI gene annotations, Excel] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_proteins.txt JGI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_merged.txt CJVI Full genome, 5 contigs fused, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_ORFs.txt CJVI gene sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_proteins.txt CJVI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/GeneLengths.xls 3-way comparison, Excel] &lt;br&gt;<br /> [[Venn_diagrams]] Venn diagram of 3-way comparison<br /> <br /> &lt;br&gt;<br /> <br /> == RNA Genes ==<br /> <br /> *[[tRNA Genes Check List]]&lt;br&gt;<br /> *[[rRNA operon]]&lt;br&gt;<br /> *[[2 misc. RNA genes]] (short summary list)&lt;br&gt;<br /> *[[Missing tRNA-trp gene found]]&lt;br&gt;<br /> <br /> == Other Resources ==<br /> *[[Consensus Shine Dalgarno]] Excel File for ''H. utahensis'' &lt;br&gt;<br /> *[[References]]&lt;br&gt;<br /> *[[Gene Annotation Template]]&lt;br&gt;<br /> *[[General Questions]]&lt;br&gt;<br /> *[[Page for Annotated Genes]]&lt;br&gt;<br /> *[http://www.bio.davidson.edu/courses/genomics/2008/Win/ec/ Search EC number in RAST, JGI or Manatee] &lt;br&gt;<br /> *[http://gcat.davidson.edu/Wideloache/Webfiles/ecNumBlast.html Blast an EC number against the H. utahensis genome]&lt;br&gt;<br /> <br /> == Research Questions ==<br /> #How do the three systems compare for finding ORFs and RNA genes?<br /> #Is there a pattern of missed genes for any of the 3 sites? <br /> #Do the three systems differ in their ability to find good start codons and Shine-Dalgarno sequences? [We need a standard set of genes for comparison. Only highly conserved or a range of genes?]<br /> # Were Shine-Dalgarno sequences calculated for our species or default values used? If default, what sequence?<br /> #Can we fill any holes in their automated annotation? Is there a mechanism for users to add in genes?<br /> #How do the 3 sites compare for ease of use?<br /> #What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working?<br /> #How does each of the 3 sites compare for pathway detection and visualization? <br /> #Do they find the origin of replication? Can we find it? <br /> <br /> * How do the 3 systems compare when one gene is called hypothetical and the other calls it a functional protein? How can they vary and who is getting it closer to correct (however you define that, possibly by date of matched entry: Pallavi and Mary)<br /> * Why did one system call a gene when the other two did not? (Matt and Lara)<br /> * How do the 3 sites compare for ease of use? What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working? (Samantha and Nick)<br /> * Where is the origin of replication and did the 3 systems attempt to identify this?<br /> * Did the 3 systems utilize Shine-Dalgarno sequences to help them call start codons? Did they utilize our species's consensus Shine-Dalgarno? (Peter)<br /> * We need to fill in the [[Venn diagrams]] for our 3-way comparison. Let's compare the size of ORFs and generate a [[Gene Length Histograms|graph comparing the distributions]] for all 3. (Max and Will - they also take requests). <br /> <br /> &lt;hr&gt;<br /> =Our Favorites=<br /> == My favorite genes==<br /> Pallavi - Monooxygenase vs. Peroxiredoxin<br /> <br /> Mary - JGI gene 2500588521 (922976...924046) [[Media:My favorite gene.ppt]]<br /> <br /> Max - [http://app.sliderocket.com/app/FullPlayer.aspx?id=f2058b94-845f-4a11-94eb-142f251a7fea JGI gene 2500587636 (2-1849)]<br /> <br /> Samantha - JGI gene 2500575882 (80504-80878) [[Media:Earl.ppt]]<br /> <br /> Nick - JGI gene 2300587691 (69942...72866) [[Media:Gene presentation.ppt]]<br /> <br /> Will - JGI gene 2500590430 (2847205..2854335)<br /> <br /> Jay - JGI gene 2500588397 (806410..807321) [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Fav_Gene/FavoriteGenePresentation.pptx Co/Zn/Cd PowerPoint]<br /> <br /> Matt - Transcriptional Regulator nrdR (3109722..3110204 + 7274..7765)<br /> <br /> Peter - tRNA intron endonuclease [[Media:TRNAtrpintronendonuclease.ppt]]<br /> <br /> Laura - 16S Small ribosomal subunit, JGI gene 2500590728 (2397347..2398825)<br /> <br /> == My Favorite Pathways==<br /> Pallavi - Carbohydrate Metabolism<br /> <br /> Jay - Membrane Transport<br /> <br /> Will - Signal Transduction<br /> <br /> Max -energy<br /> <br /> ''Suggestions by Kjeld''&lt;br&gt;<br /> '''[[Cellulase]]''' by Pallavi&lt;br&gt;<br /> I think it would be very interesting to look for genes involved in cellulose degradation: endocellulases, exocellolases (=cellobiohydrolases) and b-glucosidases.<br /> Many cellulose degrades produce a range of each type. A cellolulyic system able to function at 4.6 M of NaCl is an interesting one. We either did not observed (or look for cellulose degradation). However, these systems are normally inducible and you need to test several substrates and inducers. It would be nice to have a compilation of putative “cellulase” genes.<br /> There are several good recent reviews on cellulases (also mentioning E.C. numbers and enzyme families) that your students could consult.<br /> <br /> '''[[Chitinase]]''' by Matt&lt;br&gt;<br /> Apparently you detected a chitinase but according to our records it does not gorw on N-acetyl-glucosamine which is somewhat strange. It grows on glucose though. <br /> <br /> '''[[Lipases]]''' by Mary&lt;br&gt;<br /> Lipases (/esterases) would also be interesting to look for – some lipases have important industrial applications.<br /> <br /> '''[[Amylases]]''' by Samantha&lt;br&gt;<br /> We did not observed growth on starch. Did you find any “amylase-coding genes”?<br /> <br /> '''[[Xylose (glucose) isomerase)]]''' by Nick&lt;br&gt;<br /> An enzyme of great commercial value. <br /> <br /> '''[[Amino acids]]''' lead by Laura and assisted by Max, Jay, Nick and Samantha&lt;br&gt;<br /> According to our records AX-2 is able to grow in a “defined medium”. This is at variance with your “holes” for synthesis of amino acids. However, there could have been some “carry over” of amino acids when inoculating a culture grown in complex medium (e.g. containing yeast extract). However, we are normally aware of this problem and do repeated culturing to dilute out potential growth factors present in yeast extract.<br /> <br /> '''[[Proteases]]''' by Peter&lt;br&gt;<br /> We did not detect protease activity – albeit only checking a few substrates.<br /> <br /> '''[[Protein Export]]''' by Malcolm &lt;br&gt;<br /> We need to know how these proteins might reach outside the cell which is where the food would be and thus the digestive enzymes or importers need to reach the outside world or the cell membrane.<br /> <br /> = Student-created tutorials: =<br /> == Tutorials for Annotating Genomes ==<br /> <br /> # Will DeLoache - [http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/BioPerlTutorial/BioPerl.htm BioPerl Installation] &lt;br&gt;<br /> # Max Win - [http://www.bio.davidson.edu/courses/genomics/2008/Win/perl.html Introduction to Perl for non-programmers.(with step by step explanations,simple exercises and solutions)]&lt;br&gt;<br /> # Pallavi - Conserved Domains Database (CDD) [[Media:CDDtutorial.doc]] &lt;br&gt;<br /> # Mary - Protein Data Bank (PDB) [[Media:PDB Tutorial.doc]] &lt;br&gt;<br /> # Laura Voss - Pfam Database [http://www.bio.davidson.edu/Courses/Bio343/Pfam_tutorial.doc Pfam Tutorial] &lt;br&gt;<br /> # Samantha Simpson - [http://www.bio.davidson.edu/courses/genomics/2008/Simpson/Tutorial.html NCBI BLAST]&lt;br&gt;<br /> # Peter Bakke - [[Media:ShineDalgarnoTutorial.doc]]&lt;br&gt;<br /> # Jay McNair - [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Origin_Tutorial/OriginTutorial.doc Origin of Replication Tutorial]&lt;br&gt;<br /> # Nick Carney - Navigating the JGI Database [[Media:NavigatingJGItutorial.doc]]&lt;br&gt;<br /> # Matt Lotz - SEED Viewer - [[Media:SEEDTutorial.doc]] &lt;br&gt;<br /> == Pathway Tutorials==<br /> [http://www.pathguide.org/ Pathguide] - a possible source of tutorials and extensive information<br /> [http://www.bigre.ulb.ac.be/Users/didier/pathfinding/ Shortest Path Tool]<br /> <br /> *Pallavi: I will compare RAST and KEGG in pathway annotations and use Glycolysis/Gluconeogenesis as my example<br /> <br /> &lt;hr&gt;<br /> <br /> =Glossary words (A - Z):=<br /> [[#A| A ]] [[#B| B ]] [[#C| C ]] [[#D| D ]] [[#E| E ]] [[#F| F ]] [[#G| G ]] [[#H| H ]] [[#I| I ]] [[#J| J ]] [[#K| K ]] [[#L| L ]] [[#M| M ]] [[#N| N ]] [[#O| O ]] [[#P| P ]] [[#Q| Q ]] [[#R| R ]] [[#S| S ]] [[#T| T ]] [[#U| U ]] [[#V| V ]] [[#W| W ]] [[#X| X ]] [[#Y| Y ]] [[#Z| Z ]] <br /> <br /> == A ==<br /> '''Accession Number''' - a unique identifier given to DNA and protein sequences to allow for tracking of sequence information within a single database [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics)] (Will).<br /> <br /> '''Antisense (RNA or DNA)'''-a piece of DNA or RNA that binds to a complementary sequence of DNA or RNA. These segments of genetic material can be used to identify the existence of a disease gene and they can also be used to bind to specific DNA or mRNA sequences to inhibit their function ([http://biotech.fyicenter.com/glossary/Bioinformatics_Glossary.html 5] Pallavi).<br /> <br /> '''&lt;i&gt;Arabidopsis thaliana&lt;/i&gt;''' - the scientific name for the thale cress plant; it was the first plant to have its genome sequenced, and is a model organism for understanding plant biology and genetics ([http://en.wikipedia.org/wiki/Thale_cress Wikipedia.org], Jay)<br /> <br /> == B ==<br /> '''BAC''' - &lt;i&gt;b&lt;/i&gt;acterial &lt;i&gt;a&lt;/i&gt;rticifical &lt;i&gt;c&lt;/i&gt;hromosome, a DNA construct used for transforming or cloning segments of DNA and often used to sequence the genetic code of organisms ([http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome Wikipedia.org], Jay)<br /> <br /> '''bioinformatics''' - the multi-disciplinary approach of using biology, computer science and mathematics to solve or better understand biological problems [http://en.wikipedia.org/wiki/Bioinformatics] (Matt)<br /> <br /> '''BLAST''' - (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. [http://blast.ncbi.nlm.nih.gov/Blast.cgi] (Mary)<br /> <br /> '''bioperl'''- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications such as accessing sequence data from local and remote databases, transforming formats of database, manipulating individual sequences, searching for similar sequences, searching for genes and other structures on genomic DNA, or developing a machine readable sequence annotations. [http://en.wikipedia.org/wiki/BioPerl] (Wikipedia, Max Win)<br /> <br /> == C ==<br /> '''carbon fixation''' - using carbon dioxide to create organic materials [http://en.wikipedia.org/wiki/Carbon_fixation] (Samantha)&lt;BR&gt;<br /> <br /> '''CDD''' (Conserved Domains Database)- a database used to identify the conserved domains present in a protein query sequence [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml] (Mary)<br /> <br /> '''chaperonin''' - a protein complex that assists some newly formed polypeptide chains by folding them into their final, functional, three-dimensional form [http://en.wikipedia.org/wiki/Chaperonins] (Matt)<br /> <br /> '''chemotaxis''' - the process in which cells will seek out or flee from a high concentration of certain chemicals and is found in both uni- and multicellular organisms. This process is used to avoid toxins or find food in unicelllular organisms or tasks such as reproduction in multicellular organisms [http://en.wikipedia.org/wiki/Chemotaxis] (Nick)<br /> <br /> '''chemotaxonomy''' - the attempt to classify and identify organisms according to demonstrable differences and similarities in their biochemical compositions [http://en.wikipedia.org/wiki/Chemotaxonomy] (Mary)<br /> <br /> '''ClustalW''' - A web-based or command line tool that performs multiple sequence alignments to determine evolutionary relationships between three or more sequences [http://en.wikipedia.org/wiki/Clustal] (Will).<br /> <br /> '''COG''' (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs ([http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml COG] Pallavi) &lt;br&gt;<br /> <br /> '''concatemer''' - long continuous DNA molecule that contains the same DNA sequence repeated in series [http://en.wikipedia.org/wiki/Concatemer](Samantha)&lt;BR&gt;<br /> <br /> '''contigs''' (contiguous DNA)- overlapping DNA segments that as a collection from a longer and gapless segment of DNA. (Discovery Genomics, Proteomics and Bioinformatics [http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''coverage''' - refers to the number of times, on average, any piece of DNA in a sequenced genome has been individually sequenced (Lecture, Jay)<br /> <br /> '''CPAN (Comprehensive Perl Archive Network)''' - an archive of over 12,200 modules of software written in Perl, as well as documentation for it. It contains a module called CPAN (or CPAN.pm) which is used as an installer for Perl modules such as BioPerl [http://en.wikipedia.org/wiki/CPAN](Will).<br /> <br /> '''Cytogenetics'''-the study of normal and abnormal chromosomes. This involves studying the causes of chromosomal abnormalities and looking at the structure of chromosomes ([http://www.vivo.colostate.edu/hbooks/genetics/medgen/chromo/index.html 7] Pallavi).<br /> <br /> == D ==<br /> '''''de novo'' synthesis''' - the synthesis of complex molecules from simple molecules (e.g. sugars and nucleotides), rather than from recycled molecules; from the latin &quot;of the new&quot; [http://en.wikipedia.org/wiki/De_novo_synthesis] (Matt)<br /> <br /> '''dehydrogenase''' - a type of enzyme that oxidizes a substrate by transferring one or more protons and a pair of electrons to an acceptor. [http://en.wikipedia.org/wiki/Dehydrogenase] (Peter)<br /> <br /> '''diatom''' - a major group of eukaryotic algae, and one of the most common types of phytoplankton. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica called a frustule. These frustules show a wide diversity in form, but usually consist of two asymmetrical sides with a split between them. [http://en.wikipedia.org/wiki/Diatom] (Mary)<br /> <br /> '''domain (protein)''' - the structural and functional groups of a protein, which can exist independently of the protein itself. Domains typically perform a specific function, such as binding to promoters or substrates, and many proteins can have one or several domains in common. Evolutionarily-linked proteins are more likely to have domains in common. Domains are used to organize proteins into families. ([http://en.wikipedia.org/wiki/Domain_(protein) Wikipedia article], Laura)<br /> <br /> '''dot plot'''-graphical display comparing sequence conservation between two genomes with dots indicating strings of identical bases. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> == E ==<br /> <br /> '''EC number''' (Enzyme Commission Number)- a numerical classification scheme for enzymes, based on the chemical reactions they catalyze [http://en.wikipedia.org/wiki/EC_number] (Mary)<br /> <br /> '''E-value''' (Expect value)- When performing a BLAST search, you will obtain an E-value for each sequence that is retrieved. And E-value can be thought of as the probability that two sequences are similar to each other by chance. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''Extremophile''' - an organism that thrives in and may even require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth [http://en.wikipedia.org/wiki/Extremophile] (Will).<br /> <br /> == F ==<br /> <br /> '''FASTA format''' - a format used to convey either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented by single-letter codes. The sequence name and other descriptors often precede the amino acid sequence. [http://en.wikipedia.org/wiki/FASTA_format] (Nick)&lt;br&gt;<br /> <br /> '''family (protein)''' - a group of evolutionarily-related proteins, often with one or several domains in common. Families are organized by domain overlap, structural/functional similarity, and sequence similarity. ([http://en.wikipedia.org/wiki/Protein_family Wikipedia article] and lecture, Laura)<br /> <br /> '''finished genome''' - a genome that has been sequenced at least partly by hand, resulting at least 99.99% sequence accuracy (Lecture, Jay)&lt;br&gt;<br /> <br /> '''fusion mRNA'''-mRNA that results from the transcription of a gene after a chromosomal translocation event. This results in an mRNA sequence that comes from two different genes (Rowley and Blumenthal 2008 ''Science'' Pallavi)<br /> <br /> == G ==<br /> <br /> '''GC Content''' - the percentage of bases within a certain sequence of DNA (e.g. a gene or a genome) that are either guanine or cytosine; a higher GC content is characteristic of a coding region of a gene; differences in GC content between a gene and a genome can be used as evidence for horizontal gene transfer [http://en.wikipedia.org/wiki/GC-content] (Matt)&lt;br&gt;<br /> <br /> '''GC-skew''' – uneven distribution of guanine and cytosine bases between the two strands of DNA where GC base pairs occur. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''gene amplification''' - production of multiple copies of a gene in order to amplify the amount of protein that the gene encodes for [http://www.medterms.com/script/main/art.asp?articlekey=13537] [http://www.answers.com/topic/gene-amplification] (Matt)<br /> <br /> '''gene fusion'''-occurs when DNA segments of two different genes come together. Can result in hybrid proteins ([http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html 9] Pallavi)<br /> <br /> '''gene knockout''' - a process in which a gene is deactivated within a test organism in order to better understand the function of the gene in that organism [http://en.wikipedia.org/wiki/Gene_knockout] (Matt)<br /> <br /> '''gene oncology'''- a collaborative effort of investigators to unify and standardize terms associated with the role a gene or protein plays in an organism. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''glaucophyte''' - freshwater algae that have not been studied well [http://en.wikipedia.org/wiki/Glaucophyte](Samantha)&lt;br&gt;<br /> <br /> == H ==<br /> <br /> '''haemolysin or hemolysin''' - a chemical produced by a bacteria that causes lysis of red blood cells [http://en.wikipedia.org/wiki/Hemolysis_(microbiology)] (Nick)<br /> <br /> '''halophile''' - an organism, most often of the Archaea domain, that lives in environments containing high concentrations of salt [http://en.wikipedia.org/wiki/Halophile] (Matt)<br /> <br /> '''haplotype'''-collection of alleles that travel together (Lecture, Pallavi)<br /> <br /> '''haptophyte''' - phylum of algae [http://en.wikipedia.org/wiki/Haptophyte](Samantha)<br /> <br /> '''heterokont''' - major line of eukaryotes consisting of about 10,500 known species, most of which are algae [http://en.wikipedia.org/wiki/Heterokont](Samantha)<br /> <br /> '''Hidden Markov Model''' - a statistical model used in protein recognition databases such as Pfam. A Hidden Markov Model keeps track of several variables and possible variations thereof, such as the possible amino acid sequences that make up a protein domain (since there can be some variance in an amino acid sequence) or the variations in the component sounds that make up a word, and uses those points to match a given sequence to the word, domain, or other complex sequence it most closely matches. An HMM in speech recognition software, for example, can identify that a certain set of sounds make up a certain word, even with the variations in pronunciation and accent that different people will give those sounds. ([http://en.wikipedia.org/wiki/Hidden_Markov_Model Wikipedia] and lecture, Laura) <br /> <br /> '''HMM Logo''' - a graphical representation of an HMM, detailing the possible amino acid sequences, the relative frequencies and probabilities of each amino acid in the sequence, the relative contribution each amino acid has to the overall protein family, and the charge or nature of the amino acids themselves. ([http://www.sanger.ac.uk/Software/analysis/logomat-m/help.shtml How to read HMM Logos, on Pfam], Laura)<br /> <br /> '''homeobox''' - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades [http://en.wikipedia.org/wiki/Homeobox](Samantha)<br /> <br /> '''homodimer''' - a protein made of paired identical polypeptides ([http://www.answers.com/topic/homodimer Answers.com], Jay)<br /> <br /> '''horizontal gene transfer'''-DNA transmission between species and incorporation of the DNA into the recipient's genome ([http://www.csrees.usda.gov/nea/biotech/res/biotechnology_res_glossary.html horizontal gene transfer] Pallavi)<br /> <br /> '''''Hox'' gene'''-a gene that contains a homeobox region that is involved in morphogenesis along the cranio-caudal body axis ([http://www.uprightape.net/UA_Glossary.html 4] Pallavi)<br /> <br /> '''hydrolase''' - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often take part in subsequent reactions [http://en.wikipedia.org/wiki/Hydrolase] (Nick)<br /> <br /> == I ==<br /> <br /> '''ideogram''' - in genomics, usually describes a stylized representation of a chromosome with banding patterns (Campbell-Heyer Genomics textbook, Jay)<br /> <br /> '''identities''' - in a BLAST output, the number and fraction of total residues which are identical in a given alignment [www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''indole'''-a chemical compound that is produced from the break down of tryptophan ([http://medical-dictionary.thefreedictionary.com/indole indole] Pallavi)<br /> <br /> '''inclusion body''' - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [http://en.wikipedia.org/wiki/Inclusion_body] (Nick)<br /> <br /> '''intron''' - a region of DNA in a gene that is not part of the final coding sequence for the protein. [http://en.wikipedia.org/wiki/Intron] (Peter)<br /> <br /> '''isoelectric point''' - the pH at which a molecule is neutral [http://en.wikipedia.org/wiki/Isoelectric_point] (Nick)<br /> <br /> '''isozymes''' - members of a gene family with very similar cellular roles (Cambpell-Heyer Genomics textbook, Jay)<br /> <br /> == J ==<br /> <br /> == K ==<br /> '''KEGG (Kyoto Encyclopedia of Genes and Genomes)''' - a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The Pathway database records networks of molecular interactions in the cells, and variants of them specific to particular organisms [http://en.wikipedia.org/wiki/KEGG](Will).<br /> <br /> '''kinase''' - a type of enzyme that transfers a phosphate group from a high-energy donor molecule to a target molecule in a process called phosphorylation. [http://en.wikipedia.org/wiki/Kinase] (Peter)<br /> <br /> == L ==<br /> <br /> == M ==<br /> '''Manatee''' - a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. This on-going, open source initiative was developed with two missions. One, to allow biologists the ability to functionally annotate their genomes using a powerful, stand-alone web application with a robustly designed relational annotation database. And secondly, to invite outside developers the opportunity to contribute their own ideas and requirements to enhance Manatee's ability to accomplish biological goals [http://manatee.sourceforge.net/](Will). &lt;br&gt;<br /> <br /> '''microsatellites'''-stretches of repetitive, short DNA segments that can be used to track the inheritance of certain traits within families ([http://www.clanlindsay.com/genetic_dna_glossary.htm 3] Pallavi)<br /> <br /> '''minisatellites'''-segments of DNA that can be used for individual identification (ex. DNA fingerprinting) or in determining relationships between people (ex. paternity cases) ([http://www.clanlindsay.com/genetic_dna_glossary.htm 2] Pallavi).<br /> <br /> '''motif''' - a sequence of amino acids or nucleotides that performs a particular role and is often conserved in other species or molecules. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''mycoplasma''' - genus of bacteria that lack a cell wall [http://en.wikipedia.org/wiki/Mycoplasma] (Nick)<br /> <br /> == N ==<br /> <br /> '''NORFs''' (nonannotated open reading frame) - on open reading frame that was considered not to be a real gene when the genome was annotated.( Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''nucleomorph''' - reduced eukaryotic nuclei found in plastids [http://en.wikipedia.org/wiki/Nucleomorph](Samantha)<br /> <br /> == O ==<br /> '''object-oriented programming''' - a programming paradigm in which collections of data, associated with operations on that data, are modularly defined and then built upon (CSC 121 Lecture, Will). <br /> <br /> '''open reading frame (ORF)'''-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) [http://www.fao.org/DOCREP/003/X3910E/X3910E18.htm ORF] (Pallavi)<br /> <br /> '''operon''' - a segment of DNA involving an operator, promoter, and one or more genes that operate as a single unit during transcription [http://en.wikipedia.org/wiki/Operon] (Nick)<br /> <br /> '''optical mapping'''-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome [http://www.geocities.com/bioinformaticsweb/genomicglossary.html optical mapping] (Pallavi)<br /> <br /> '''ortholog'''-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)<br /> <br /> '''oxidoreductase''' - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [http://en.wikipedia.org/wiki/Oxidoreductase] (Nick)<br /> <br /> == P ==<br /> <br /> '''paralog'''-identical DNA sequences within a species (Lecture, Pallavi)<br /> <br /> '''p-arm''' - the shorter arm of a chromosome's two arms separated by the centromere (compare to q-arm, the longer arm) ([http://www.medterms.com/script/main/art.asp?articlekey=4715 MedTerms Dictionary], Jay)<br /> <br /> '''Perl''' - Developed by Larry Wall in 1987, Perl is a [http://en.wikipedia.org/wiki/High-level_programming_language high-level programming language] used frequently by biologists and bioinformaticists [http://en.wikipedia.org/wiki/Perl] (Will). <br /> <br /> '''periplasmic space''' - the space between the inner cytoplasmic membrane and external outer membrane in bacteria or archaea. [http://en.wikipedia.org/wiki/Periplasmic_space] (Peter)<br /> <br /> '''Pfam''' - a database for protein domain families that matches amino acid sequences or nucleotide sequences to the related group of proteins to which they most likely belong. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura)<br /> <br /> '''plasmid''' - an extra-chromosomal DNA molecule that is capable of replicating independently of the chromosomal DNA. Commonly found in bacteria and archaea. [http://en.wikipedia.org/wiki/Plasmid](Peter)<br /> <br /> '''plastid''' - major organelles in plants or algae [http://en.wikipedia.org/wiki/Plastid](Samantha)<br /> <br /> '''pleomorphism''' - the occurrence of two or more structural forms during a life cycle [http://en.wikipedia.org/wiki/Pleomorphism] (Mary)<br /> <br /> '''phylogenetic tree''' - a diagram showing the evolutionary relationships between biological species that are thought to share a common ancestor [http://en.wikipedia.org/wiki/Phylogenetic_tree] (Nick)<br /> <br /> '''phylotypes''' – a term intended to resolve the challenge of “species” when classifying prokaryotes using DNA sequence comparisons. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''positives''' - in a BLAST output, the number and fraction of residues for which the alignment scores have positive rather than negative values [http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''proteome''' - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions [http://en.wikipedia.org/wiki/Proteome](Samantha)<br /> <br /> '''PSORT''' - a prediction server that judges where a mature protein could be in the cell, based on its transmembrane domains, its predicted mature amino acid composition, and its signal sequences. ([http://psort.ims.u-tokyo.ac.jp/form.html PSORT], Laura)<br /> <br /> '''psuedogenes'''-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)<br /> <br /> '''purine''' - a category of nitrogenous base consisting of a pyrimidine ring fused to an imidazole ring. Notable purine bases are adenine and guanine. [http://en.wikipedia.org/wiki/Purine] (Peter)<br /> <br /> '''pyrimidine''' - a category of nitrogenous base consisting of a heterocyclic aromatic ring containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Notable pyrimidine bases are cytosine, thymine, and uracil. [http://en.wikipedia.org/wiki/Pyrimidine] (Peter)<br /> <br /> == Q ==<br /> <br /> '''q-arm''' - the longer arm of a chromosome's two arms separated by the centromere (compare to p-arm, the shorter arm) ([http://www.medterms.com/script/main/art.asp?articlekey=5152 MedTerms Dictionary], Jay)&lt;br&gt;<br /> <br /> '''query sequence''' - the sequence (whether amino acid or nucleotide) entered into a database’s search function and checked against the database entries. ([http://en.wikipedia.org/wiki/BLAST BLAST on Wikipedia], Laura)<br /> <br /> == R ==<br /> <br /> '''RAST''' - (Rapid Annotation using Subsystem Technology)- a fully-automated service for annotating bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree. ([http://rast.nmpdr.org/], Max Win)<br /> <br /> '''rDNA'''-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. ([http://en.wikipedia.org/wiki/Ribosomal_DNA rDNA] Pallavi)<br /> <br /> '''residue (protein)''' - the remaining portion of an amino acid after a water molecule has been removed and it has been incorporated into a protein. Functional residues, referred to in Pfam, are the residues that perform some specific identifiable function or are part of a domain, and can be conserved across evolutionarily-related proteins. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura) &lt;br&gt;<br /> <br /> '''retropseudogenes'''-these are genes that have been reverse-transcribed from mRNA and the resulting DNA sequence is incorporated back into the genome. They are non-functional segments of DNA and can be distinguished from pseudogenes in that they do not have intron sequences. ([http://genome.cshlp.org/cgi/content/full/10/5/672 1] Pallavi)<br /> <br /> '''retrotransposons''' - RNA transcribed back into DNA and added into the genome [http://en.wikipedia.org/wiki/Retrotransposon](Samantha)<br /> <br /> '''ribonuclease''' - a nuclease that catalyzes the degradation of RNA into smaller components [http://en.wikipedia.org/wiki/Ribonuclease] (Mary)<br /> <br /> == S ==<br /> '''Serovar'''-a subdivision of a species based on the characteristics of their cell surface antigens ([http://www.biology-online.org/dictionary/Serovar serovar] Pallavi)<br /> <br /> '''scaffold''' - a section of a sequenced genome composed of contigs that are in the right order but not necessarily connected ([http://www.medterms.com/script/main/art.asp?articlekey=25223 MedTerms Dictionary], Jay)<br /> <br /> '''&quot;Shadow enhancers&quot;'''-secondary enhancers that are thought to be important for natural selection to occur in regulatory DNA segments. They evolve much faster than primary enhancers, which suggests that they are under fewer functional constraints (Wray and Babbit 2008 ''Science'' Pallavi)<br /> <br /> '''Shine-Dalgarno sequence''' - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and [http://en.wikipedia.org/wiki/Shine-dalgarno Wikipedia article], Laura)&lt;br&gt;<br /> Note: The Shine-Dalgarno consensus sequence for our genome is ccGGAGGt.<br /> <br /> '''SignalP''' - a prediction server that judges whether or not a query protein is a signal peptide. SignalP measures each amino acid against the amino acid sequences of probable signal peptide matches and predicts the cleavage site of the signal peptide. ([http://www.cbs.dtu.dk/services/SignalP-3.0/output.php SignalP Output explained], Laura)<br /> <br /> '''signal peptide''' - a short peptide chain that directs the post-translational transport of a protein [http://en.wikipedia.org/wiki/Signal_peptide] (Matt)<br /> <br /> '''Smith-Waterman alignment''' - A well-known algorithm for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure [http://en.wikipedia.org/wiki/Smith_waterman](Will).<br /> <br /> '''SNP (Single Nucleotide Polymorphism)''' - a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual) [http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism](Will).<br /> <br /> '''symporter''' - an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane. [http://en.wikipedia.org/wiki/Symporter] (Peter)<br /> <br /> '''synteny''' - a neologism from the Greek for &quot;on the same ribbon&quot;. Genes that are syntenic in one species are on the same chromosome; genes that are syntenic across species retain the same order on respective chromosomes as a result of descent from a common ancestor ([http://www.answers.com/synteny Answers.com], Jay)<br /> <br /> '''synthetase''' - a type of enzyme that creates a new covalent bond and requires direct input of energy from a high-energy phosphate. [http://books.google.com/books?id=bB8XnCykRmIC&amp;pg=PA522&amp;lpg=PA522&amp;dq=%22synthetase+is+an+enzyme%22&amp;source=web&amp;ots=wkws4ksMsg&amp;sig=zWLkDIk7T78hcf9S84nWs3u5Apw&amp;hl=en&amp;sa=X&amp;oi=book_result&amp;resnum=9&amp;ct=result] (Peter)<br /> <br /> == T ==<br /> '''transferase''' - an enzyme that catalyzes the transfer of a functional group from one molecule (the donor) to another (the acceptor) [http://en.wikipedia.org/wiki/Transferase] (Matt)<br /> <br /> '''transmembrane helix''' - a single transmembrane alpha helix of a transmembrane protein, usually about twenty amino acids in length. They are usually predicted by hydrophobicity. [http://en.wikipedia.org/wiki/Transmembrane_domain](Mary)<br /> <br /> '''transposons / transposable elements''' - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. [http://en.wikipedia.org/wiki/Transposon](Samantha)<br /> <br /> '''Transposon Mutagenesis'''-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene ([http://cancerweb.ncl.ac.uk/cgi-bin/omd?transposon+mutagenesis transposon mutagenesis] Pallavi)<br /> <br /> '''Trans-splicing'''-fragmented exon sequences fuse to form a mature species of mRNA. This process results in fusion mRNA ([http://www.representinggenes.org/Glossary.html 8] Pallavi).<br /> <br /> '''tRNA splicing endonuclease''' - an enzyme that cleaves intervening sequences of precursor tRNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?splicing+endonuclease] (Peter)&lt;br&gt;<br /> <br /> == U ==<br /> <br /> == V ==<br /> '''Vertical gene transfer'''-the transmission or absorption of genetic material that is associated with sexual reproduction and, thus, acknowledges species-specific boundaries ([http://www.gmo-compass.org/eng/glossary/#G 6] Pallavi)<br /> <br /> == W ==<br /> <br /> '''whole genome shotgun sequencing''' - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. [http://en.wikipedia.org/wiki/Whole_genome_shotgun](Samantha)<br /> &lt;br&gt;<br /> <br /> == X ==<br /> '''xenolog''' - homologs that are created by horizontal gene transfer between two different species [http://en.wikipedia.org/wiki/Xenolog#Xenology] (Matt)&lt;br&gt;<br /> <br /> == Y ==<br /> <br /> == Z ==<br /> <br /> &lt;BR&gt;</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Halorhabdus_utahensis_Genome&diff=7092 2008-11-04T16:14:21Z

