GcatWiki - User contributions [en]

IGEM 2009 Project

2009-07-13T21:19:01Z

Alyn the violist:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences] 
[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers] 
[http://www.staff.uni-bayreuth.de/~btc914/search/index.html Align E. coli tRNA sequences] 
[http://media.pearsoncmg.com/bc/bc_campbell_genomics_2/medialib/jmol/trna/index.html Compare 2 tRNA structures] 

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="120"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"| [http://gcat.davidson.edu/GcatWiki/index.php/What_naming_system_are_we_going_to_use_for_the_suppressor_tRNAs%3F Codon Short Name]
!width="150"|tRNA Status
!width="150"|5mer+XFP Status
!width="150"|5mer+Drug resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || '''2 verified clones''' , both ligated with pBad || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| '''1 clone 100% match''', putting pBAD upstream || 9 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 2 clones being resequenced || 6 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''1 clone 100% match''', putting pBAD upstream || 7 5mer+RFPs sequencing || 7 5mer+Tets sequencing
|-
| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || '''4 clones 100%match''', pBad is upstream clone || 4 5mer+RFPs sequencing || 6 5mer+Tets sequencing
|-
| Clif Davis|| 5mer codon || Anticodon Sequence || Leu3|| tRNA Status || 5mer+RFP Status || 2 5mer+CAT sequenced-99% Match with a Conservative Mutation
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

IGEM 2009 Project

2009-07-13T21:18:37Z

Alyn the violist:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences] 
[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers] 
[http://www.staff.uni-bayreuth.de/~btc914/search/index.html Align E. coli tRNA sequences] 
[http://media.pearsoncmg.com/bc/bc_campbell_genomics_2/medialib/jmol/trna/index.html Compare 2 tRNA structures] 

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="120"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"| [http://gcat.davidson.edu/GcatWiki/index.php/What_naming_system_are_we_going_to_use_for_the_suppressor_tRNAs%3F Codon Short Name]
!width="150"|tRNA Status
!width="150"|5mer+XFP Status
!width="150"|5mer+Drug resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || '''2 verified clones''' , both ligated with pBad || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| '''1 clone 100% match''', putting pBAD upstream || 9 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 2 clones being resequenced || 6 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''1 clone 100% match''', putting pBAD upstream || 7 5mer+RFPs sequencing || 7 5mer+Tets sequencing
|-
| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || ""4 clones 100%match"", pBad is upstream clone || 4 5mer+RFPs sequencing || 6 5mer+Tets sequencing
|-
| Clif Davis|| 5mer codon || Anticodon Sequence || Leu3|| tRNA Status || 5mer+RFP Status || 2 5mer+CAT sequenced-99% Match with a Conservative Mutation
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

IGEM 2009 Project

2009-06-27T16:00:36Z

Alyn the violist:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences] 
[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers] 
[http://www.staff.uni-bayreuth.de/~btc914/search/index.html Align E. coli tRNA sequences] 
[http://media.pearsoncmg.com/bc/bc_campbell_genomics_2/medialib/jmol/trna/index.html Compare 2 tRNA structures] 

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="120"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"| [http://gcat.davidson.edu/GcatWiki/index.php/What_naming_system_are_we_going_to_use_for_the_suppressor_tRNAs%3F Codon Short Name]
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || 2 clones being resequenced || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || 1 clone being resequenced || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| '''1 clone 100% match''', putting pBAD upstream || 9 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 2 clones being re-sequenced || 6 5mer+RFPs sequencing || 5 5mer+Tets sequencing
|-
| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''1 clone 100% match''', putting pBAD upstream || 7 5mer+RFPs sequencing || 7 5mer+Tets sequencing
|-
| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || 5 clones being sequenced || 4 5mer+RFPs being sequenced || 6 5mer+Tets being sequenced
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

IGEM 2009 Project

2009-06-23T03:39:04Z

Alyn the violist:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]

[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="200"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"|Codon Short Name
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || 4 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || 3 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
|-
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| 1 clone being sequenced || Gel purifying 5mer+RFP || Gel purifying 5mer+Tet Resistance
|-
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 3 clones being sequenced || Cleaning/Concentrating 5mer+ RFP || Cleaning+Conc 5mer +Tet
|-
| Leland Taylor || CCCUC || CUGAGGGUC || Pro || 2 clones being sequenced || Transformed 5mer+RFP || Transformed 5mer+Tet
|-
| Alyndria Thompson|| CGGUC || UUGACCGAC || Arg|| 5 clones being sequenced || Transformed || Transformed
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

IGEM 2009 Project

2009-06-19T21:57:12Z

Alyn the violist:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]

[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="200"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"|Codon Short Name
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || 4 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || 3 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
|-
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| 1 clone being sequenced || Gel purifying 5mer+RFP || Gel purifying 5mer+Tet Resistance
|-
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 3 clones being sequenced || Cleaning/Concentrating 5mer+ RFP || Cleaning+Conc 5mer +Tet
|-
| Leland Taylor || CCCUC || CUGAGGGUC || Pro || 2 clones being sequenced || Transformed 5mer+RFP || Transformed 5mer+Tet
|-
| Alyndria Thompson|| CGGUC || UUGACCGAC || Arg|| 5 clones to be verified || Ready for Digestion || Ready for Digestion
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

How are we going to build the 5-mer BioBricks?