<p>LaHeyer: /* Pathway Tutorials */</p> <hr /> <div>This page will be used by Davidson College students in the [http://www.bio.davidson.edu/Courses/Bio343/LabMethods.html Genomics Laboratory course].<br /> __NOTOC__<br /> == Links to Multiple Databases ==<br /> *[http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&amp;page=taxonDetail&amp;taxon_oid=2500575004 JGI IMG EDU] &lt;br&gt; public access &lt;br&gt; *[[Media:JGIAnnotation.xls|JGI Annotation Excel Spreadsheet]]<br /> *[http://www.tigr.org/tigr-scripts/prok_manatee/shared/login.cgi Manatee at JCVI] &lt;br&gt; use the davidson number sent by email as username and password (database is nthu01 - this is case sensitive) &lt;br&gt; *[[Media:ManateeAnnotation.xls|Manatee Annotation Excel Spreadsheet]]<br /> *[http://rast.nmpdr.org/ SEED view via RAST] &lt;br&gt; use the username and password combination sent to you by SEED &lt;br&gt; *[[Media:RastAnnotation.xls|RAST Annotation Excel Spreadsheet]]&lt;br&gt; *[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=18261238 RAST Publication in PubMed]<br /> *[http://www.genome.jp/kegg/kaas/ KEGG]&lt;br&gt; We can submit our genes to KEGG to have it mapped out, but SEED and Manatee may already do this. Do we want to ask them to upload it into their database? &lt;br&gt;<br /> *[http://wishart.biology.ualberta.ca/basys/cache/135af8726ad6f61ec4c5f1e9c4d139ac/index.html BASYs]&lt;br&gt;&lt;br&gt;<br /> *[http://gcat.davidson.edu/Registry/compare/ Pairwise comparisons of All Three Annotations]<br /> <br /> <br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI_5contigs.txt JGI Full genome, 5 separate contigs &amp; 3.1 Mbp, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.txt JGI gene DNA sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_genes.xls JGI gene annotations, Excel] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/JGI2500575004_proteins.txt JGI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_merged.txt CJVI Full genome, 5 contigs fused, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_ORFs.txt CJVI gene sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/h_utahensis_proteins.txt CJVI protein sequences, FASTA] &lt;br&gt;<br /> [http://www.bio.davidson.edu/Courses/Bio343/sequences/GeneLengths.xls 3-way comparison, Excel] &lt;br&gt;<br /> [[Venn_diagrams]] Venn diagram of 3-way comparison<br /> <br /> &lt;br&gt;<br /> <br /> == RNA Genes ==<br /> <br /> *[[tRNA Genes Check List]]&lt;br&gt;<br /> *[[rRNA operon]]&lt;br&gt;<br /> *[[2 misc. RNA genes]] (short summary list)&lt;br&gt;<br /> *[[Missing tRNA-trp gene found]]&lt;br&gt;<br /> <br /> == Other Resources ==<br /> *[[Consensus Shine Dalgarno]] Excel File for ''H. utahensis'' &lt;br&gt;<br /> *[[References]]&lt;br&gt;<br /> *[[Gene Annotation Template]]&lt;br&gt;<br /> *[[General Questions]]&lt;br&gt;<br /> *[[Page for Annotated Genes]]&lt;br&gt;<br /> *[http://www.bio.davidson.edu/courses/genomics/2008/Win/ec/ Search EC number in RAST, JGI or Manatee] &lt;br&gt;<br /> *[http://gcat.davidson.edu/Wideloache/Webfiles/ecNumBlast.html Blast an EC number against the H. utahensis genome]&lt;br&gt;<br /> <br /> == Research Questions ==<br /> #How do the three systems compare for finding ORFs and RNA genes?<br /> #Is there a pattern of missed genes for any of the 3 sites? <br /> #Do the three systems differ in their ability to find good start codons and Shine-Dalgarno sequences? [We need a standard set of genes for comparison. Only highly conserved or a range of genes?]<br /> # Were Shine-Dalgarno sequences calculated for our species or default values used? If default, what sequence?<br /> #Can we fill any holes in their automated annotation? Is there a mechanism for users to add in genes?<br /> #How do the 3 sites compare for ease of use?<br /> #What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working?<br /> #How does each of the 3 sites compare for pathway detection and visualization? <br /> #Do they find the origin of replication? Can we find it? <br /> <br /> * How do the 3 systems compare when one gene is called hypothetical and the other calls it a functional protein? How can they vary and who is getting it closer to correct (however you define that, possibly by date of matched entry: Pallavi and Mary)<br /> * Why did one system call a gene when the other two did not? (Matt and Lara)<br /> * How do the 3 sites compare for ease of use? What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working? (Samantha and Nick)<br /> * Where is the origin of replication and did the 3 systems attempt to identify this?<br /> * Did the 3 systems utilize Shine-Dalgarno sequences to help them call start codons? Did they utilize our species's consensus Shine-Dalgarno? (Peter)<br /> * We need to fill in the [[Venn diagrams]] for our 3-way comparison. Let's compare the size of ORFs and generate a [[Gene Length Histograms|graph comparing the distributions]] for all 3. (Max and Will - they also take requests). <br /> <br /> &lt;hr&gt;<br /> =Our Favorites=<br /> == My favorite genes==<br /> Pallavi - Monooxygenase vs. Peroxiredoxin<br /> <br /> Mary - JGI gene 2500588521 (922976...924046) [[Media:My favorite gene.ppt]]<br /> <br /> Max - [http://app.sliderocket.com/app/FullPlayer.aspx?id=f2058b94-845f-4a11-94eb-142f251a7fea JGI gene 2500587636 (2-1849)]<br /> <br /> Samantha - JGI gene 2500575882 (80504-80878) [[Media:Earl.ppt]]<br /> <br /> Nick - JGI gene 2300587691 (69942...72866) [[Media:Gene presentation.ppt]]<br /> <br /> Will - JGI gene 2500590430 (2847205..2854335)<br /> <br /> Jay - JGI gene 2500588397 (806410..807321) [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Fav_Gene/FavoriteGenePresentation.pptx Co/Zn/Cd PowerPoint]<br /> <br /> Matt - Transcriptional Regulator nrdR (3109722..3110204 + 7274..7765)<br /> <br /> Peter - tRNA intron endonuclease [[Media:TRNAtrpintronendonuclease.ppt]]<br /> <br /> Laura - 16S Small ribosomal subunit, JGI gene 2500590728 (2397347..2398825)<br /> <br /> == My Favorite Pathways==<br /> Pallavi - Carbohydrate Metabolism<br /> <br /> Jay - Membrane Transport<br /> <br /> Will - Signal Transduction<br /> <br /> Max -energy<br /> <br /> ''Suggestions by Kjeld''&lt;br&gt;<br /> '''[[Cellulase]]''' by Pallavi&lt;br&gt;<br /> I think it would be very interesting to look for genes involved in cellulose degradation: endocellulases, exocellolases (=cellobiohydrolases) and b-glucosidases.<br /> Many cellulose degrades produce a range of each type. A cellolulyic system able to function at 4.6 M of NaCl is an interesting one. We either did not observed (or look for cellulose degradation). However, these systems are normally inducible and you need to test several substrates and inducers. It would be nice to have a compilation of putative “cellulase” genes.<br /> There are several good recent reviews on cellulases (also mentioning E.C. numbers and enzyme families) that your students could consult.<br /> <br /> '''[[Chitinase]]''' by Matt&lt;br&gt;<br /> Apparently you detected a chitinase but according to our records it does not gorw on N-acetyl-glucosamine which is somewhat strange. It grows on glucose though. <br /> <br /> '''[[Lipases]]''' by Mary&lt;br&gt;<br /> Lipases (/esterases) would also be interesting to look for – some lipases have important industrial applications.<br /> <br /> '''[[Amylases]]''' by Samantha&lt;br&gt;<br /> We did not observed growth on starch. Did you find any “amylase-coding genes”?<br /> <br /> '''[[Xylose (glucose) isomerase)]]''' by Nick&lt;br&gt;<br /> An enzyme of great commercial value. <br /> <br /> '''[[Amino acids]]''' lead by Laura and assisted by Max, Jay, Nick and Samantha&lt;br&gt;<br /> According to our records AX-2 is able to grow in a “defined medium”. This is at variance with your “holes” for synthesis of amino acids. However, there could have been some “carry over” of amino acids when inoculating a culture grown in complex medium (e.g. containing yeast extract). However, we are normally aware of this problem and do repeated culturing to dilute out potential growth factors present in yeast extract.<br /> <br /> '''[[Proteases]]''' by Peter&lt;br&gt;<br /> We did not detect protease activity – albeit only checking a few substrates.<br /> <br /> '''[[Protein Export]]''' by Malcolm &lt;br&gt;<br /> We need to know how these proteins might reach outside the cell which is where the food would be and thus the digestive enzymes or importers need to reach the outside world or the cell membrane.<br /> <br /> = Student-created tutorials: =<br /> == Tutorials for Annotating Genomes ==<br /> <br /> # Will DeLoache - [http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/BioPerlTutorial/BioPerl.htm BioPerl Installation] &lt;br&gt;<br /> # Max Win - [http://www.bio.davidson.edu/courses/genomics/2008/Win/perl.html Introduction to Perl for non-programmers.(with step by step explanations,simple exercises and solutions)]&lt;br&gt;<br /> # Pallavi - Conserved Domains Database (CDD) [[Media:CDDtutorial.doc]] &lt;br&gt;<br /> # Mary - Protein Data Bank (PDB) [[Media:PDB Tutorial.doc]] &lt;br&gt;<br /> # Laura Voss - Pfam Database [http://www.bio.davidson.edu/Courses/Bio343/Pfam_tutorial.doc Pfam Tutorial] &lt;br&gt;<br /> # Samantha Simpson - [http://www.bio.davidson.edu/courses/genomics/2008/Simpson/Tutorial.html NCBI BLAST]&lt;br&gt;<br /> # Peter Bakke - [[Media:ShineDalgarnoTutorial.doc]]&lt;br&gt;<br /> # Jay McNair - [http://www.bio.davidson.edu/courses/genomics/2008/McNair/Origin_Tutorial/OriginTutorial.doc Origin of Replication Tutorial]&lt;br&gt;<br /> # Nick Carney - Navigating the JGI Database [[Media:NavigatingJGItutorial.doc]]&lt;br&gt;<br /> # Matt Lotz - SEED Viewer - [[Media:SEEDTutorial.doc]] &lt;br&gt;<br /> == Pathway Tutorials==<br /> [http://www.pathguide.org/ Pathguide] - a possible source of tutorials and extensive information<br /> <br /> *Pallavi: I will compare RAST and KEGG in pathway annotations and use Glycolysis/Gluconeogenesis as my example<br /> <br /> &lt;hr&gt;<br /> <br /> =Glossary words (A - Z):=<br /> [[#A| A ]] [[#B| B ]] [[#C| C ]] [[#D| D ]] [[#E| E ]] [[#F| F ]] [[#G| G ]] [[#H| H ]] [[#I| I ]] [[#J| J ]] [[#K| K ]] [[#L| L ]] [[#M| M ]] [[#N| N ]] [[#O| O ]] [[#P| P ]] [[#Q| Q ]] [[#R| R ]] [[#S| S ]] [[#T| T ]] [[#U| U ]] [[#V| V ]] [[#W| W ]] [[#X| X ]] [[#Y| Y ]] [[#Z| Z ]] <br /> <br /> == A ==<br /> '''Accession Number''' - a unique identifier given to DNA and protein sequences to allow for tracking of sequence information within a single database [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics)] (Will).<br /> <br /> '''Antisense (RNA or DNA)'''-a piece of DNA or RNA that binds to a complementary sequence of DNA or RNA. These segments of genetic material can be used to identify the existence of a disease gene and they can also be used to bind to specific DNA or mRNA sequences to inhibit their function ([http://biotech.fyicenter.com/glossary/Bioinformatics_Glossary.html 5] Pallavi).<br /> <br /> '''&lt;i&gt;Arabidopsis thaliana&lt;/i&gt;''' - the scientific name for the thale cress plant; it was the first plant to have its genome sequenced, and is a model organism for understanding plant biology and genetics ([http://en.wikipedia.org/wiki/Thale_cress Wikipedia.org], Jay)<br /> <br /> == B ==<br /> '''BAC''' - &lt;i&gt;b&lt;/i&gt;acterial &lt;i&gt;a&lt;/i&gt;rticifical &lt;i&gt;c&lt;/i&gt;hromosome, a DNA construct used for transforming or cloning segments of DNA and often used to sequence the genetic code of organisms ([http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome Wikipedia.org], Jay)<br /> <br /> '''bioinformatics''' - the multi-disciplinary approach of using biology, computer science and mathematics to solve or better understand biological problems [http://en.wikipedia.org/wiki/Bioinformatics] (Matt)<br /> <br /> '''BLAST''' - (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. [http://blast.ncbi.nlm.nih.gov/Blast.cgi] (Mary)<br /> <br /> '''bioperl'''- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications such as accessing sequence data from local and remote databases, transforming formats of database, manipulating individual sequences, searching for similar sequences, searching for genes and other structures on genomic DNA, or developing a machine readable sequence annotations. [http://en.wikipedia.org/wiki/BioPerl] (Wikipedia, Max Win)<br /> <br /> == C ==<br /> '''carbon fixation''' - using carbon dioxide to create organic materials [http://en.wikipedia.org/wiki/Carbon_fixation] (Samantha)&lt;BR&gt;<br /> <br /> '''CDD''' (Conserved Domains Database)- a database used to identify the conserved domains present in a protein query sequence [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml] (Mary)<br /> <br /> '''chaperonin''' - a protein complex that assists some newly formed polypeptide chains by folding them into their final, functional, three-dimensional form [http://en.wikipedia.org/wiki/Chaperonins] (Matt)<br /> <br /> '''chemotaxis''' - the process in which cells will seek out or flee from a high concentration of certain chemicals and is found in both uni- and multicellular organisms. This process is used to avoid toxins or find food in unicelllular organisms or tasks such as reproduction in multicellular organisms [http://en.wikipedia.org/wiki/Chemotaxis] (Nick)<br /> <br /> '''chemotaxonomy''' - the attempt to classify and identify organisms according to demonstrable differences and similarities in their biochemical compositions [http://en.wikipedia.org/wiki/Chemotaxonomy] (Mary)<br /> <br /> '''ClustalW''' - A web-based or command line tool that performs multiple sequence alignments to determine evolutionary relationships between three or more sequences [http://en.wikipedia.org/wiki/Clustal] (Will).<br /> <br /> '''COG''' (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs ([http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml COG] Pallavi) &lt;br&gt;<br /> <br /> '''concatemer''' - long continuous DNA molecule that contains the same DNA sequence repeated in series [http://en.wikipedia.org/wiki/Concatemer](Samantha)&lt;BR&gt;<br /> <br /> '''contigs''' (contiguous DNA)- overlapping DNA segments that as a collection from a longer and gapless segment of DNA. (Discovery Genomics, Proteomics and Bioinformatics [http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''coverage''' - refers to the number of times, on average, any piece of DNA in a sequenced genome has been individually sequenced (Lecture, Jay)<br /> <br /> '''CPAN (Comprehensive Perl Archive Network)''' - an archive of over 12,200 modules of software written in Perl, as well as documentation for it. It contains a module called CPAN (or CPAN.pm) which is used as an installer for Perl modules such as BioPerl [http://en.wikipedia.org/wiki/CPAN](Will).<br /> <br /> '''Cytogenetics'''-the study of normal and abnormal chromosomes. This involves studying the causes of chromosomal abnormalities and looking at the structure of chromosomes ([http://www.vivo.colostate.edu/hbooks/genetics/medgen/chromo/index.html 7] Pallavi).<br /> <br /> == D ==<br /> '''''de novo'' synthesis''' - the synthesis of complex molecules from simple molecules (e.g. sugars and nucleotides), rather than from recycled molecules; from the latin &quot;of the new&quot; [http://en.wikipedia.org/wiki/De_novo_synthesis] (Matt)<br /> <br /> '''dehydrogenase''' - a type of enzyme that oxidizes a substrate by transferring one or more protons and a pair of electrons to an acceptor. [http://en.wikipedia.org/wiki/Dehydrogenase] (Peter)<br /> <br /> '''diatom''' - a major group of eukaryotic algae, and one of the most common types of phytoplankton. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica called a frustule. These frustules show a wide diversity in form, but usually consist of two asymmetrical sides with a split between them. [http://en.wikipedia.org/wiki/Diatom] (Mary)<br /> <br /> '''domain (protein)''' - the structural and functional groups of a protein, which can exist independently of the protein itself. Domains typically perform a specific function, such as binding to promoters or substrates, and many proteins can have one or several domains in common. Evolutionarily-linked proteins are more likely to have domains in common. Domains are used to organize proteins into families. ([http://en.wikipedia.org/wiki/Domain_(protein) Wikipedia article], Laura)<br /> <br /> '''dot plot'''-graphical display comparing sequence conservation between two genomes with dots indicating strings of identical bases. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> == E ==<br /> <br /> '''EC number''' (Enzyme Commission Number)- a numerical classification scheme for enzymes, based on the chemical reactions they catalyze [http://en.wikipedia.org/wiki/EC_number] (Mary)<br /> <br /> '''E-value''' (Expect value)- When performing a BLAST search, you will obtain an E-value for each sequence that is retrieved. And E-value can be thought of as the probability that two sequences are similar to each other by chance. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''Extremophile''' - an organism that thrives in and may even require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth [http://en.wikipedia.org/wiki/Extremophile] (Will).<br /> <br /> == F ==<br /> <br /> '''FASTA format''' - a format used to convey either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented by single-letter codes. The sequence name and other descriptors often precede the amino acid sequence. [http://en.wikipedia.org/wiki/FASTA_format] (Nick)&lt;br&gt;<br /> <br /> '''family (protein)''' - a group of evolutionarily-related proteins, often with one or several domains in common. Families are organized by domain overlap, structural/functional similarity, and sequence similarity. ([http://en.wikipedia.org/wiki/Protein_family Wikipedia article] and lecture, Laura)<br /> <br /> '''finished genome''' - a genome that has been sequenced at least partly by hand, resulting at least 99.99% sequence accuracy (Lecture, Jay)&lt;br&gt;<br /> <br /> '''fusion mRNA'''-mRNA that results from the transcription of a gene after a chromosomal translocation event. This results in an mRNA sequence that comes from two different genes (Rowley and Blumenthal 2008 ''Science'' Pallavi)<br /> <br /> == G ==<br /> <br /> '''GC Content''' - the percentage of bases within a certain sequence of DNA (e.g. a gene or a genome) that are either guanine or cytosine; a higher GC content is characteristic of a coding region of a gene; differences in GC content between a gene and a genome can be used as evidence for horizontal gene transfer [http://en.wikipedia.org/wiki/GC-content] (Matt)&lt;br&gt;<br /> <br /> '''GC-skew''' – uneven distribution of guanine and cytosine bases between the two strands of DNA where GC base pairs occur. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''gene amplification''' - production of multiple copies of a gene in order to amplify the amount of protein that the gene encodes for [http://www.medterms.com/script/main/art.asp?articlekey=13537] [http://www.answers.com/topic/gene-amplification] (Matt)<br /> <br /> '''gene fusion'''-occurs when DNA segments of two different genes come together. Can result in hybrid proteins ([http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html 9] Pallavi)<br /> <br /> '''gene knockout''' - a process in which a gene is deactivated within a test organism in order to better understand the function of the gene in that organism [http://en.wikipedia.org/wiki/Gene_knockout] (Matt)<br /> <br /> '''gene oncology'''- a collaborative effort of investigators to unify and standardize terms associated with the role a gene or protein plays in an organism. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''glaucophyte''' - freshwater algae that have not been studied well [http://en.wikipedia.org/wiki/Glaucophyte](Samantha)&lt;br&gt;<br /> <br /> == H ==<br /> <br /> '''haemolysin or hemolysin''' - a chemical produced by a bacteria that causes lysis of red blood cells [http://en.wikipedia.org/wiki/Hemolysis_(microbiology)] (Nick)<br /> <br /> '''halophile''' - an organism, most often of the Archaea domain, that lives in environments containing high concentrations of salt [http://en.wikipedia.org/wiki/Halophile] (Matt)<br /> <br /> '''haplotype'''-collection of alleles that travel together (Lecture, Pallavi)<br /> <br /> '''haptophyte''' - phylum of algae [http://en.wikipedia.org/wiki/Haptophyte](Samantha)<br /> <br /> '''heterokont''' - major line of eukaryotes consisting of about 10,500 known species, most of which are algae [http://en.wikipedia.org/wiki/Heterokont](Samantha)<br /> <br /> '''Hidden Markov Model''' - a statistical model used in protein recognition databases such as Pfam. A Hidden Markov Model keeps track of several variables and possible variations thereof, such as the possible amino acid sequences that make up a protein domain (since there can be some variance in an amino acid sequence) or the variations in the component sounds that make up a word, and uses those points to match a given sequence to the word, domain, or other complex sequence it most closely matches. An HMM in speech recognition software, for example, can identify that a certain set of sounds make up a certain word, even with the variations in pronunciation and accent that different people will give those sounds. ([http://en.wikipedia.org/wiki/Hidden_Markov_Model Wikipedia] and lecture, Laura) <br /> <br /> '''HMM Logo''' - a graphical representation of an HMM, detailing the possible amino acid sequences, the relative frequencies and probabilities of each amino acid in the sequence, the relative contribution each amino acid has to the overall protein family, and the charge or nature of the amino acids themselves. ([http://www.sanger.ac.uk/Software/analysis/logomat-m/help.shtml How to read HMM Logos, on Pfam], Laura)<br /> <br /> '''homeobox''' - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades [http://en.wikipedia.org/wiki/Homeobox](Samantha)<br /> <br /> '''homodimer''' - a protein made of paired identical polypeptides ([http://www.answers.com/topic/homodimer Answers.com], Jay)<br /> <br /> '''horizontal gene transfer'''-DNA transmission between species and incorporation of the DNA into the recipient's genome ([http://www.csrees.usda.gov/nea/biotech/res/biotechnology_res_glossary.html horizontal gene transfer] Pallavi)<br /> <br /> '''''Hox'' gene'''-a gene that contains a homeobox region that is involved in morphogenesis along the cranio-caudal body axis ([http://www.uprightape.net/UA_Glossary.html 4] Pallavi)<br /> <br /> '''hydrolase''' - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often take part in subsequent reactions [http://en.wikipedia.org/wiki/Hydrolase] (Nick)<br /> <br /> == I ==<br /> <br /> '''ideogram''' - in genomics, usually describes a stylized representation of a chromosome with banding patterns (Campbell-Heyer Genomics textbook, Jay)<br /> <br /> '''identities''' - in a BLAST output, the number and fraction of total residues which are identical in a given alignment [www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''indole'''-a chemical compound that is produced from the break down of tryptophan ([http://medical-dictionary.thefreedictionary.com/indole indole] Pallavi)<br /> <br /> '''inclusion body''' - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [http://en.wikipedia.org/wiki/Inclusion_body] (Nick)<br /> <br /> '''intron''' - a region of DNA in a gene that is not part of the final coding sequence for the protein. [http://en.wikipedia.org/wiki/Intron] (Peter)<br /> <br /> '''isoelectric point''' - the pH at which a molecule is neutral [http://en.wikipedia.org/wiki/Isoelectric_point] (Nick)<br /> <br /> '''isozymes''' - members of a gene family with very similar cellular roles (Cambpell-Heyer Genomics textbook, Jay)<br /> <br /> == J ==<br /> <br /> == K ==<br /> '''KEGG (Kyoto Encyclopedia of Genes and Genomes)''' - a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The Pathway database records networks of molecular interactions in the cells, and variants of them specific to particular organisms [http://en.wikipedia.org/wiki/KEGG](Will).<br /> <br /> '''kinase''' - a type of enzyme that transfers a phosphate group from a high-energy donor molecule to a target molecule in a process called phosphorylation. [http://en.wikipedia.org/wiki/Kinase] (Peter)<br /> <br /> == L ==<br /> <br /> == M ==<br /> '''Manatee''' - a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. This on-going, open source initiative was developed with two missions. One, to allow biologists the ability to functionally annotate their genomes using a powerful, stand-alone web application with a robustly designed relational annotation database. And secondly, to invite outside developers the opportunity to contribute their own ideas and requirements to enhance Manatee's ability to accomplish biological goals [http://manatee.sourceforge.net/](Will). &lt;br&gt;<br /> <br /> '''microsatellites'''-stretches of repetitive, short DNA segments that can be used to track the inheritance of certain traits within families ([http://www.clanlindsay.com/genetic_dna_glossary.htm 3] Pallavi)<br /> <br /> '''minisatellites'''-segments of DNA that can be used for individual identification (ex. DNA fingerprinting) or in determining relationships between people (ex. paternity cases) ([http://www.clanlindsay.com/genetic_dna_glossary.htm 2] Pallavi).<br /> <br /> '''motif''' - a sequence of amino acids or nucleotides that performs a particular role and is often conserved in other species or molecules. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''mycoplasma''' - genus of bacteria that lack a cell wall [http://en.wikipedia.org/wiki/Mycoplasma] (Nick)<br /> <br /> == N ==<br /> <br /> '''NORFs''' (nonannotated open reading frame) - on open reading frame that was considered not to be a real gene when the genome was annotated.( Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''nucleomorph''' - reduced eukaryotic nuclei found in plastids [http://en.wikipedia.org/wiki/Nucleomorph](Samantha)<br /> <br /> == O ==<br /> '''object-oriented programming''' - a programming paradigm in which collections of data, associated with operations on that data, are modularly defined and then built upon (CSC 121 Lecture, Will). <br /> <br /> '''open reading frame (ORF)'''-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) [http://www.fao.org/DOCREP/003/X3910E/X3910E18.htm ORF] (Pallavi)<br /> <br /> '''operon''' - a segment of DNA involving an operator, promoter, and one or more genes that operate as a single unit during transcription [http://en.wikipedia.org/wiki/Operon] (Nick)<br /> <br /> '''optical mapping'''-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome [http://www.geocities.com/bioinformaticsweb/genomicglossary.html optical mapping] (Pallavi)<br /> <br /> '''ortholog'''-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)<br /> <br /> '''oxidoreductase''' - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [http://en.wikipedia.org/wiki/Oxidoreductase] (Nick)<br /> <br /> == P ==<br /> <br /> '''paralog'''-identical DNA sequences within a species (Lecture, Pallavi)<br /> <br /> '''p-arm''' - the shorter arm of a chromosome's two arms separated by the centromere (compare to q-arm, the longer arm) ([http://www.medterms.com/script/main/art.asp?articlekey=4715 MedTerms Dictionary], Jay)<br /> <br /> '''Perl''' - Developed by Larry Wall in 1987, Perl is a [http://en.wikipedia.org/wiki/High-level_programming_language high-level programming language] used frequently by biologists and bioinformaticists [http://en.wikipedia.org/wiki/Perl] (Will). <br /> <br /> '''periplasmic space''' - the space between the inner cytoplasmic membrane and external outer membrane in bacteria or archaea. [http://en.wikipedia.org/wiki/Periplasmic_space] (Peter)<br /> <br /> '''Pfam''' - a database for protein domain families that matches amino acid sequences or nucleotide sequences to the related group of proteins to which they most likely belong. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura)<br /> <br /> '''plasmid''' - an extra-chromosomal DNA molecule that is capable of replicating independently of the chromosomal DNA. Commonly found in bacteria and archaea. [http://en.wikipedia.org/wiki/Plasmid](Peter)<br /> <br /> '''plastid''' - major organelles in plants or algae [http://en.wikipedia.org/wiki/Plastid](Samantha)<br /> <br /> '''pleomorphism''' - the occurrence of two or more structural forms during a life cycle [http://en.wikipedia.org/wiki/Pleomorphism] (Mary)<br /> <br /> '''phylogenetic tree''' - a diagram showing the evolutionary relationships between biological species that are thought to share a common ancestor [http://en.wikipedia.org/wiki/Phylogenetic_tree] (Nick)<br /> <br /> '''phylotypes''' – a term intended to resolve the challenge of “species” when classifying prokaryotes using DNA sequence comparisons. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''positives''' - in a BLAST output, the number and fraction of residues for which the alignment scores have positive rather than negative values [http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''proteome''' - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions [http://en.wikipedia.org/wiki/Proteome](Samantha)<br /> <br /> '''PSORT''' - a prediction server that judges where a mature protein could be in the cell, based on its transmembrane domains, its predicted mature amino acid composition, and its signal sequences. ([http://psort.ims.u-tokyo.ac.jp/form.html PSORT], Laura)<br /> <br /> '''psuedogenes'''-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)<br /> <br /> '''purine''' - a category of nitrogenous base consisting of a pyrimidine ring fused to an imidazole ring. Notable purine bases are adenine and guanine. [http://en.wikipedia.org/wiki/Purine] (Peter)<br /> <br /> '''pyrimidine''' - a category of nitrogenous base consisting of a heterocyclic aromatic ring containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Notable pyrimidine bases are cytosine, thymine, and uracil. [http://en.wikipedia.org/wiki/Pyrimidine] (Peter)<br /> <br /> == Q ==<br /> <br /> '''q-arm''' - the longer arm of a chromosome's two arms separated by the centromere (compare to p-arm, the shorter arm) ([http://www.medterms.com/script/main/art.asp?articlekey=5152 MedTerms Dictionary], Jay)&lt;br&gt;<br /> <br /> '''query sequence''' - the sequence (whether amino acid or nucleotide) entered into a database’s search function and checked against the database entries. ([http://en.wikipedia.org/wiki/BLAST BLAST on Wikipedia], Laura)<br /> <br /> == R ==<br /> <br /> '''RAST''' - (Rapid Annotation using Subsystem Technology)- a fully-automated service for annotating bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree. ([http://rast.nmpdr.org/], Max Win)<br /> <br /> '''rDNA'''-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. ([http://en.wikipedia.org/wiki/Ribosomal_DNA rDNA] Pallavi)<br /> <br /> '''residue (protein)''' - the remaining portion of an amino acid after a water molecule has been removed and it has been incorporated into a protein. Functional residues, referred to in Pfam, are the residues that perform some specific identifiable function or are part of a domain, and can be conserved across evolutionarily-related proteins. ([http://pfam.sanger.ac.uk/help Pfam Help], Laura) &lt;br&gt;<br /> <br /> '''retropseudogenes'''-these are genes that have been reverse-transcribed from mRNA and the resulting DNA sequence is incorporated back into the genome. They are non-functional segments of DNA and can be distinguished from pseudogenes in that they do not have intron sequences. ([http://genome.cshlp.org/cgi/content/full/10/5/672 1] Pallavi)<br /> <br /> '''retrotransposons''' - RNA transcribed back into DNA and added into the genome [http://en.wikipedia.org/wiki/Retrotransposon](Samantha)<br /> <br /> '''ribonuclease''' - a nuclease that catalyzes the degradation of RNA into smaller components [http://en.wikipedia.org/wiki/Ribonuclease] (Mary)<br /> <br /> == S ==<br /> '''Serovar'''-a subdivision of a species based on the characteristics of their cell surface antigens ([http://www.biology-online.org/dictionary/Serovar serovar] Pallavi)<br /> <br /> '''scaffold''' - a section of a sequenced genome composed of contigs that are in the right order but not necessarily connected ([http://www.medterms.com/script/main/art.asp?articlekey=25223 MedTerms Dictionary], Jay)<br /> <br /> '''&quot;Shadow enhancers&quot;'''-secondary enhancers that are thought to be important for natural selection to occur in regulatory DNA segments. They evolve much faster than primary enhancers, which suggests that they are under fewer functional constraints (Wray and Babbit 2008 ''Science'' Pallavi)<br /> <br /> '''Shine-Dalgarno sequence''' - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and [http://en.wikipedia.org/wiki/Shine-dalgarno Wikipedia article], Laura)&lt;br&gt;<br /> Note: The Shine-Dalgarno consensus sequence for our genome is ccGGAGGt.<br /> <br /> '''SignalP''' - a prediction server that judges whether or not a query protein is a signal peptide. SignalP measures each amino acid against the amino acid sequences of probable signal peptide matches and predicts the cleavage site of the signal peptide. ([http://www.cbs.dtu.dk/services/SignalP-3.0/output.php SignalP Output explained], Laura)<br /> <br /> '''signal peptide''' - a short peptide chain that directs the post-translational transport of a protein [http://en.wikipedia.org/wiki/Signal_peptide] (Matt)<br /> <br /> '''Smith-Waterman alignment''' - A well-known algorithm for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure [http://en.wikipedia.org/wiki/Smith_waterman](Will).<br /> <br /> '''SNP (Single Nucleotide Polymorphism)''' - a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual) [http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism](Will).<br /> <br /> '''symporter''' - an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane. [http://en.wikipedia.org/wiki/Symporter] (Peter)<br /> <br /> '''synteny''' - a neologism from the Greek for &quot;on the same ribbon&quot;. Genes that are syntenic in one species are on the same chromosome; genes that are syntenic across species retain the same order on respective chromosomes as a result of descent from a common ancestor ([http://www.answers.com/synteny Answers.com], Jay)<br /> <br /> '''synthetase''' - a type of enzyme that creates a new covalent bond and requires direct input of energy from a high-energy phosphate. [http://books.google.com/books?id=bB8XnCykRmIC&amp;pg=PA522&amp;lpg=PA522&amp;dq=%22synthetase+is+an+enzyme%22&amp;source=web&amp;ots=wkws4ksMsg&amp;sig=zWLkDIk7T78hcf9S84nWs3u5Apw&amp;hl=en&amp;sa=X&amp;oi=book_result&amp;resnum=9&amp;ct=result] (Peter)<br /> <br /> == T ==<br /> '''transferase''' - an enzyme that catalyzes the transfer of a functional group from one molecule (the donor) to another (the acceptor) [http://en.wikipedia.org/wiki/Transferase] (Matt)<br /> <br /> '''transmembrane helix''' - a single transmembrane alpha helix of a transmembrane protein, usually about twenty amino acids in length. They are usually predicted by hydrophobicity. [http://en.wikipedia.org/wiki/Transmembrane_domain](Mary)<br /> <br /> '''transposons / transposable elements''' - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. [http://en.wikipedia.org/wiki/Transposon](Samantha)<br /> <br /> '''Transposon Mutagenesis'''-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene ([http://cancerweb.ncl.ac.uk/cgi-bin/omd?transposon+mutagenesis transposon mutagenesis] Pallavi)<br /> <br /> '''Trans-splicing'''-fragmented exon sequences fuse to form a mature species of mRNA. This process results in fusion mRNA ([http://www.representinggenes.org/Glossary.html 8] Pallavi).<br /> <br /> '''tRNA splicing endonuclease''' - an enzyme that cleaves intervening sequences of precursor tRNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?splicing+endonuclease] (Peter)&lt;br&gt;<br /> <br /> == U ==<br /> <br /> == V ==<br /> '''Vertical gene transfer'''-the transmission or absorption of genetic material that is associated with sexual reproduction and, thus, acknowledges species-specific boundaries ([http://www.gmo-compass.org/eng/glossary/#G 6] Pallavi)<br /> <br /> == W ==<br /> <br /> '''whole genome shotgun sequencing''' - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. [http://en.wikipedia.org/wiki/Whole_genome_shotgun](Samantha)<br /> &lt;br&gt;<br /> <br /> == X ==<br /> '''xenolog''' - homologs that are created by horizontal gene transfer between two different species [http://en.wikipedia.org/wiki/Xenolog#Xenology] (Matt)&lt;br&gt;<br /> <br /> == Y ==<br /> <br /> == Z ==<br /> <br /> &lt;BR&gt;</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Halorhabdus_utahensis_Genome&diff=6563 2008-09-23T14:50:22Z

<p>LaHeyer: /* Links to our 3 Databases */</p> <hr /> <div>This page will be used by Davidson College students in the [http://www.bio.davidson.edu/Courses/Bio343/LabMethods.html Genomics Laboratory course].<br /> <br /> == Links to our 3 Databases ==<br /> *[http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&amp;page=taxonDetail&amp;taxon_oid=2500575004 JGI IMG EDU] &lt;br&gt; public access<br /> *[http://www.tigr.org/tigr-scripts/prok_manatee/shared/login.cgi Manatee at JCVI] &lt;br&gt; use the davidson number sent by email as username and password (database is nthu01)<br /> *[http://rast.nmpdr.org/ SEED view via RAST] &lt;br&gt; use the username and password combination sent to you by SEED<br /> &lt;br&gt;<br /> <br /> == RNA Genes ==<br /> <br /> *[[tRNA Genes Check List]]&lt;br&gt;<br /> *[[rRNA operon]]&lt;br&gt;<br /> *[[2 misc. RNA genes]] (short summary list)&lt;br&gt;<br /> <br /> == Other Resources ==<br /> *[[Consensus Shine Dalgarno]] Excel File for ''H. utahensis'' &lt;br&gt;<br /> *[[References]]&lt;br&gt;<br /> *[[Gene Annotation Template]]&lt;br&gt;<br /> *[[General Questions]]&lt;br&gt;<br /> *[[Page for Annotated Genes]]&lt;br&gt;<br /> <br /> == Tutorials for Annotating Genomes ==<br /> <br /> # Will DeLoache- BioPerl Installation &lt;br&gt;<br /> # Max Win- Introduction to Perl for non-programmers.(with step by step explanations,simple exercises and solutions)&lt;br&gt;<br /> # Pallavi-Conserved Domains Database (CDD) &lt;br&gt;<br /> # Mary- Protein Data Bank &lt;br&gt;<br /> # Laura Voss - Pfam Database &lt;br&gt;<br /> # Samantha Simpson - NCBI Blast (protein, nucleotide, and blast2) &lt;br&gt;<br /> <br /> == Research Questions ==<br /> #How do the three systems compare for finding ORFs and RNA genes?<br /> #Is there a pattern of missed genes for any of the 3 sites? <br /> #Do the three systems differ in their ability to find good start codons and Shine-Dalgarno sequences? [We need a standard set of genes for comparison. Only highly conserved or a range of genes?]<br /> # Were Shine-Dalgarno sequences calculated for our species or default values used? If default, what sequence?<br /> #Can we fill any holes in their automated annotation? Is there a mechanism for users to add in genes?<br /> #How do the 3 sites compare for ease of use?<br /> #What are the strengths and weakness of each system? What did they publish as their special features and how do we see these working?<br /> #How does each of the 3 sites compare for pathway detection and visualization? <br /> #Do they find the origin of replication? Can we find it? <br /> <br /> &lt;hr&gt;<br /> <br /> == This is a list of glossary words (A - Z): ==<br /> [[#A| A ]] [[#B| B ]] [[#C| C ]] [[#D| D ]] [[#E| E ]] [[#F| F ]] [[#G| G ]] [[#H| H ]] [[#I| I ]] [[#J| J ]] [[#K| K ]] [[#L| L ]] [[#M| M ]] [[#N| N ]] [[#O| O ]] [[#P| P ]] [[#Q| Q ]] [[#R| R ]] [[#S| S ]] [[#T| T ]] [[#U| U ]] [[#V| V ]] [[#W| W ]] [[#X| X ]] [[#Y| Y ]] [[#Z| Z ]] <br /> <br /> == A ==<br /> '''Accession Number''' - a unique identifier given to DNA and protein sequences to allow for tracking of sequence information within a single database [http://en.wikipedia.org/wiki/Accession_number_(bioinformatics)] (Will).<br /> <br /> '''&lt;i&gt;Arabidopsis thaliana&lt;/i&gt;''' - the scientific name for the thale cress plant; it was the first plant to have its genome sequenced, and is a model organism for understanding plant biology and genetics ([http://en.wikipedia.org/wiki/Thale_cress Wikipedia.org], Jay)<br /> <br /> == B ==<br /> '''BAC''' - &lt;i&gt;b&lt;/i&gt;acterial &lt;i&gt;a&lt;/i&gt;rticifical &lt;i&gt;c&lt;/i&gt;hromosome, a DNA construct used for transforming or cloning segments of DNA and often used to sequence the genetic code of organisms ([http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome Wikipedia.org], Jay)<br /> <br /> '''bioinformatics''' - the multi-disciplinary approach of using biology, computer science and mathematics to solve or better understand biological problems [http://en.wikipedia.org/wiki/Bioinformatics] (Matt)<br /> <br /> '''BLAST''' - (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. [http://blast.ncbi.nlm.nih.gov/Blast.cgi] (Mary)<br /> <br /> '''bioperl'''- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications such as accessing sequence data from local and remote databases, transforming formats of database, manipulating individual sequences, searching for similar sequences, searching for genes and other structures on genomic DNA, or developing a machine readable sequence annotations. [http://en.wikipedia.org/wiki/BioPerl] (Wikipedia, Max Win)<br /> <br /> == C ==<br /> '''carbon fixation''' - using carbon dioxide to create organic materials [http://en.wikipedia.org/wiki/Carbon_fixation] (Samantha)&lt;BR&gt;<br /> <br /> '''CDD''' (Conserved Domains Database)- a database used to identify the conserved domains present in a protein query sequence [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml] (Mary)<br /> <br /> '''chaperonin''' - a protein complex that assists some newly formed polypeptide chains by folding them into their final, functional, three-dimensional form [http://en.wikipedia.org/wiki/Chaperonins] (Matt)<br /> <br /> '''chemotaxis''' - the process in which cells will seek out or flee from a high concentration of certain chemicals and is found in both uni- and multicellular organisms. This process is used to avoid toxins or find food in unicelllular organisms or tasks such as reproduction in multicellular organisms [http://en.wikipedia.org/wiki/Chemotaxis] (Nick)<br /> <br /> '''chemotaxonomy''' - the attempt to classify and identify organisms according to demonstrable differences and similarities in their biochemical compositions [http://en.wikipedia.org/wiki/Chemotaxonomy] (Mary)<br /> <br /> '''ClustalW''' - A web-based or command line tool that performs multiple sequence alignment to determine evolutionary relationships between three or more sequences [http://en.wikipedia.org/wiki/Clustal] (Will).<br /> <br /> '''COG''' (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs ([http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml COG] Pallavi) &lt;br&gt;<br /> <br /> '''concatemer''' - long continuous DNA molecule that contains the same DNA sequence repeated in series [http://en.wikipedia.org/wiki/Concatemer](Samantha)&lt;BR&gt;<br /> <br /> '''contigs''' (contiguous DNA)- overlapping DNA segments that as a collection from a longer and gapless segment of DNA. (Discovery Genomics, Proteomics and Bioinformatics [http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''coverage''' - refers to the number of times, on average, any piece of DNA in a sequenced genome has been individually sequenced (Lecture, Jay)<br /> <br /> '''CPAN (Comprehensive Perl Archive Network)''' - an archive of over 12,200 modules of software written in Perl, as well as documentation for it. It contains a module called CPAN (or CPAN.pm) which is used as an installer for Perl modules such as BioPerl [http://en.wikipedia.org/wiki/CPAN](Will).<br /> <br /> == D ==<br /> '''''de novo'' synthesis''' - the synthesis of complex molecules from simple molecules (e.g. sugars and nucleotides), rather than from recycled molecules; from the latin &quot;of the new&quot; [http://en.wikipedia.org/wiki/De_novo_synthesis] (Matt)<br /> <br /> '''dehydrogenase''' - a type of enzyme that oxidizes a substrate by transferring one or more protons and a pair of electrons to an acceptor. [http://en.wikipedia.org/wiki/Dehydrogenase] (Peter)<br /> <br /> '''diatom''' - a major group of eukaryotic algae, and one of the most common types of phytoplankton. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica called a frustule. These frustules show a wide diversity in form, but usually consist of two asymmetrical sides with a split between them. [http://en.wikipedia.org/wiki/Diatom] (Mary)<br /> <br /> '''dot plot'''-graphical display comparing sequence conservation between two genomes with dots indicating strings of identical bases. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> == E ==<br /> <br /> '''EC number''' (Enzyme Commission Number)- a numerical classification scheme for enzymes, based on the chemical reactions they catalyze [http://en.wikipedia.org/wiki/EC_number] (Mary)<br /> <br /> '''E-value''' (Expect value)- When performing a BLAST search, you will obtain an E-value for each sequence that is retrieved. And E-value can be thought of as the probability that two sequences are similar to each other by chance. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''Extremophile''' - an organism that thrives in and may even require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth [http://en.wikipedia.org/wiki/Extremophile] (Will).<br /> <br /> == F ==<br /> <br /> '''FASTA format''' - a format used to convey either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented by single-letter codes. The sequence name and other descriptors often precede the amino acide sequence. [http://en.wikipedia.org/wiki/FASTA_format] (Nick)&lt;br&gt;<br /> <br /> '''finished genome''' - a genome that has been sequenced at least partly by hand, resulting at least 99.99% sequence accuracy (Lecture, Jay)&lt;br&gt;<br /> <br /> == G ==<br /> <br /> '''GC Content''' - the percentage of bases within a certain sequence of DNA (e.g. a gene or a genome) that are either guanine or cytosine; a higher GC content is characteristic of a coding region of a gene; differences in GC content between a gene and a genome can be used as evidence for horizontal gene transfer [http://en.wikipedia.org/wiki/GC-content] (Matt)&lt;br&gt;<br /> <br /> '''GC-skew''' – uneven distribution of guanine and cytosine bases between the two strands of DNA where GC base pairs occur. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''gene amplification''' - production of multiple copies of a gene in order to amplify the amount of protein that the gene encodes for [http://www.medterms.com/script/main/art.asp?articlekey=13537] [http://www.answers.com/topic/gene-amplification] (Matt)<br /> <br /> '''gene knockout''' - a process in which a gene is deactivated within a test organism in order to better understand the function of the gene in that organism [http://en.wikipedia.org/wiki/Gene_knockout] (Matt)<br /> <br /> '''gene oncology'''- a collaborative effort of investigators to unify and standardize terms associated with the role a gene or protein plays in an organism. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''glaucophyte''' - freshwater algae that have not been studied well [http://en.wikipedia.org/wiki/Glaucophyte](Samantha)&lt;br&gt;<br /> <br /> == H ==<br /> <br /> '''haemolysin or hemolysin''' - a chemical produced by a bacteria that causes lysis of red blood cells [http://en.wikipedia.org/wiki/Hemolysis_(microbiology)] (Nick)<br /> <br /> '''halophile''' - an organism, most often of the Archaea domain, that lives in environments containing high concentrations of salt [http://en.wikipedia.org/wiki/Halophile] (Matt)<br /> <br /> '''haplotype'''-collection of alleles that travel together (Lecture, Pallavi)<br /> <br /> '''haptophyte''' - phylum of algae [http://en.wikipedia.org/wiki/Haptophyte](Samantha)<br /> <br /> '''heterokont''' - major line of eukaryotes consisting of about 10,500 known species, most of which are algae [http://en.wikipedia.org/wiki/Heterokont](Samantha)<br /> <br /> '''homeobox''' - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades [http://en.wikipedia.org/wiki/Homeobox](Samantha)<br /> <br /> '''homodimer''' - a protein made of paired identical polypeptides ([http://www.answers.com/topic/homodimer Answers.com], Jay)<br /> <br /> '''horizontal gene transfer'''-DNA transmission between species and incorporation of the DNA into the recipient's genome ([http://www.csrees.usda.gov/nea/biotech/res/biotechnology_res_glossary.html horizontal gene transfer] Pallavi)<br /> <br /> '''hydrolase''' - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often take part in subsequent reactions [http://en.wikipedia.org/wiki/Hydrolase] (Nick)<br /> <br /> == I ==<br /> <br /> '''ideogram''' - in genomics, usually describes a stylized representation of a chromosome with banding patterns (Campbell-Heyer Genomics textbook, Jay)<br /> <br /> '''identities''' - in a BLAST output, the number and fraction of total residues which are identical in a given alignment [www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''indole'''-a chemical compound that is produced from the break down of tryptophan ([http://medical-dictionary.thefreedictionary.com/indole indole] Pallavi)<br /> <br /> '''inclusion body''' - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [http://en.wikipedia.org/wiki/Inclusion_body] (Nick)<br /> <br /> '''intron''' - a region of DNA in a gene that is not part of the final coding sequence for the protein. [http://en.wikipedia.org/wiki/Intron] (Peter)<br /> <br /> '''isoelectric point''' - the pH at which a molecule is neutral [http://en.wikipedia.org/wiki/Isoelectric_point] (Nick)<br /> <br /> '''isozymes''' - members of a gene family with very similar cellular roles (Cambpell-Heyer Genomics textbook, Jay)<br /> <br /> == J ==<br /> <br /> == K ==<br /> '''KEGG (Kyoto Encyclopedia of Genes and Genomes)''' - a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The Pathway database records networks of molecular interactions in the cells, and variants of them specific to particular organisms [http://en.wikipedia.org/wiki/KEGG](Will).<br /> <br /> '''kinase''' - a type of enzyme that transfers a phosphate group from a high-energy donor molecule to a target molecule in a process called phosphorylation. [http://en.wikipedia.org/wiki/Kinase] (Peter)<br /> <br /> == L ==<br /> <br /> == M ==<br /> '''Manatee''' - a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. This on-going, open source initiative was developed with two missions. One, to allow biologists the ability to functionally annotate their genomes using a powerful, stand-alone web application with a robustly designed relational annotation database. And secondly, to invite outside developers the opportunity to contribute their own ideas and requirements to enhance Manatee's ability to accomplish biological goals [http://manatee.sourceforge.net/](Will).<br /> <br /> '''motif''' - a sequence of amino acids or nucleotides that performs a particular role and is often conserved in other species or molecules. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''mycoplasma''' - genus of bacteria that lack a cell wall [http://en.wikipedia.org/wiki/Mycoplasma] (Nick)<br /> <br /> == N ==<br /> <br /> '''NORFs''' (nonannotated open reading frame) - on open reading frame that was considered not to be a real gene when the genome was annotated.( Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''nucleomorph''' - reduced eukaryotic nuclei found in plastids [http://en.wikipedia.org/wiki/Nucleomorph](Samantha)<br /> <br /> == O ==<br /> '''object-oriented programming''' - a programming paradigm in which collections of data, associated with operations on that data, are modularly defined and then built upon (CSC 121 Lecture, Will). <br /> <br /> '''open reading frame (ORF)'''-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) [http://www.fao.org/DOCREP/003/X3910E/X3910E18.htm ORF] (Pallavi)<br /> <br /> '''operon''' - a segment of DNA involving an operator, promoter, and one or more genes that operate as a single unit during transcription [http://en.wikipedia.org/wiki/Operon] (Nick)<br /> <br /> '''optical mapping'''-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome [http://www.geocities.com/bioinformaticsweb/genomicglossary.html optical mapping] (Pallavi)<br /> <br /> '''ortholog'''-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)<br /> <br /> '''oxidoreductase''' - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [http://en.wikipedia.org/wiki/Oxidoreductase] (Nick)<br /> <br /> == P ==<br /> <br /> '''paralog'''-identical DNA sequences within a species (Lecture, Pallavi)<br /> <br /> '''p-arm''' - the shorter arm of a chromosome's two arms separated by the centromere (compare to q-arm, the longer arm) ([http://www.medterms.com/script/main/art.asp?articlekey=4715 MedTerms Dictionary], Jay)<br /> <br /> '''Perl''' - Developed by Larry Wall in 1987, Perl is a [http://en.wikipedia.org/wiki/High-level_programming_language high-level programming language] used frequently by biologists and bioinformaticists [http://en.wikipedia.org/wiki/Perl] (Will). <br /> <br /> '''periplasmic space''' - the space between the inner cytoplasmic membrane and external outer membrane in bacteria or archaea. [http://en.wikipedia.org/wiki/Periplasmic_space] (Peter)<br /> <br /> '''plasmid''' - an extra-chromosomal DNA molecule that is capable of replicating independently of the chromosomal DNA. Commonly found in bacteria and archaea. [http://en.wikipedia.org/wiki/Plasmid](Peter)<br /> <br /> '''plastid''' - major organelles in plants or algae [http://en.wikipedia.org/wiki/Plastid](Samantha)<br /> <br /> '''pleomorphism''' - the occurrence of two or more structural forms during a life cycle [http://en.wikipedia.org/wiki/Pleomorphism] (Mary)<br /> <br /> '''phylogenetic tree''' - a diagram showing the evolutionary relationships between biological species that are thought to share a common ancestor [http://en.wikipedia.org/wiki/Phylogenetic_tree] (Nick)<br /> <br /> '''phylotypes''' – a term intended to resolve the challenge of “species” when classifying prokaryotes using DNA sequence comparisons. (Discovery Genomics, Proteomics and Bioinformatics[http://wps.aw.com/bc_campbell_genomics_2/43/11232/2875502.cw/index.html], Max Win)<br /> <br /> '''positives''' - in a BLAST output, the number and fraction of residues for which the alignment scores have positive rather than negative values [http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml] (Mary)<br /> <br /> '''proteome''' - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions [http://en.wikipedia.org/wiki/Proteome](Samantha)<br /> <br /> '''psuedogenes'''-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)<br /> <br /> '''purine''' - a category of nitrogenous base consisting of a pyrimidine ring fused to an imidazole ring. Notable purine bases are adenine and guanine. [http://en.wikipedia.org/wiki/Purine] (Peter)<br /> <br /> '''pyrimidine''' - a category of nitrogenous base consisting of a heterocyclic aromatic ring containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Notable pyrimidine bases are cytosine, thymine, and uracil. [http://en.wikipedia.org/wiki/Pyrimidine] (Peter)<br /> <br /> == Q ==<br /> <br /> '''q-arm''' - the longer arm of a chromosome's two arms separated by the centromere (compare to p-arm, the shorter arm) ([http://www.medterms.com/script/main/art.asp?articlekey=5152 MedTerms Dictionary], Jay)<br /> <br /> == R ==<br /> <br /> '''RAST''' - (Rapid Annotation using Subsystem Technology)- a fully-automated service for annotating bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree. ([http://rast.nmpdr.org/], Max Win)<br /> <br /> '''rDNA'''-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. ([http://en.wikipedia.org/wiki/Ribosomal_DNA rDNA] Pallavi)<br /> <br /> '''retrotransposons''' - RNA transcribed back into DNA and added into the genome [http://en.wikipedia.org/wiki/Retrotransposon](Samantha)<br /> <br /> '''ribonuclease''' - a nuclease that catalyzes the degradation of RNA into smaller components [http://en.wikipedia.org/wiki/Ribonuclease] (Mary)<br /> <br /> == S ==<br /> '''Serovar'''-a subdivision of a species based on the characteristics of their cell surface antigens ([http://www.biology-online.org/dictionary/Serovar serovar] Pallavi)<br /> <br /> '''scaffold''' - a section of a sequenced genome composed of contigs that are in the right order but not necessarily connected ([http://www.medterms.com/script/main/art.asp?articlekey=25223 MedTerms Dictionary], Jay)<br /> <br /> '''Shine-Dalgarno sequence''' - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and [http://en.wikipedia.org/wiki/Shine-dalgarno Wikipedia article], Laura)&lt;br&gt;<br /> Note: The Shine-Dalgarno consensus sequence for our genome is TAGGAGG.<br /> <br /> '''signal peptide''' - a short peptide chain that directs the post-translational transport of a protein [http://en.wikipedia.org/wiki/Signal_peptide] (Matt)<br /> <br /> '''Smith-Waterman alignment''' - A well-known algorithm for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure [http://en.wikipedia.org/wiki/Smith_waterman](Will).<br /> <br /> '''SNP (Single Nucleotide Polymorphism)''' - a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual) [http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism](Will).<br /> <br /> '''symporter''' - an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane. [http://en.wikipedia.org/wiki/Symporter] (Peter)<br /> <br /> '''synteny''' - a neologism from the Greek for &quot;on the same ribbon&quot;. Genes that are syntenic in one species are on the same chromosome; genes that are syntenic across species retain the same order on respective chromosomes as a result of descent from a common ancestor ([http://www.answers.com/synteny Answers.com], Jay)<br /> <br /> '''synthetase''' - a type of enzyme that creates a new covalent bond and requires direct input of energy from a high-energy phosphate. [http://books.google.com/books?id=bB8XnCykRmIC&amp;pg=PA522&amp;lpg=PA522&amp;dq=%22synthetase+is+an+enzyme%22&amp;source=web&amp;ots=wkws4ksMsg&amp;sig=zWLkDIk7T78hcf9S84nWs3u5Apw&amp;hl=en&amp;sa=X&amp;oi=book_result&amp;resnum=9&amp;ct=result] (Peter)<br /> <br /> == T ==<br /> '''transferase''' - an enzyme that catalyzes the transfer of a functional group from one molecule (the donor) to another (the acceptor) [http://en.wikipedia.org/wiki/Transferase] (Matt)<br /> <br /> '''transmembrane helix''' - a single transmembrane alpha helix of a transmembrane protein, usually about twenty amino acids in length. They are usually predicted by hydrophobicity. [http://en.wikipedia.org/wiki/Transmembrane_domain](Mary)<br /> <br /> '''transposons / transposable elements''' - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. [http://en.wikipedia.org/wiki/Transposon](Samantha)<br /> <br /> '''Transposon Mutagenesis'''-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene ([http://cancerweb.ncl.ac.uk/cgi-bin/omd?transposon+mutagenesis transposon mutagenesis] Pallavi)<br /> <br /> '''tRNA splicing endonuclease''' - an enzyme that cleaves intervening sequences of precursor tRNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?splicing+endonuclease] (Peter)&lt;br&gt;<br /> <br /> == U ==<br /> <br /> == V ==<br /> <br /> == W ==<br /> <br /> '''whole genome shotgun sequencing''' - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. [http://en.wikipedia.org/wiki/Whole_genome_shotgun](Samantha)<br /> &lt;br&gt;<br /> <br /> == X ==<br /> '''xenolog''' - homologs that are created by horizontal gene transfer between two different species [http://en.wikipedia.org/wiki/Xenolog#Xenology] (Matt)&lt;br&gt;<br /> <br /> == Y ==<br /> <br /> == Z ==<br /> <br /> &lt;BR&gt;<br /> &lt;HR&gt;<br /> &lt;HR&gt;<br /> <br /> == This is a list of the student-created tutorials: ==</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=TRNA_Genes_Check_List&diff=6075 2008-09-02T02:26:25Z