2009-06-04T14:29:54Z

Alyn the violist:

[http://gcat.davidson.edu/GcatWiki/images/c/c0/InsertingLC.doc Inserting 5mers]

How are we going to build the 5-mer BioBricks?

2009-06-04T14:29:39Z

Alyn the violist:

[[http://gcat.davidson.edu/GcatWiki/images/c/c0/InsertingLC.doc Inserting 5mers]]

File:InsertingLC.doc

2009-06-04T14:28:20Z

Alyn the violist:

Examples of Metabolic Pathways in E.coli

2009-05-27T18:45:50Z

Alyn the violist:

Metabolic Pathways:

[http://biocyc.org/ECOL316407/NEW-IMAGE?object=Degradation]

Examples of Metabolic Pathways in E.coli

2009-05-27T18:42:40Z

Alyn the violist:

Metaboic Pathways:

[http://biocyc.org/ECOL316407/NEW-IMAGE?object=Degradation]

Examples of Metabolic Pathways in E.coli

2009-05-27T18:41:48Z

Alyn the violist:

Metaboic Pathways:

http://biocyc.org/ECOL316407/NEW-IMAGE?object=Degradation

Missouri Western/Davidson iGEM2009

2009-05-27T18:41:13Z

Alyn the violist:

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-alog Freezer Stocks] 

We need to learn more about these topics:
<center>'''Biology-based'''</center>

#[[Plasmid Creation]]
#[[What is msDNA?]]
#[[How is msDNA normally produced?]] Olivia/Alyndria
#[[How many copies are carried per cell?]] Alyndria
#[[What would we need to do to turn this into a BioBrick device?]] Romina
#[[ How could we swap out msDNA sequences?]] Shamita
#[[What role can physical modeling of protein structure play in our project?]]
#[[What role can physical modeling of proteins play in our project? Eric Sawyer]]
#[[What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik]]
#[[Can we use promoter strength/opposite directions to subtract? Clif Davis]]
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
#[[How is msDNA stored in E. coli?]] Olivia
#[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]] Shamita
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
#[[What are other available reverse transcriptases?]] Leland
#[[What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun]]
#[[What is the relationship between 3-SAT and map coloring? Ashley Schnoor]]
#[[What activators are there that turn on a promoter without any help?]]
#[[Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon]]
#[[Could we do something with clocks/counting?]]
#[[Could we have/use multiple synthetic organelles in a cell?]]
#[[What ideas from previous iGEM teams are useful to us?]]
#[[Examples of Metabolic Pathways in E.coli]]

<center>'''Math-based'''</center>
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
#[[What interesting challenges or problems does origami offer?]]
#[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]
#[[What has been done before and how can we improve upon that?]]
#[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]
#[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]
#[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]

#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
#[[What are some linear algebra applications for DNA origami?]]
#[[How can we use origami to solve 3-SAT problems?]]

<center>'''Behavior-based'''</center>
#[[What constructs are we testing?]]
#[[What school districts do we have access to?]]
#[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]
#[[Do you need any more input from the veterans before the survey is ready?]]

<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
#[[Can we solve a 3-SAT problem with supressor logic?]]

<center>'''Hin/Hix System'''</center>
Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks.
[http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf Hin/Hix Animation]

Missouri Western/Davidson iGEM2009

2009-05-27T18:40:54Z

Alyn the violist:

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-alog Freezer Stocks] 

We need to learn more about these topics:
<center>'''Biology-based'''</center>

#[[Plasmid Creation]]
#[[What is msDNA?]]
#[[How is msDNA normally produced?]] Olivia/Alyndria
#[[How many copies are carried per cell?]] Alyndria
#[[What would we need to do to turn this into a BioBrick device?]] Romina
#[[ How could we swap out msDNA sequences?]] Shamita
#[[What role can physical modeling of protein structure play in our project?]]
#[[What role can physical modeling of proteins play in our project? Eric Sawyer]]
#[[What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik]]
#[[Can we use promoter strength/opposite directions to subtract? Clif Davis]]
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
#[[How is msDNA stored in E. coli?]] Olivia
#[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]] Shamita
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
#[[What are other available reverse transcriptases?]] Leland
#[[What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun]]
#[[What is the relationship between 3-SAT and map coloring? Ashley Schnoor]]
#[[What activators are there that turn on a promoter without any help?]]
#[[Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon]]
#[[Could we do something with clocks/counting?]]
#[[Could we have/use multiple synthetic organelles in a cell?]]
#[[What ideas from previous iGEM teams are useful to us?]]
#[]Examples of Metabolic Pathways in E.coli]]