<p>LaHeyer: </p> <hr /> <div>As you find your anticodons, please change the 3 letter codon in the table to '''''bold and italics'''''. For example, if you find 5' GGG 3' is your anticodon, then it will bind to the codon CCC listed in the table and you will convert the '''''CCC''''' to bold and italics. To keep track of the 5' to 3' portion, use the genetic code and the amino acid automatically assigned to your tRNA gene to make sure you don't have it reversed. <br /> <br /> &lt;center&gt;<br /> &lt;h1&gt;Table of Standard Genetic Code&lt;/h1&gt;<br /> &lt;hr&gt;<br /> <br /> &lt;table border&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;th colspan=1&gt;T&lt;/th&gt;<br /> &lt;th colspan=1&gt;C&lt;/th&gt;<br /> &lt;th colspan=1&gt;A&lt;/th&gt;<br /> &lt;th colspan=1&gt;G&lt;/th&gt;<br /> &lt;/tr&gt;<br /> <br /> <br /> &lt;tr&gt;<br /> &lt;th rowspan=1&gt;T&lt;/th&gt;<br /> &lt;td&gt;<br /> TTT Phe (F)&lt;br&gt;<br /> '''''TTC''''' Phe (F)&lt;br&gt;<br /> '''''TTA''''' Leu (L)&lt;br&gt;<br /> TTG Leu (L)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> <br /> &lt;td&gt; <br /> TCT Ser (S)&lt;br&gt;<br /> '''''TCC''''' Ser (S)&lt;br&gt; <br /> '''''TCA''''' Ser (S)&lt;br&gt;<br /> '''''TCG''''' Ser (S)&lt;br&gt;<br /> <br /> &lt;/td&gt; <br /> <br /> &lt;td&gt;<br /> TAT Tyr (Y)&lt;br&gt;<br /> '''''TAC''''' Tyr (Y)&lt;br&gt;<br /> &lt;font color=&quot;#FF0000&quot;&gt;TAA&lt;/font&gt; Stop &lt;br&gt;<br /> &lt;font color=&quot;#FF0000&quot;&gt;TAG&lt;/font&gt; Stop &lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> <br /> TGT Cys (C)&lt;br&gt;<br /> '''''TGC''''' Cys (C)&lt;br&gt;<br /> &lt;font color=&quot;#FF0000&quot;&gt;TGA&lt;/font&gt; Stop &lt;br&gt;<br /> TGG Trp (W)&lt;br&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> <br /> <br /> &lt;tr&gt;<br /> &lt;th rowspan=1&gt;C&lt;/th&gt;<br /> <br /> &lt;td&gt;<br /> CTT Leu (L)&lt;br&gt;<br /> CTC Leu (L)&lt;br&gt;<br /> '''''CTA''''' Leu (L)&lt;br&gt;<br /> '''''CTG''''' Leu (L)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> CCT Pro (P)&lt;br&gt;<br /> CCC Pro (P)&lt;br&gt;<br /> '''''CCA''''' Pro (P)&lt;br&gt;<br /> '''''CCG''''' Pro (P)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> CAT His (H)&lt;br&gt;<br /> '''''CAC''''' His (H)&lt;br&gt;<br /> '''''CAA''''' Gln (Q)&lt;br&gt;<br /> '''''CAG''''' Gln (Q)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> CGT Arg (R)&lt;br&gt;<br /> CGC Arg (R)&lt;br&gt;<br /> CGA Arg (R)&lt;br&gt;<br /> '''''CGG''''' Arg (R)&lt;br&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> <br /> <br /> &lt;tr&gt;<br /> &lt;th rowspan=1&gt;A&lt;/th&gt;<br /> <br /> &lt;td&gt;<br /> ATT Ile (I)&lt;br&gt;<br /> ATC Ile (I)&lt;br&gt;<br /> ATA Ile (I)&lt;br&gt;<br /> &lt;font color=&quot;#00CC00&quot;&gt;'''''ATG'''''&lt;/font&gt; Met (M)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> ACT Thr (T)&lt;br&gt;<br /> '''''ACC''''' Thr (T)&lt;br&gt;<br /> '''''ACA''''' Thr (T)&lt;br&gt;<br /> '''''ACG''''' Thr (T)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> AAT Asn (N)&lt;br&gt; <br /> AAC Asn (N)&lt;br&gt;<br /> '''''AAA''''' Lys (K)&lt;br&gt;<br /> '''''AAG''''' Lys (K&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> AGT Ser (S)&lt;br&gt;<br /> &lt;b&gt;AGC&lt;/b&gt; Ser (S)&lt;br&gt;<br /> '''''AGA''''' Arg (R)&lt;br&gt;<br /> '''''AGG''''' Arg (R)&lt;br&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> <br /> <br /> &lt;tr&gt;<br /> &lt;th rowspan=1&gt;G&lt;/th&gt;<br /> <br /> &lt;td&gt;<br /> GTT Val (V)&lt;br&gt;<br /> '''''GTC''''' Val (V)&lt;br&gt;<br /> '''''GTA''''' Val (V)&lt;br&gt;<br /> GTG Val (V)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> GCT Ala (A)&lt;br&gt;<br /> '''''GCC''''' Ala (A)&lt;br&gt;<br /> '''''GCA''''' Ala (A)&lt;br&gt;<br /> '''''GCG''''' Ala (A)&lt;br&gt;<br /> <br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> GAT Asp (D)&lt;br&gt;<br /> '''''GAC''''' Asp (D)&lt;br&gt;<br /> &lt;b&gt;GAA&lt;/b&gt; Glu (E)&lt;br&gt;<br /> '''''GAG''''' Glu (E)&lt;br&gt;<br /> &lt;/td&gt;<br /> <br /> &lt;td&gt;<br /> GGT Gly (G)&lt;br&gt;<br /> GGC Gly (G)&lt;br&gt;<br /> &lt;b&gt;GGA&lt;/b&gt; Gly (G)&lt;br&gt;<br /> '''''GGG''''' Gly (G)&lt;br&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> <br /> &lt;/table&gt;<br /> &lt;/center&gt;</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Contact_A_Team_Member&diff=5463 2008-06-24T12:52:48Z