<center>'''Math-based'''</center>
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
#[[What interesting challenges or problems does origami offer?]]
#[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]
#[[What has been done before and how can we improve upon that?]]
#[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]
#[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]
#[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]

#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
#[[What are some linear algebra applications for DNA origami?]]
#[[How can we use origami to solve 3-SAT problems?]]

<center>'''Behavior-based'''</center>
#[[What constructs are we testing?]]
#[[What school districts do we have access to?]]
#[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]
#[[Do you need any more input from the veterans before the survey is ready?]]

<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
#[[Can we solve a 3-SAT problem with supressor logic?]]

<center>'''Hin/Hix System'''</center>
Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks.
[http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf Hin/Hix Animation]

How many copies are carried per cell?

2009-04-25T18:24:33Z

Alyn the violist:

msDNA exists in several hundreds of copies per cell in bacterial cells. Because of this, it was named '''multicopy''' single-stranded DNA.

[http://rss.sciencedirect.com/getMessage?registrationId=IADJJDLJJCDRQAHNKADSIEFOJEDRIIJKISFRLIDMRJ Ahmed 2003 msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron]

--[[User:Alyn the violist|Alyn the violist]] 14:24, 25 April 2009 (EDT)

How many copies are carried per cell?

2009-04-25T18:24:12Z

Alyn the violist:

msDNA exists in several hundreds of copies per cell in bacterial cells. Because of this, it was named '''multicopy''' single-stranded DNA.

[http://rss.sciencedirect.com/getMessage?registrationId=IADJJDLJJCDRQAHNKADSIEFOJEDRIIJKISFRLIDMRJ Ahmed 2003 msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron]
--[[User:Alyn the violist|Alyn the violist]] 14:24, 25 April 2009 (EDT)

How is msDNA normally produced?

2009-04-25T18:23:23Z

Alyn the violist:

This page has a lot of very good history about msDNA.
[ msDNA History and References]

[http://content.karger.com/produktedb/produkte.asp?typ=fulltext&file=CGR20051101_4491 Here is a 2005 paper on msDNA.]

----

How is msDNA [multicopy single-stranded DNA] normally produced?

In some strains of E. coli, msDNA linked to RNA is produced by a reverse transcriptase (RT) encoded by a retron.[1] The retron is a genetic substructure containing the gene for reverse transcriptase (RT) as well as the msr-msd region (msr gene codes for msdRNA/ msd gene codes for msDNA) of the transcript, which serves as a template as well as a primer for the RT reaction. Bacterial reverse transcriptases (RTs) are distinctive amongst other RTs in terms of the priming reactions for cDNA (complementary DNA) synthesis. Because the single RNA molecule is used as both template and starting point for DNA replication, the RT forms an unusual 2′,5′-phosphodiester linkage between an internal G residue of the RNA molecule and the 5′ end of the cDNA to initiate cDNA . In this process the bacterial RTs synthesize msDNA. [2]
Lampson confirmed that the msDNA contained the DNA-RNA duplex and that the RNA molecule existed as a template for AT in his study of a clinical strain of E. coli (Cl-1).This msDNA formed a secondary hairpin structure, and the RNA portion formed a stem-and loop structure.[3]

(1)[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45R89PJ-11&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=2125bd75cb17285d5060c988b4b0d75c Lima 1995 Isolation and Characterization of Host Mutants Defective in msDNA Synthesis: Role of Ribonuclease H in msDNA Synthesis]

(2) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45KKVK8-R&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=3e647c1471bc1217f7dbc6cb6bd6181b Lima 1997 A Novel Retron That Produces RNA-less msDNA inEscherichia coliUsing Reverse Transcriptase,]

(3) [http://www.bio.cmu.edu/Courses/03441/TermPapers/97TermPapers/RT/msdna.html REVERSE TRANSCRIPTASE IN E.COLI msDNA]

--[[User:Alyn the violist|Alyn the violist]] 14:23, 25 April 2009 (EDT)

How many copies are carried per cell?

2009-04-25T18:21:49Z

Alyn the violist:

[Alyndria]

msDNA exists in several hundreds of copies per cell in bacterial cells. Because of this, it was named '''multicopy''' single-stranded DNA.

[http://rss.sciencedirect.com/getMessage?registrationId=IADJJDLJJCDRQAHNKADSIEFOJEDRIIJKISFRLIDMRJ Ahmed 2003 msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron]

How many copies are carried per cell?