<p>LaHeyer: /* Davidson */</p> <hr /> <div>== Davidson ==<br /> '''Biology''' <br /> <br /> Dr. Malcolm Campbell<br /> <br /> macampbell@davidson.edu<br /> <br /> <br /> James Barron<br /> <br /> james.barron@pipeline.hamptonu.edu<br /> <br /> <br /> <br /> Erin Feeney<br /> <br /> erfeeney@davidson.edu<br /> <br /> <br /> <br /> Pallavi Penumetcha<br /> <br /> papenumetcha@davidson.edu<br /> <br /> <br /> <br /> <br /> <br /> '''Math'''<br /> <br /> Dr. Laurie Heyer<br /> <br /> laheyer@davidson.edu<br /> <br /> <br /> <br /> Kelly Davis<br /> <br /> kedavis@davidson.edu<br /> <br /> <br /> <br /> Kristi Muscalino<br /> <br /> krmuscalino@davidson.edu<br /> <br /> <br /> <br /> Madeline Parra<br /> <br /> maparra@davidson.edu<br /> <br /> <br /> <br /> Karlesha Roland<br /> <br /> karlesha.roland@yahoo.com<br /> <br /> == Missouri Western ==<br /> '''Biology''' <br /> <br /> Dr. Todd Eckdahl<br /> <br /> eckdahl@missouriwestern.edu<br /> <br /> <br /> Robert Cool<br /> <br /> rcool@missouriwestern.edu<br /> <br /> <br /> Xiao Zhu<br /> <br /> Xzhu@missouriwestern.edu<br /> <br /> <br /> Andrew Gordon<br /> <br /> ajg714@hotmail.com<br /> <br /> <br /> Alicia Allen<br /> <br /> aallen10@missouriwestern.edu<br /> <br /> <br /> '''Math'''<br /> <br /> Dr. Jeff Poet<br /> <br /> poet@missouriwestern.edu<br /> <br /> <br /> Aaron Lewis<br /> <br /> masterwizard_32@hotmail.com<br /> <br /> <br /> John Igo<br /> <br /> john_igo@hotmail.com</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Team_Projects&diff=5296 2008-06-16T14:18:12Z