2009-04-25T18:21:06Z

Alyn the violist:

#4How many copies are carried per cell? [Alyndria]

msDNA exists in several hundreds of copies per cell in bacterial cells. Because of this, it was named multicopy single-stranded DNA.

[http://rss.sciencedirect.com/getMessage?registrationId=IADJJDLJJCDRQAHNKADSIEFOJEDRIIJKISFRLIDMRJ Ahmed 2003 msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron]

How is msDNA normally produced?

2009-04-23T01:57:35Z

Alyn the violist:

This page has a lot of very good history about msDNA.
[ msDNA History and References]

[http://content.karger.com/produktedb/produkte.asp?typ=fulltext&file=CGR20051101_4491 Here is a 2005 paper on msDNA.]

How is msDNA [multicopy single-stranded DNA] normally produced?
[Alyndria]

In some strains of E. coli, msDNA linked to RNA is produced by a reverse transcriptase (RT) encoded by a retron.[1] The retron is a genetic substructure containing the gene for reverse transcriptase (RT) as well as the msr-msd region (msr gene codes for msdRNA/ msd gene codes for msDNA) of the transcript, which serves as a template as well as a primer for the RT reaction. Bacterial reverse transcriptases (RTs) are distinctive amongst other RTs in terms of the priming reactions for cDNA (complementary DNA) synthesis. Because the single RNA molecule is used as both template and starting point for DNA replication, the RT forms an unusual 2′,5′-phosphodiester linkage between an internal G residue of the RNA molecule and the 5′ end of the cDNA to initiate cDNA . In this process the bacterial RTs synthesize msDNA. [2]
Lampson confirmed that the msDNA contained the DNA-RNA duplex and that the RNA molecule existed as a template for AT in his study of a clinical strain of E. coli (Cl-1).This msDNA formed a secondary hairpin structure, and the RNA portion formed a stem-and loop structure.[3]

(1)[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45R89PJ-11&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=2125bd75cb17285d5060c988b4b0d75c Lima 1995 Isolation and Characterization of Host Mutants Defective in msDNA Synthesis: Role of Ribonuclease H in msDNA Synthesis]

(2) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45KKVK8-R&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=3e647c1471bc1217f7dbc6cb6bd6181b Lima 1997 A Novel Retron That Produces RNA-less msDNA inEscherichia coliUsing Reverse Transcriptase,]

(3) [http://www.bio.cmu.edu/Courses/03441/TermPapers/97TermPapers/RT/msdna.html REVERSE TRANSCRIPTASE IN E.COLI msDNA]

How is msDNA normally produced?

2009-04-23T01:54:46Z

Alyn the violist:

This page has a lot of very good history about msDNA.
[ msDNA History and References]

[http://content.karger.com/produktedb/produkte.asp?typ=fulltext&file=CGR20051101_4491 Here is a 2005 paper on msDNA.]

How is msDNA [multicopy single-stranded DNA] normally produced?
[Alyndria]

In some strains of E. coli, msDNA linked to RNA is produced by a reverse transcriptase (RT) encoded by a retron.[1] The retron is a genetic substructure containing the gene for reverse transcriptase (RT) as well as the msr-msd region (msr gene codes for msdRNA/ msd gene codes for msDNA) of the transcript, which serves as a template as well as a primer for the RT reaction. Bacterial reverse transcriptases (RTs) are distinctive amongst other RTs in terms of the priming reactions for cDNA (complementary DNA) synthesis. Because the single RNA molecule is used as both template and starting point for DNA replication, the RT forms an unusual 2′,5′-phosphodiester linkage between an internal G residue of the RNA molecule and the 5′ end of the cDNA to initiate cDNA . In this process the bacterial RTs synthesize msDNA. [2]
Lampson confirmed that the msDNA contained the DNA-RNA duplex and that the RNA molecule existed as a template for AT in his study of a clinical strain of E. coli (Cl-1).This msDNA formed a secondary hairpin structure, and the RNA portion formed a stem-and loop structure.[3]

(1)[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45R89PJ-11&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=2125bd75cb17285d5060c988b4b0d75c Lima 1995 Isolation and Characterization of Host Mutants Defective in msDNA Synthesis: Role of Ribonuclease H in msDNA Synthesis]
(2) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPF-45KKVK8-R&_user=6646248&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000070315&_version=1&_urlVersion=0&_userid=6646248&md5=3e647c1471bc1217f7dbc6cb6bd6181b Lima 1997 A Novel Retron That Produces RNA-less msDNA inEscherichia coliUsing Reverse Transcriptase,]
(3) [http://www.bio.cmu.edu/Courses/03441/TermPapers/97TermPapers/RT/msdna.html REVERSE TRANSCRIPTASE IN E.COLI msDNA]