<p>LaHeyer: /* Erin + Karlesha + Kelly + Samantha - Modeling Circuits */</p> <hr /> <div>Here is a list of Team Projects We Want to Work On<br /> == James, Max and Madeline - PCR Primer with BB ends == <br /> '''(needs tweaking for output)'''<br /> == James and Madeline - tilt and and diffusion of Amp&lt;sup&gt;R&lt;/sup&gt; and chemical messengers. ==<br /> [[Image:XOR_AMC2.jpg]]&lt;br&gt;<br /> [[Image:XOR_AMC3A.jpg]]&lt;br&gt;<br /> [[Image:XOR_AMC3B.jpg]]&lt;br&gt;<br /> <br /> == Erin + Karlesha + Samantha - Modeling Circuits ==<br /> <br /> == Kelly + Karlesha - Gel Percent Optimizer ==<br /> == Kristi and Math team - Hash Function issues ==<br /> == Pallavi - Lac promoter and protein optimization ==<br /> == James and Erin - make new promoters for XOR Davidson version ==<br /> [[Designing_XOR_Gates_-_two_campus_approach]]&lt;br&gt;<br /> [[Image:XOR_AMC1.jpg]]&lt;br&gt;<br /> == James - make new pLsr reverse primer == <br /> '''(done!)'''<br /> == James, Pallavi, Erin - analyze sequence data files ==<br /> == Madeline - encyclopedia project ==</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Math_Modeling_Pages&diff=4779 2008-05-22T00:00:16Z

<p>LaHeyer: </p> <hr /> <div>This is the place for math modelers to post ideas, papers, examples and computer programs.<br /> <br /> == Papers ==<br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.<br /> <br /> == Engineering agar ==<br /> [http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Math_Modeling_Pages&diff=4778 2008-05-21T23:15:39Z

<p>LaHeyer: </p> <hr /> <div>This is the place for math modelers to post ideas, papers, examples and computer programs.<br /> <br /> == Papers ==<br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Math_Modeling_Pages&diff=4777 2008-05-21T22:54:54Z

<p>LaHeyer: </p> <hr /> <div>This is the place for math modelers to post ideas, papers, examples and computer programs.<br /> <br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways]</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4776 2008-05-21T22:52:31Z

<p>LaHeyer: </p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> ==[[Wet Lab Pages]]==<br /> <br /> ==[[Math Modeling Pages]]==<br /> <br /> == Las/Rhl cell signaling system ==<br /> '''Responsible''': Robert Cool, Alicia Allen, and Erin Feeney<br /> <br /> '''Las System'''<br /> <br /> '''Signal Molecule''': An AHL called PAI-1 (N-3-oxododecanoyl-l-hsl)(3-oxo-C12-hsl)<br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa gram(-) possibly E.coli (see article 3)<br /> <br /> '''Receiver protein''': LasR<br /> <br /> '''Effect of binding''': TXN activation of virulence genes, lasA, lasB, apr, toxR<br /> <br /> '''Synthase''': LasI enzyme<br /> <br /> '''Target Genes''': lasI, lasA, lasB, apr, toxR<br /> <br /> '''Regulation''': unknown<br /> <br /> <br /> '''References'''<br /> <br /> &quot;Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes&quot; <br /> <br /> JP Pearson, EC Pesci and BH Iglewski <br /> [http://jb.asm.org/cgi/reprint/179/18/5756?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;titleabstract=las&amp;searchid=1&amp;FIRSTINDEX=0&amp;resourcetype=HWCIT]<br /> <br /> <br /> &quot;Regulation of Pseudomonas Quinolone Signal Synthesis in Pseudomonas aeruginosa&quot;<br /> <br /> Dana S. Wade, M. Worth Calfee, Edson R. Rocha, Elizabeth A. Ling, Elana Engstrom, James P. Coleman, and Everett C. Pesci<br /> [http://jb.asm.org/cgi/content/full/187/13/4372?view=long&amp;pmid=15968046 2]<br /> <br /> <br /> Posttranscriptional Control of Quorum-Sensing-Dependent Virulence Genes by DksA in Pseudomonas aeruginosa<br /> <br /> Florence Jude,Thilo Köhler,Pavel Branny,Karl Perron,Matthias P. Mayer,Rachel Comte, and Christian van Delden<br /> [http://jb.asm.org/cgi/content/full/185/12/3558?view=long&amp;pmid=12775693 3]<br /> <br /> Pending: [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1447470]<br /> <br /> '''Rhl System''' <br /> <br /> &lt;br&gt;<br /> '''Signal Molecule''': An AHL called PAI-2, Plasminogen activator inhibitor-2, N-butanoyl-homoserine lactone (C4HSL) <br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa, gram(-)<br /> <br /> '''Receiver Protein''': Rhl R <br /> <br /> '''Effect of Binding''': activation of Rhamnosyl Transferase, then making RL (rhamnolipid) <br /> <br /> '''Synthase''': RhlA and RhlB <br /> <br /> '''Target Genes''': pqsABCDE and phnAB<br /> <br /> '''Regulation''': unknown<br /> <br /> '''References'''<br /> <br /> [http://jb.asm.org/cgi/reprint/189/13/4827 background information on Las and Rhl]<br /> <br /> [[Image:Las_rhl.gif]]<br /> <br /> '''Parts Needed''':<br /> <br /> LasR + pro/term<br /> <br /> RhlR + pro/term<br /> <br /> RhlI + pro/term<br /> <br /> pqsABCDE + pro/term<br /> <br /> pqsR<br /> <br /> pqsH + pro/term<br /> <br /> phnAB<br /> <br /> LasI<br /> <br /> RBS<br /> <br /> == Lux cell signaling system ==<br /> <br /> '''Responsible:''' Andrew Gordon and Pallavi Penumetcha<br /> <br /> '''Signal molecule:''' ''N''-acyl-homoserine lactone (AHL) Generic term for a variety of species specific hormone-like molecules <br /> <br /> '''Bacterial species:''' discovered in ''Vibrio fischeri'' known to work in ''E. coli''<br /> <br /> '''Receiver protein:''' LuxR protein receives signal from AHL; also has some control over transciption of luciferase<br /> <br /> '''Signal molecule synthase:''' LuxI; also has some control over transciption of luciferase<br /> <br /> '''Additional Information:''' &quot;Quorum Quenching&quot; aiiA (intracellular) lactonase reduces AHL concentration<br /> <br /> [[Image:800px-Luxrreceiverschematic.png]]<br /> <br /> '''Resources'''<br /> <br /> [http://partsregistry.org/Lux Lux Operon Pathway]<br /> <br /> [http://partsregistry.org/AHL AHL signaling molecules by species; some are specific to gram pos but may affect gram negs]<br /> <br /> '''References'''<br /> <br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522112 Quorum Quenching to control Lux Pathway]<br /> <br /> '''Parts Needed''':<br /> <br /> LuxR + pro/term<br /> <br /> RBS<br /> <br /> LuxI + pro/term<br /> <br /> LuxI sender<br /> <br /> == Lsr cell signaling system ==<br /> <br /> '''Responsible''': Kelly Davis, Xiao Zhu<br /> <br /> '''Signal molecule''': AI-2, furanosyl borate diester, derived from the ribosyl part of S-ribosylhomocysteine, [http://www.biomedcentral.com/content/pdf/1471-2148-4-36.pdf]<br /> <br /> '''Bacterial species''': discovered in Vibrio harveyi, but interspecies signalling occurs, Escherichia coli E24377A (strain: E24377A) (for lsrK), Escherichia coli str. K-12 substr. DH10B (strain: K-12, substrain: DH10B) (for lsrR)<br /> <br /> '''Receiver protein''': LsrR protein receives signal from sensor protein<br /> <br /> '''Signal molecule synthase''': Pfs enzyme, then LuxS autoinducer synthase<br /> <br /> '''Target genes''': lsr operon, including ABC transporter and LsrK kinase<br /> <br /> '''Regulation''': LsrR represses the lsr operon, derepression by phospho-AI-2<br /> <br /> '''References'''<br /> <br /> [http://web.ebscohost.com/ehost/detail?vid=1&amp;hid=116&amp;sid=edfbf2f7-b0c8-40c3-8227-1cc94f134972%40sessionmgr108 Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium]<br /> <br /> [http://www.microbialcellfactories.com/content/pdf/1475-2859-1-5.pdf Review of AI-2 and other systems]<br /> <br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22733&amp;blobtype=pdf E. coli produces a signal that can substitute for AI-2]<br /> <br /> [http://jb.asm.org/cgi/content/full/187/1/238?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;titleabstract=quorum+sensing+AI-2&amp;searchid=1&amp;FIRSTINDEX=0&amp;resourcetype=HWCIT Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli]<br /> <br /> '''Resources'''<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&amp;cmd=Retrieve&amp;dopt=full_report&amp;list_uids=5586283 lsrK gene in Entrez] <br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&amp;Cmd=ShowDetailView&amp;TermToSearch=6062136&amp;ordinalpos=9&amp;itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum#summary lsrR gene in Entrez]<br /> <br /> [http://BioCyc.org/ECOLI/substring-search?type=NIL&amp;object=lsr lsr genes in EcoCyc]<br /> <br /> <br /> &lt;br&gt;<br /> '''Parts Needed:'''<br /> <br /> LsrR pro/term<br /> <br /> LsrK<br /> <br /> LsrACDB (transport)<br /> <br /> LsrFGE (catabolic)<br /> <br /> LuxS<br /> <br /> Pfs enzyme (?)<br /> <br /> '''Note:'''<br /> lsrB encodes the periplasmic AI-2 binding protein<br /> <br /> lsrC &amp; lsrD encode the channel proteins<br /> <br /> lsrA encodes the ATPase that provides energy for AI-2 transport <br /> <br /> lsrF is similar to genes specifying aldolases<br /> <br /> lsrG encodes a protein with an unknown function. <br /> <br /> There is no lsrE in the E. coli lsr operon<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&amp;id=55669965 R-THMF]<br /> <br /> http://www.nature.com/nrmicro/journal/v3/n5/images/nrmicro1146-f2.gif<br /> <br /> == Fec cell signaling system ==<br /> Responsible: Xiao Zhu<br /> <br /> '''Ferric Dicitrate Transport System'''<br /> The inducer, ferric citrate, binds to an outer membrane transport protein, FecA, and without further transport elicits a signal that is transmitted across the outer membrane (by FecA), the periplasm, and the cytoplasmic membrane (by FecBCDE and FecR) into the cytoplasm. Signal transfer across the three subcellular compartments is mediated by the outer membrane transport protein (FecA) that interacts in the periplasm with a cytoplasmic transmembrane protein (FecR). FecR is required for activation of a sigma factor (FecI) which belongs to the extracytoplasmic function (ECF)sigma factor family.<br /> &lt;br/&gt;<br /> Only iron not iron complex enters the cytoplasm. FecA is the TonB energy transducing system-dependent. <br /> &lt;br/&gt;<br /> '''Signaling Molecule:''' FeC (ferric dicitrate)<br /> &lt;br/&gt;<br /> '''Bacteria species:''' E.coli, Pseudomonas putida, P. aeruginosa, Serratia marcescens, Klebsiella pneumoniae, Aerobacter aerogenes, Bordetella pertussis, B. bronchseptica, B. avium, and Ralstonia solanacearum.<br /> &lt;br/&gt;<br /> '''Receptor Protein: ''' FecA<br /> &lt;br/&gt;<br /> '''Effect of binding:''' the conformational changes that FecA undergoes when binding to ferric citrate:The alpha helix in loop 7 unravels, and the loop moves by up to 11 angstroms ; Loop 8 moves up to 15 angstroms.<br /> http://www.rsc.org/ej/CS/2007/b617040b/b617040b-f13.gif<br /> &lt;br/&gt;<br /> '''Sensor Producer:''' N/A<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> Harvard iGEM'07 team worked with Fec system, the results were not favorable. [http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing :We believe that overexpression of the Fec system killed the cells, possibly by disturbing the cell membranes.]<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> [http://pathway.gramene.org/ECOLI/NEW-IMAGE?type=REACTION&amp;object=RXN0-2261 More detailed information about Fec]<br /> &lt;br/&gt;<br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=215624&amp;blobtype=pdf Exogenous Induction of the Iron Dicitrate Transport System of Escherichia coli K-12]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/183/1/162 Control of the Ferric Citrate Transport System of Escherichia coli:Mutations in Region2.1 of the FecI ECF Sigma Factor Suppress Mutations in the FecR Transmembrane Regulatory Protein]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/189/19/6913 Docking of the Periplasmic FecB Binding Protein to the FecCD Transmembrane Proteins in the Ferric Citrate Transport System of Escherichia coli]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/abstract/185/6/1870 Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box]<br /> <br /> == Signal molecules ==<br /> <br /> [[Image:QSsignals.gif|QSsignals.gif]]<br /> <br /> <br /> '''Gram (-) bacteria use:'''<br /> <br /> 3-oxo-C6-HSL, N-(3-oxohexanoyl)-L-homoserine lactone, an AHL<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> HHQ, 2-heptyl-4(1H)-quinolone, an AQ<br /> <br /> '''Gram (+) bacteria use:'''<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> A-Factor, 2-isocapryloyl-3-hydroxymethyl--butyrolactone<br /> <br /> PQS, pseudomonas quinolone signal, 2-heptyl-3-hydroxy-4(1H)-quinolone<br /> <br /> DSF, ‘diffusible factor’, cis-11-methyl-2-dodecenoic acid<br /> <br /> 3OH-PAME, hydroxyl-palmitic acid methyl ester; <br /> <br /> AIP-1, staphylococcal autoinducing peptide 1<br /> <br /> == E. coli Signaling ==<br /> <br /> &quot;As yet no AHL-producing Escherichia coli or Salmonella strains have been identified, although both organisms possess an AHL receptor (SdiA) of the LuxR protein class and respond to AHLs produced by other bacteria.&quot; [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Williams 2007]<br /> <br /> <br /> <br /> == Cell signaling resources ==<br /> [http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]<br /> <br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> [http://journals.royalsociety.org/content/m5hgygq1t6daxy72/fulltext.pdf Quorum Sensing and the Population Control of Virulence]<br /> <br /> == Davidson Journal Club ==<br /> <br /> [http://www.bio.davidson.edu/courses/synthetic/papers/Stochastic_Cells.pdf Stochasticity and Gene Expression --- Dr. Campbell]<br /> <br /> [http://gcat.davidson.edu/iGEM08/cryptography_graph.pdf Hash Function --- Dr. Heyer]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4714 2008-05-21T00:53:47Z

<p>LaHeyer: /* Temporary section for IM names */</p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> ==[[Wet Lab Pages]]==<br /> <br /> == Temporary section for IM names ==<br /> <br /> heyermath &lt;br&gt;<br /> genomicsguy &lt;br&gt;<br /> lookinformammoth &lt;br&gt;<br /> toddeckdahl &lt;br&gt;<br /> aba767 &lt;br&gt;<br /> Awake714 &lt;br&gt;<br /> evelynzx &lt;br&gt;<br /> johnigo25 &lt;br&gt;<br /> masterwizard_32@hotmail.com &lt;br&gt;<br /> rcoolbassman &lt;br&gt;<br /> <br /> == Las/Rhl cell signaling system ==<br /> '''Responsible''': Robert Cool<br /> <br /> '''Las System'''<br /> <br /> '''Signal Molecule''': An AHL called PAI-1 (N-3-oxododecanoyl-l-hsl)(3-oxo-C12-hsl)<br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa gram(-) possibly E.coli (see article 3)<br /> <br /> '''Receiver protein''': LasR<br /> <br /> '''Effect of binding''': TXN activation of virulence genes, lasA, lasB, apr, toxR<br /> <br /> '''Synthase''': LasI enzyme<br /> <br /> '''Target Genes''': lasI, lasA, lasB, apr, toxR<br /> <br /> '''Regulation''': unknown<br /> <br /> <br /> '''References'''<br /> <br /> &quot;Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes&quot; <br /> <br /> JP Pearson, EC Pesci and BH Iglewski <br /> [http://jb.asm.org/cgi/reprint/179/18/5756?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;titleabstract=las&amp;searchid=1&amp;FIRSTINDEX=0&amp;resourcetype=HWCIT]<br /> <br /> <br /> &quot;Regulation of Pseudomonas Quinolone Signal Synthesis in Pseudomonas aeruginosa&quot;<br /> <br /> Dana S. Wade, M. Worth Calfee, Edson R. Rocha, Elizabeth A. Ling, Elana Engstrom, James P. Coleman, and Everett C. Pesci<br /> [http://jb.asm.org/cgi/content/full/187/13/4372?view=long&amp;pmid=15968046 2]<br /> <br /> <br /> Posttranscriptional Control of Quorum-Sensing-Dependent Virulence Genes by DksA in Pseudomonas aeruginosa<br /> <br /> Florence Jude,Thilo Köhler,Pavel Branny,Karl Perron,Matthias P. Mayer,Rachel Comte, and Christian van Delden<br /> [http://jb.asm.org/cgi/content/full/185/12/3558?view=long&amp;pmid=12775693 3]<br /> <br /> <br /> '''Rhl System''' <br /> <br /> &lt;br&gt;<br /> '''Signal Molecule''': An AHL called PAI-2, Plasminogen activator inhibitor-2, N-butanoyl-homoserine lactone (C4HSL) <br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa, gram(-)<br /> <br /> '''Receiver Protein''': Rhl R <br /> <br /> '''Effect of Binding''': activation of Rhamnosyl Transferase, then making RL (rhamnolipid) <br /> <br /> '''Synthase''': RhlA and RhlB <br /> <br /> '''Target Genes''': pqsABCDE and phnAB<br /> <br /> '''Regulation''': unknown<br /> <br /> '''References'''<br /> <br /> [http://jb.asm.org/cgi/reprint/189/13/4827 background information on Las and Rhl]<br /> <br /> [[Image:Las_rhl.gif]]<br /> <br /> '''Parts Needed''':<br /> <br /> LasR + pro/term<br /> <br /> RhlR + pro/term<br /> <br /> RhlI + pro/term<br /> <br /> pqsABCDE + pro/term<br /> <br /> pqsR<br /> <br /> pqsH + pro/term<br /> <br /> phnAB<br /> <br /> LasI<br /> <br /> RBS<br /> <br /> == Lux cell signaling system ==<br /> <br /> '''Responsible:''' Andrew Gordon<br /> <br /> '''Signal molecule:''' ''N''-acyl-homoserine lactone (AHL) Generic term for a variety of species specific hormone-like molecules <br /> <br /> '''Bacterial species:''' discovered in ''Vibrio fischeri'' known to work in ''E. coli''<br /> <br /> '''Receiver protein:''' LuxR protein receives signal from AHL; also has some control over transciption of luciferase<br /> <br /> '''Signal molecule synthase:''' LuxI; also has some control over transciption of luciferase<br /> <br /> '''Additional Information:''' &quot;Quorum Quenching&quot; lactonase reduces AHL concentration<br /> <br /> [[Image:800px-Luxrreceiverschematic.png]]<br /> <br /> '''Resources'''<br /> <br /> [http://partsregistry.org/Lux Lux Operon Pathway]<br /> <br /> [http://partsregistry.org/AHL AHL signaling molecules by species; some are specific to gram pos but may affect gram negs]<br /> <br /> '''References'''<br /> <br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522112 Quorum Quenching to control Lux Pathway]<br /> <br /> '''Parts Needed''':<br /> <br /> LuxR + pro/term<br /> <br /> RBS<br /> <br /> LuxI + pro/term<br /> <br /> LuxI sender<br /> <br /> == Lsr cell signaling system ==<br /> <br /> '''Responsible''': Kelly Davis, Xiao Zhu<br /> <br /> '''Signal molecule''': AI-2, furanosyl borate diester, derived from the ribosyl part of S-ribosylhomocysteine, [http://www.biomedcentral.com/content/pdf/1471-2148-4-36.pdf]<br /> <br /> '''Bacterial species''': discovered in Vibrio harveyi, but interspecies signalling occurs, Escherichia coli E24377A (strain: E24377A) (for lsrK), Escherichia coli str. K-12 substr. DH10B (strain: K-12, substrain: DH10B) (for lsrR)<br /> <br /> '''Receiver protein''': LsrR protein receives signal from sensor protein<br /> <br /> '''Signal molecule synthase''': Pfs enzyme, then LuxS autoinducer synthase<br /> <br /> '''Target genes''': lsr operon, including ABC transporter and LsrK kinase<br /> <br /> '''Regulation''': LsrR represses the lsr operon, derepression by phospho-AI-2<br /> <br /> '''References'''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/14622426 Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium]<br /> <br /> [http://www.microbialcellfactories.com/content/pdf/1475-2859-1-5.pdf Review of AI-2 and other systems]<br /> <br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22733&amp;blobtype=pdf E. coli produces a signal that can substitute for AI-2]<br /> <br /> '''Resources'''<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&amp;cmd=Retrieve&amp;dopt=full_report&amp;list_uids=5586283 lsrK gene in Entrez] <br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&amp;Cmd=ShowDetailView&amp;TermToSearch=6062136&amp;ordinalpos=9&amp;itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum#summary lsrR gene in Entrez]<br /> <br /> [http://BioCyc.org/ECOLI/substring-search?type=NIL&amp;object=lsr lsr genes in EcoCyc]<br /> <br /> &lt;br&gt;<br /> '''Parts Needed:'''<br /> &lt;br/&gt;<br /> LsrR pro/term<br /> &lt;br/&gt;<br /> LsrK<br /> &lt;br/&gt;<br /> LsrACDB (transport)<br /> &lt;br/&gt;<br /> LsrFGE (catabolic)<br /> &lt;br/&gt;<br /> LuxS<br /> &lt;br/&gt;<br /> Pfs enzyme (?)<br /> <br /> http://www.nature.com/nrmicro/journal/v3/n5/images/nrmicro1146-f2.gif<br /> <br /> == Fec cell signaling system ==<br /> Responsible: Xiao Zhu<br /> <br /> '''Ferric Dicitrate Transport System'''<br /> The inducer, ferric citrate, binds to an outer membrane transport protein, FecA, and without further transport elicits a signal that is transmitted across the outer membrane (by FecA), the periplasm, and the cytoplasmic membrane (by FecBCDE and FecR) into the cytoplasm. Signal transfer across the three subcellular compartments is mediated by the outer membrane transport protein (FecA) that interacts in the periplasm with a cytoplasmic transmembrane protein (FecR). FecR is required for activation of a sigma factor (FecI) which belongs to the extracytoplasmic function (ECF)sigma factor family.<br /> &lt;br/&gt;<br /> Only iron not iron complex enters the cytoplasm. FecA is the TonB energy transducing system-dependent. <br /> &lt;br/&gt;<br /> '''Signaling Molecule:''' FeC (ferric dicitrate)<br /> &lt;br/&gt;<br /> '''Bacteria species:''' E.coli, Pseudomonas putida, P. aeruginosa, Serratia marcescens, Klebsiella pneumoniae, Aerobacter aerogenes, Bordetella pertussis, B. bronchseptica, B. avium, and Ralstonia solanacearum.<br /> &lt;br/&gt;<br /> '''Receptor Protein: ''' FecA<br /> &lt;br/&gt;<br /> '''Effect of binding:''' the conformational changes that FecA undergoes when binding to ferric citrate:The alpha helix in loop 7 unravels, and the loop moves by up to 11 angstroms ; Loop 8 moves up to 15 angstroms.<br /> http://www.rsc.org/ej/CS/2007/b617040b/b617040b-f13.gif<br /> &lt;br/&gt;<br /> '''Sensor Producer:''' N/A<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> Harvard iGEM'07 team worked with Fec system, the results were not favorable. [http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing :We believe that overexpression of the Fec system killed the cells, possibly by disturbing the cell membranes.]<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> [http://pathway.gramene.org/ECOLI/NEW-IMAGE?type=REACTION&amp;object=RXN0-2261 More detailed information about Fec]<br /> &lt;br/&gt;<br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=215624&amp;blobtype=pdf Exogenous Induction of the Iron Dicitrate Transport System of Escherichia coli K-12]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/183/1/162 Control of the Ferric Citrate Transport System of Escherichia coli:Mutations in Region2.1 of the FecI ECF Sigma Factor Suppress Mutations in the FecR Transmembrane Regulatory Protein]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/189/19/6913 Docking of the Periplasmic FecB Binding Protein to the FecCD Transmembrane Proteins in the Ferric Citrate Transport System of Escherichia coli]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/abstract/185/6/1870 Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box]<br /> <br /> == Signal molecules ==<br /> <br /> [[Image:QSsignals.gif|QSsignals.gif]]<br /> <br /> <br /> '''Gram (-) bacteria use:'''<br /> <br /> 3-oxo-C6-HSL, N-(3-oxohexanoyl)-L-homoserine lactone, an AHL<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> HHQ, 2-heptyl-4(1H)-quinolone, an AQ<br /> <br /> '''Gram (+) bacteria use:'''<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> A-Factor, 2-isocapryloyl-3-hydroxymethyl--butyrolactone<br /> <br /> PQS, pseudomonas quinolone signal, 2-heptyl-3-hydroxy-4(1H)-quinolone<br /> <br /> DSF, ‘diffusible factor’, cis-11-methyl-2-dodecenoic acid<br /> <br /> 3OH-PAME, hydroxyl-palmitic acid methyl ester; <br /> <br /> AIP-1, staphylococcal autoinducing peptide 1<br /> <br /> == E. coli Signaling ==<br /> <br /> &quot;As yet no AHL-producing Escherichia coli or Salmonella strains have been identified, although both organisms possess an AHL receptor (SdiA) of the LuxR protein class and respond to AHLs produced by other bacteria.&quot; [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Williams 2007]<br /> <br /> <br /> <br /> == Cell signaling resources ==<br /> [http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]<br /> <br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> [http://journals.royalsociety.org/content/m5hgygq1t6daxy72/fulltext.pdf Quorum Sensing and the Population Control of Virulence]<br /> <br /> == Davidson Journal Club ==<br /> <br /> [http://www.bio.davidson.edu/courses/synthetic/papers/Stochastic_Cells.pdf Stochasticity and Gene Expression --- Dr. Campbell]<br /> <br /> [http://gcat.davidson.edu/iGEM08/cryptography_graph.pdf Hash Function --- Dr. Heyer]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4713 2008-05-21T00:41:47Z

<p>LaHeyer: /* Temporary section for IM names */</p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> ==[[Wet Lab Pages]]==<br /> <br /> == Temporary section for IM names ==<br /> <br /> heyermath &lt;br&gt;<br /> genomicsguy &lt;br&gt;<br /> lookinformammoth &lt;br&gt;<br /> toddeckdahl &lt;br&gt;<br /> aba767 &lt;br&gt;<br /> Awake714 &lt;br&gt;<br /> evelynzx &lt;br&gt;<br /> johnigo25 &lt;br&gt;<br /> masterwizard_32@hotmail.com &lt;br&gt;<br /> rcoolbassman &lt;br&gt;<br /> proud2Bnerdie &lt;br&gt;<br /> nextdrb&lt;br&gt;<br /> lesheebaby&lt;br&gt;<br /> tanglingirl&lt;br&gt;<br /> thetakris422&lt;br&gt;<br /> SwimnAfgurl3&lt;br&gt;<br /> caesymax@gmail.com&lt;br&gt;<br /> palpen9&lt;br&gt;<br /> ncsam3110&lt;br&gt;<br /> <br /> == Las/Rhl cell signaling system ==<br /> '''Responsible''': Robert Cool<br /> <br /> '''Las System'''<br /> <br /> '''Signal Molecule''': An AHL called PAI-1 (N-3-oxododecanoyl-l-hsl)(3-oxo-C12-hsl)<br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa gram(-) possibly E.coli (see article 3)<br /> <br /> '''Receiver protein''': LasR<br /> <br /> '''Effect of binding''': TXN activation of virulence genes, lasA, lasB, apr, toxR<br /> <br /> '''Synthase''': LasI enzyme<br /> <br /> '''Target Genes''': lasI, lasA, lasB, apr, toxR<br /> <br /> '''Regulation''': unknown<br /> <br /> <br /> '''References'''<br /> <br /> &quot;Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes&quot; <br /> <br /> JP Pearson, EC Pesci and BH Iglewski <br /> [http://jb.asm.org/cgi/reprint/179/18/5756?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;titleabstract=las&amp;searchid=1&amp;FIRSTINDEX=0&amp;resourcetype=HWCIT]<br /> <br /> <br /> &quot;Regulation of Pseudomonas Quinolone Signal Synthesis in Pseudomonas aeruginosa&quot;<br /> <br /> Dana S. Wade, M. Worth Calfee, Edson R. Rocha, Elizabeth A. Ling, Elana Engstrom, James P. Coleman, and Everett C. Pesci<br /> [http://jb.asm.org/cgi/content/full/187/13/4372?view=long&amp;pmid=15968046 2]<br /> <br /> <br /> Posttranscriptional Control of Quorum-Sensing-Dependent Virulence Genes by DksA in Pseudomonas aeruginosa<br /> <br /> Florence Jude,Thilo Köhler,Pavel Branny,Karl Perron,Matthias P. Mayer,Rachel Comte, and Christian van Delden<br /> [http://jb.asm.org/cgi/content/full/185/12/3558?view=long&amp;pmid=12775693 3]<br /> <br /> <br /> '''Rhl System''' <br /> <br /> &lt;br&gt;<br /> '''Signal Molecule''': An AHL called PAI-2, Plasminogen activator inhibitor-2, N-butanoyl-homoserine lactone (C4HSL) <br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa, gram(-)<br /> <br /> '''Receiver Protein''': Rhl R <br /> <br /> '''Effect of Binding''': activation of Rhamnosyl Transferase, then making RL (rhamnolipid) <br /> <br /> '''Synthase''': RhlA and RhlB <br /> <br /> '''Target Genes''': pqsABCDE and phnAB<br /> <br /> '''Regulation''': unknown<br /> <br /> '''References'''<br /> <br /> [http://jb.asm.org/cgi/reprint/189/13/4827 background information on Las and Rhl]<br /> <br /> [[Image:Las_rhl.gif]]<br /> <br /> '''Parts Needed''':<br /> <br /> LasR + pro/term<br /> <br /> RhlR + pro/term<br /> <br /> RhlI + pro/term<br /> <br /> pqsABCDE + pro/term<br /> <br /> pqsR<br /> <br /> pqsH + pro/term<br /> <br /> phnAB<br /> <br /> LasI<br /> <br /> RBS<br /> <br /> == Lux cell signaling system ==<br /> <br /> '''Responsible:''' Andrew Gordon<br /> <br /> '''Signal molecule:''' ''N''-acyl-homoserine lactone (AHL) Generic term for a variety of species specific hormone-like molecules <br /> <br /> '''Bacterial species:''' discovered in ''Vibrio fischeri'' known to work in ''E. coli''<br /> <br /> '''Receiver protein:''' LuxR protein receives signal from AHL; also has some control over transciption of luciferase<br /> <br /> '''Signal molecule synthase:''' LuxI; also has some control over transciption of luciferase<br /> <br /> '''Additional Information:''' &quot;Quorum Quenching&quot; lactonase reduces AHL concentration<br /> <br /> [[Image:800px-Luxrreceiverschematic.png]]<br /> <br /> '''Resources'''<br /> <br /> [http://partsregistry.org/Lux Lux Operon Pathway]<br /> <br /> [http://partsregistry.org/AHL AHL signaling molecules by species; some are specific to gram pos but may affect gram negs]<br /> <br /> '''References'''<br /> <br /> [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522112 Quorum Quenching to control Lux Pathway]<br /> <br /> '''Parts Needed''':<br /> <br /> LuxR + pro/term<br /> <br /> RBS<br /> <br /> LuxI + pro/term<br /> <br /> LuxI sender<br /> <br /> == Lsr cell signaling system ==<br /> <br /> '''Responsible''': Kelly Davis, Xiao Zhu<br /> <br /> '''Signal molecule''': AI-2, furanosyl borate diester, derived from the ribosyl part of S-ribosylhomocysteine, [http://www.biomedcentral.com/content/pdf/1471-2148-4-36.pdf]<br /> <br /> '''Bacterial species''': discovered in Vibrio harveyi, but interspecies signalling occurs, Escherichia coli E24377A (strain: E24377A) (for lsrK), Escherichia coli str. K-12 substr. DH10B (strain: K-12, substrain: DH10B) (for lsrR)<br /> <br /> '''Receiver protein''': LsrR protein receives signal from sensor protein<br /> <br /> '''Signal molecule synthase''': Pfs enzyme, then LuxS autoinducer synthase<br /> <br /> '''Target genes''': lsr operon, including ABC transporter and LsrK kinase<br /> <br /> '''Regulation''': LsrR represses the lsr operon, derepression by phospho-AI-2<br /> <br /> '''References'''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/14622426 Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium]<br /> <br /> [http://www.microbialcellfactories.com/content/pdf/1475-2859-1-5.pdf Review of AI-2 and other systems]<br /> <br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22733&amp;blobtype=pdf E. coli produces a signal that can substitute for AI-2]<br /> <br /> '''Resources'''<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&amp;cmd=Retrieve&amp;dopt=full_report&amp;list_uids=5586283 lsrK gene in Entrez] <br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&amp;Cmd=ShowDetailView&amp;TermToSearch=6062136&amp;ordinalpos=9&amp;itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum#summary lsrR gene in Entrez]<br /> <br /> [http://BioCyc.org/ECOLI/substring-search?type=NIL&amp;object=lsr lsr genes in EcoCyc]<br /> <br /> &lt;br&gt;<br /> '''Parts Needed:'''<br /> &lt;br/&gt;<br /> LsrR pro/term<br /> &lt;br/&gt;<br /> LsrK<br /> &lt;br/&gt;<br /> LsrACDB (transport)<br /> &lt;br/&gt;<br /> LsrFGE (catabolic)<br /> &lt;br/&gt;<br /> LuxS<br /> &lt;br/&gt;<br /> Pfs enzyme (?)<br /> <br /> http://www.nature.com/nrmicro/journal/v3/n5/images/nrmicro1146-f2.gif<br /> <br /> == Fec cell signaling system ==<br /> Responsible: Xiao Zhu<br /> <br /> '''Ferric Dicitrate Transport System'''<br /> The inducer, ferric citrate, binds to an outer membrane transport protein, FecA, and without further transport elicits a signal that is transmitted across the outer membrane (by FecA), the periplasm, and the cytoplasmic membrane (by FecBCDE and FecR) into the cytoplasm. Signal transfer across the three subcellular compartments is mediated by the outer membrane transport protein (FecA) that interacts in the periplasm with a cytoplasmic transmembrane protein (FecR). FecR is required for activation of a sigma factor (FecI) which belongs to the extracytoplasmic function (ECF)sigma factor family.<br /> &lt;br/&gt;<br /> Only iron not iron complex enters the cytoplasm. FecA is the TonB energy transducing system-dependent. <br /> &lt;br/&gt;<br /> '''Signaling Molecule:''' FeC (ferric dicitrate)<br /> &lt;br/&gt;<br /> '''Bacteria species:''' E.coli, Pseudomonas putida, P. aeruginosa, Serratia marcescens, Klebsiella pneumoniae, Aerobacter aerogenes, Bordetella pertussis, B. bronchseptica, B. avium, and Ralstonia solanacearum.<br /> &lt;br/&gt;<br /> '''Receptor Protein: ''' FecA<br /> &lt;br/&gt;<br /> '''Effect of binding:''' the conformational changes that FecA undergoes when binding to ferric citrate:The alpha helix in loop 7 unravels, and the loop moves by up to 11 angstroms ; Loop 8 moves up to 15 angstroms.<br /> http://www.rsc.org/ej/CS/2007/b617040b/b617040b-f13.gif<br /> &lt;br/&gt;<br /> '''Sensor Producer:''' N/A<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> Harvard iGEM'07 team worked with Fec system, the results were not favorable. [http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing :We believe that overexpression of the Fec system killed the cells, possibly by disturbing the cell membranes.]<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> [http://pathway.gramene.org/ECOLI/NEW-IMAGE?type=REACTION&amp;object=RXN0-2261 More detailed information about Fec]<br /> &lt;br/&gt;<br /> [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=215624&amp;blobtype=pdf Exogenous Induction of the Iron Dicitrate Transport System of Escherichia coli K-12]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/183/1/162 Control of the Ferric Citrate Transport System of Escherichia coli:Mutations in Region2.1 of the FecI ECF Sigma Factor Suppress Mutations in the FecR Transmembrane Regulatory Protein]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/full/189/19/6913 Docking of the Periplasmic FecB Binding Protein to the FecCD Transmembrane Proteins in the Ferric Citrate Transport System of Escherichia coli]<br /> &lt;br/&gt;<br /> [http://jb.asm.org/cgi/content/abstract/185/6/1870 Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box]<br /> <br /> == Signal molecules ==<br /> <br /> [[Image:QSsignals.gif|QSsignals.gif]]<br /> <br /> <br /> '''Gram (-) bacteria use:'''<br /> <br /> 3-oxo-C6-HSL, N-(3-oxohexanoyl)-L-homoserine lactone, an AHL<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> HHQ, 2-heptyl-4(1H)-quinolone, an AQ<br /> <br /> '''Gram (+) bacteria use:'''<br /> <br /> DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione<br /> <br /> A-Factor, 2-isocapryloyl-3-hydroxymethyl--butyrolactone<br /> <br /> PQS, pseudomonas quinolone signal, 2-heptyl-3-hydroxy-4(1H)-quinolone<br /> <br /> DSF, ‘diffusible factor’, cis-11-methyl-2-dodecenoic acid<br /> <br /> 3OH-PAME, hydroxyl-palmitic acid methyl ester; <br /> <br /> AIP-1, staphylococcal autoinducing peptide 1<br /> <br /> == E. coli Signaling ==<br /> <br /> &quot;As yet no AHL-producing Escherichia coli or Salmonella strains have been identified, although both organisms possess an AHL receptor (SdiA) of the LuxR protein class and respond to AHLs produced by other bacteria.&quot; [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Williams 2007]<br /> <br /> <br /> <br /> == Cell signaling resources ==<br /> [http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]<br /> <br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> [http://journals.royalsociety.org/content/m5hgygq1t6daxy72/fulltext.pdf Quorum Sensing and the Population Control of Virulence]<br /> <br /> == Davidson Journal Club ==<br /> <br /> [http://www.bio.davidson.edu/courses/synthetic/papers/Stochastic_Cells.pdf Stochasticity and Gene Expression --- Dr. Campbell]<br /> <br /> [http://gcat.davidson.edu/iGEM08/cryptography_graph.pdf Hash Function --- Dr. Heyer]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4594 2008-05-20T14:05:05Z

<p>LaHeyer: /* Stochasticity in Biology */</p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == Lux cell signaling system ==<br /> <br /> '''Responsible:''' Andrew Gordon<br /> <br /> '''Signal molecule:''' ''N''-acyl-homoserine lactone (AHL) <br /> <br /> '''Bacterial species:''' discovered in ''Vibrio fischeri'' <br /> <br /> '''Receiver protein:''' LuxR protein receives signal from AHL<br /> <br /> '''Signal molecule synthase:''' LuxI<br /> <br /> '''Additional Information:''' &quot;Quorum Quenching&quot; lactonase reduces AHL concentration<br /> <br /> Lux Operon Pathway<br /> &lt;http://partsregistry.org/Lux&gt;<br /> <br /> AHL signaling molecules by species<br /> &lt;http://partsregistry.org/AHL&gt;<br /> <br /> Quorum Quenching to control Lux Pathway<br /> &lt;http://mic.sgmjournals.org/cgi/content/full/149/8/1981&gt;<br /> &lt;http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522112&gt;<br /> <br /> == Las cell signaling system ==<br /> Responsible: Robert Cool<br /> <br /> <br /> '''Signal Molecule''': An AHL called PAI-1 (N-3-oxododecanoyl-l-hsl)(3-oxo-C12-hsl)<br /> <br /> '''Bacterial species''': Pseudomonas aeruginosa gram(-)<br /> <br /> '''Receiver protein''': LasR<br /> <br /> '''Effect of binding''': TXN activation of virulence genes, lasA, lasB, apr, toxR<br /> <br /> '''Synthase''': LasI enzyme<br /> <br /> <br /> <br /> &quot;Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes&quot; <br /> JP Pearson, EC Pesci and BH Iglewski <br /> [http://jb.asm.org/cgi/reprint/179/18/5756?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;titleabstract=las&amp;searchid=1&amp;FIRSTINDEX=0&amp;resourcetype=HWCIT]<br /> <br /> == Fec cell signaling system ==<br /> Responsible: Xiao Zhu<br /> &lt;br/&gt;<br /> <br /> &lt;br/&gt;<br /> '''Ferric Dicitrate Transport System'''<br /> Fec system is the most characterized signalling system with outermembrane receptor protein FecA. The inducer is dinuclear ferric citrate (ferric dicitrate). Fe dicitrate is transported via the TonB-dependent receptor FecA and into the cytosol via the FecBCDE periplasmic binding protein-dependent ABC(ATP binding cassette)transpot system.<br /> http://gcat.davidson.edu/GcatWiki/images/0/0c/Fec.jpg<br /> &lt;br/&gt;<br /> '''Signaling Molecule:''' FeC (ferric dicitrate)<br /> &lt;br/&gt;<br /> '''Receptor Protein: ''' FecA<br /> &lt;br/&gt;<br /> '''Effect of binding:''' the conformational changes that FecA undergoes when binding to ferric citrate:The alpha helix in loop 7 unravels, and the loop moves by up to 11 angstroms ; Loop 8 moves up to 15 angstroms.<br /> http://www.rsc.org/ej/CS/2007/b617040b/b617040b-f13.gif<br /> &lt;br/&gt;<br /> '''Sensor Producer:''' N/A<br /> &lt;br/&gt;<br /> More detailed information about Fec:<br /> &lt;br/&gt;<br /> http://pathway.gramene.org/ECOLI/NEW-IMAGE?type=REACTION&amp;object=RXN0-2261<br /> &lt;br/&gt;<br /> &quot;Exogenous Induction of the Iron Dicitrate Transport System of Escherichia coli K-12&quot;<br /> http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=215624&amp;blobtype=pdf<br /> &lt;br/&gt;<br /> &quot;Control of the Ferric Citrate Transport System of Escherichia coli...&quot;<br /> http://jb.asm.org/cgi/content/full/183/1/162<br /> <br /> == Lsr cell signaling system ==<br /> <br /> '''Responsible''': unclaimed<br /> <br /> '''Signal molecule''': AI-2, furanosyl borate diester, derived from the ribosyl part of S-ribosylhomocysteine, [http://www.biomedcentral.com/content/pdf/1471-2148-4-36.pdf]<br /> <br /> '''Bacterial species''': discovered in Vibrio harveyi, but interspecies signalling occurs<br /> <br /> '''Receiver protein''': LsrR protein receives signal from sensor protein<br /> <br /> '''Signal molecule synthase''': Pfs enzyme, then LuxS autoinducer synthase<br /> <br /> '''Target genes''': lsr operon, including ABC transporter and LsrK kinase<br /> <br /> '''Regulation''': LsrR represses the lsr operon, derepression by phospho-AI-2<br /> <br /> '''Additional References''': [http://www.microbialcellfactories.com/content/pdf/1475-2859-1-5.pdf Review of AI-2 and other systems], [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22733&amp;blobtype=pdf E. coli produces a signal that can substitute for AI-2]<br /> <br /> == Rhl cell signaling system ==<br /> Responsible: Alicia Allen<br /> &lt;br&gt;<br /> Rhl is subord. to LasR/ LasI<br /> <br /> Environmental Regulation of Pseudomonas aeruginosa PAO1 Las and Rhl Quorum-Sensing Systems <br /> <br /> (gives background information on Las and Rhl) <br /> http://jb.asm.org/cgi/reprint/189/13/4827<br /> <br /> Sensor Molecule: An AHL called PAI-2, Plasminogen activator inhibitor-2, N-butanoyl-homoserine lactone (C4HSL)<br /> <br /> Sensor Binder: Rhl R<br /> <br /> Effect of Binding: activation of Rhamnosyl Transferase, then making RL (rhamnolipid)<br /> <br /> Sensor Producer: RhlA and RhlB<br /> <br /> == Cell signaling resources ==<br /> [http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]<br /> <br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> [http://journals.royalsociety.org/content/m5hgygq1t6daxy72/fulltext.pdf Quorum Sensing and the Population Control of Virulence]<br /> <br /> == Davidson Journal Club ==<br /> <br /> [http://www.bio.davidson.edu/courses/synthetic/papers/Stochastic_Cells.pdf Stochasticity and Gene Expression --- Dr. Campbell]<br /> <br /> [http://gcat.davidson.edu/iGEM08/cryptography_graph.pdf Hash Function --- Dr. Heyer]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4535 2008-05-16T19:06:07Z

<p>LaHeyer: /* Cell signaling resources */</p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == Cell signaling resources ==<br /> [http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]<br /> <br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4510 2008-04-18T22:15:02Z

<p>LaHeyer: </p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == Cell signaling resources ==<br /> [http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]<br /> <br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> [http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]<br /> <br /> [http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4509 2008-04-18T22:07:12Z

<p>LaHeyer: /* iGEM 2007 Useful Information */</p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == Cell signaling resources ==<br /> [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]<br /> <br /> [http://www.molbio.princeton.edu/index.php?option=content&amp;task=view&amp;id=27 Bonnie Bassler lab at Princeton]<br /> <br /> [http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]<br /> <br /> [http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&amp;pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]<br /> <br /> [http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]<br /> <br /> == iGEM 2007 Useful Information ==<br /> '''Virginia Tech''' <br /> <br /> ''Engineering and Epidemic''<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.<br /> <br /> The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things. <br /> <br /> http://parts.mit.edu/igem07/index.php/Virginia_Tech<br /> <br /> <br /> '''University of Waterloo'''<br /> <br /> ''Half-Adder Logic Gate''<br /> <br /> The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.<br /> <br /> http://parts.mit.edu/igem07/index.php/Waterloo<br /> <br /> <br /> '''UCSF'''<br /> <br /> ''Project 1: Protein Scaffolds as a Molecular Breadboard''<br /> <br /> Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.<br /> <br /> http://parts.mit.edu/igem07/index.php/UCSF<br /> <br /> <br /> '''Tianjin'''<br /> <br /> ''Biological diode''<br /> <br /> In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tianjin<br /> <br /> <br /> '''Duke University'''<br /> <br /> ''Bacterial Communication With Light''<br /> <br /> http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - <br /> <br /> <br /> '''University of Cambridge'''<br /> <br /> ''BOL: Bacteria OnLine''<br /> <br /> They talk a little about making a bacterial internet, I have no idea what they mean.<br /> <br /> http://parts.mit.edu/igem07/index.php/Cambridge<br /> <br /> <br /> '''Tokyo Tech'''<br /> <br /> ''Pareto's Principle: An Ant Society''<br /> <br /> The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes &quot;balanced differentiation&quot;. Bistability and cell-cell communication are necessary to realize our model of &quot;Balanced differentiation&quot;.<br /> <br /> http://parts.mit.edu/igem07/index.php/Tokyo_Tech<br /> <br /> <br /> '''Quorum Sensing'''<br /> [http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]<br /> <br /> '''Harvard'''<br /> <br /> ''Quorum Sensing''<br /> <br /> Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.<br /> <br /> http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing<br /> <br /> <br /> '''Chiba'''<br /> <br /> ''Communication Unit''<br /> <br /> Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.<br /> <br /> http://parts.mit.edu/igem07/index.php/Chiba/Communication<br /> <br /> <br /> '''Brown'''<br /> <br /> ''Cellular Lead Sensor''<br /> <br /> -no useful information<br /> <br /> http://parts.mit.edu/igem07/index.php/Brown <br /> <br /> <br /> <br /> '''Colombia-Israel (ORT Ebin High School)'''<br /> <br /> ''A Microbial Biosensor Device'' <br /> <br /> No description left...<br /> <br /> - http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School) <br /> <br /> <br /> '''Edinburgh'''<br /> <br /> ''Division PoPper'' and ''Self Flavouring Yoghurt'' <br /> <br /> - This team is working on a project that is looking into a form of cell communication <br /> <br /> - &quot;We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication.&quot; <br /> <br /> - Could not find where on this page this info came from, but it was included with this link:<br /> ''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.'' <br /> <br /> http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21<br /> <br /> <br /> '''Imperial'''<br /> <br /> ''Infector Detector''<br /> <br /> -no useful information, but really interesting project...<br /> <br /> http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)<br /> <br /> <br /> '''Middle East Technical University'''<br /> <br /> Chase simulator <br /> <br /> This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.<br /> http://parts.mit.edu/igem07/index.php/Chase_Simulator<br /> <br /> == iGEM 2006 Useful Information ==<br /> '''UT Austin 2005/2006'''<br /> Project : Edge Detector <br /> Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&amp;group=iGEM_UTAustin<br /> <br /> Useful information: <br /> They have &quot;black boxed&quot; the light-system and used it as an input for the of the edge detection circuitry. <br /> <br /> Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.<br /> <br /> Note: Built on 2005’s work. Pretty much the same as 2005. <br /> <br /> <br /> <br /> ''' Harvard'''<br /> “Cell Surface Targeting” <br /> http://parts.mit.edu/wiki/index.php/Harvard_2006<br /> <br /> Project Overview<br /> “In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.<br /> • Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.<br /> • Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.<br /> • Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.<br /> • Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.<br /> Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”<br /> <br /> <br /> <br /> '''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.<br /> The Receivers express Green Fluorescent Protein in the vicinity of AHSL.<br /> The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.<br /> Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.<br /> <br /> http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_Calgary<br /> <br /> <br /> '''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message<br /> <br /> http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006<br /> <br /> “We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by &quot;unlocking&quot; the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”<br /> <br /> '''Mexico''': cellular automata<br /> <br /> http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006<br /> <br /> “We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”<br /> <br /> “We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”<br /> <br /> “Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”<br /> “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”<br /> <br /> <br /> <br /> '''Brown:Bacterial''' Freeze Tag<br /> http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview<br /> 2006 igem<br /> <br /> <br /> This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.<br /> <br /> TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.<br /> <br /> The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the &quot;Freeze Machine&quot;.<br /> <br /> A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the &quot;freezing&quot; of the cell.<br /> <br /> <br /> '''McGill University Split YFP'''<br /> http://parts.mit.edu/wiki/index.php/McGill_University_2006<br /> <br /> The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.<br /> <br /> <br /> '''Penn State'''<br /> http://openwetware.org/wiki/IGEM:PennState/2006<br /> <br /> The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology<br /> <br /> '''Tokyo'''<br /> http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion<br /> <br /> Our project is to make this Noughts-and-Crosses in vivo.<br /> -1. Inputs<br /> -1. Chemicals<br /> -1. To indicate each square<br /> -1. To be spreaded into all squares.<br /> -1. Outputs<br /> -1. Reporter of SYANAC: GFP<br /> Reporter of Human: RFP<br /> <br /> We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.<br /> <br /> <br /> '''BU 2006''' <br /> Project: build a functioning &quot;Biological Night-Light&quot; system<br /> <br /> Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&amp;group=iGEM2006_BU<br /> Goal<br /> Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.<br /> Ideas<br /> &quot;Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm...&quot; (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.<br /> <br /> Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete &quot;cells&quot; interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow &quot;medium&quot; range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye. <br /> <br /> '''Weiss Lab: Game of Life'''<br /> Link: http://www.princeton.edu/~rweiss/<br /> Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.<br /> <br /> Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders. <br /> <br /> <br /> '''Bangalore NCBS 2006'''<br /> Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels<br /> http://parts.mit.edu/wiki/index.php/Workshop<br /> <br /> '''Rice University 2006'''<br /> The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.<br /> http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL<br /> <br /> '''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006<br /> <br /> The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball). 
The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.<br /> <br /> 1. Parts used for generating patterns (these are parts whose function Cambridge characterized) <br /> 
(a) Constitutively expressed fluorescent proteins:<br /> ECFP: BBa_I13601<br /> GFP: BBa_J04430<br /> EYFP: BBa_I6031<br /> mRFP1: BBa_J04450 <br /> (b) Constitutive or auto-induced AHL synthesis:<br /> Lux-sender (auto-inducing): BBa_I15030<br /> Las-sender (constitutive): BBa_I0407<br /> Rhl-sender (constitutive): BBa_I0405<br /> Cin-sender (constitutive): BBa_I0409 
<br /> (c) AHL-induced fluorescence response:<br /> Lux-receiver (GFP): BBa_T9002<br /> Lux-receiver (EYFP): BBa_I13263<br /> Las-receiver (EYFP): BBa_I0426<br /> Rhl-receiver (EYFP): BBa_I0424<br /> Cin-receiver (EYFP): BBa_I0428<br /> <br /> <br /> '''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary<br /> <br /> Mammalian cell-cell signaling using LuxR and LuxI…not applicable<br /> <br /> == iGEM 2005 Useful Information ==<br /> '''Caltech'''<br /> http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&amp;direction=prev&amp;oldid=52 <br /> AND gates used to build an adder (oligo technology, Winfree lab)<br /> http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf<br /> <br /> Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf<br /> <br /> <br /> <br /> '''Cambridge''' <br /> http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page<br /> Used sender/pulse-generator from Princeton to do something?<br /> AHL signal and aTc activated promoter<br /> Important paper in PNAS where this is shown to work:<br /> http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf<br /> <br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> Bacterial wire propogates signal of AHL<br /> <br /> '''MIT 2005'''<br /> The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as &quot;how do we deploy our biosensor into a lake where it can respond to toxin levels?&quot; The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.<br /> http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver<br /> <br /> <br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1<br /> <br /> <br /> '''Penn State'''<br /> http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes<br /> <br /> ”The idea for our project grew out of one for a &quot;bacterial maze,&quot; in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a &quot;bacterial relay race.&quot;<br /> As in a conventional relay race, the signal is to &quot;go,&quot; or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).<br /> In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”<br /> <br /> <br /> '''Arizona''' <br /> “Water Color” <br /> http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006<br /> <br /> Project Details<br /> “The current name of our project is &quot;Water Color.&quot; It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.<br /> The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain &quot;color&quot; (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to &quot;erase&quot; the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”<br /> <br /> Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule<br /> <br /> <br /> '''Harvard'''<br /> http://bio.freelogy.org/wiki/IGEM_2005<br /> <br /> '''UC Berkley 2005'''<br /> http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005<br /> <br /> Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.<br /> <br /> Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as &quot;F-type&quot;, and always produces mRNA 'key 2' which unlocks RNA lock 2<br /> <br /> -1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C<br /> 1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --&gt; turn on GFP to signify &quot;message 1 received&quot;) secured by RNA lock 1.<br /> <br /> 2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, &quot;message 1 received&quot;) and simultaneously activate TraJr (start R conjugation cascade)<br /> <br /> -1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr<br /> 2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4451 2008-04-04T20:11:46Z

<p>LaHeyer: </p> <hr /> <div>&lt;font size = &quot;6&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> <br /> iGEM 2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == iGEM 2007 Useful Information ==<br /> <br /> <br /> == iGEM 2006 Useful Information ==<br /> <br /> <br /> == iGEM 2005 Useful Information ==</div>

LaHeyer http://gcat.davidson.edu/GcatWiki/index.php?title=Davidson/Missouri_Western_iGEM2008&diff=4450 2008-04-04T20:08:43Z

<p>LaHeyer: </p> <hr /> <div>&lt;font size = &quot;4&quot;&gt;&lt;center&gt;<br /> Davidson College - Missouri Western State University<br /> &lt;/center&gt;<br /> &lt;center&gt;<br /> iGem2008<br /> &lt;/center&gt;&lt;/font&gt;<br /> <br /> == iGEM 2007 Useful Information ==<br /> <br /> <br /> == iGEM 2006 Useful Information ==<br /> <br /> <br /> == iGEM 2005 Useful Information ==</div>

LaHeyer