GcatWiki - User contributions [en]

File:MWSU Gibson Assembly Presentation for Davidson.pptx

2012-07-25T13:40:04Z

Dcarr1:

Philosophy and Ethics of our Project

2012-07-18T17:52:45Z

Dcarr1:

This page is for the Philosophical and Ethical considerations surrounding our project to optimize a metabolic pathway in E. coli.

Eddie Miles- "Do we have the right to engineer living things specifically for our own benefit?" Related Article: '''Synthetic Biology: Drawing a Line in Darwin's Sand''' [http://search.ebscohost.com/login.aspx?direct=true&db=phl&AN=PHL2126216&site=ehost-live] '''Note:''' Some environmental ethicists assert that the evolutionary process serves as a normative foundation for environmental ethics, in other words, an organism's evolutionary history can/should be considered when making "ought" or "ought not" statements regarding these organisms. The main thesis of the above article is that synthetic biology, by separating an organism from its evolutionary history, is upsetting this normative foundation and that on these grounds, synthetic biology should be opposed. Although I haven't yet studied environmental ethics (first-year student here) and am not familiar with the argument for a normative value of evolutionary history, I'm initially skeptical of its relevance due to a few questions that it raises for me. For example, the assertion in the article is that this normative function tells us, at least in the case of synthetic biology, that we shouldn't "create" life due to the fact that we're separating the organism from its evolutionary history but even if the normative value of the evolutionary process can be well demonstrated, could this normative function ever tell us anything other than "don't play god"? If so, what other things can it tell us? If not, of what use is it to begin with?

'''Biology and Art'''- In what ways can synthetic biology be used to create art? What implications might our work have on the accessibility of "bioart"? How does this relate to the ethical questions that we've been considering? [http://en.wikipedia.org/wiki/BioArt]

David, Kamay, and Corinne: What unforeseeable dangers might there be in technology like Gibson Assembly, which allows the possibility of synthetically constructing any existing or new sequences of genes?

**This is a very rough summary of the things I have been thinking about in regards to the following topic. Feel free to add and edit where appropriate.**

Bioethics of Assembling Genomes(Combining the qualities of organisms and or creating new organisms)

The importance of being able to create and control life is paramount to synthetic biologists around the world. However, as be become more technologically advanced in our methods for doing this, it is of concern to our environment and scientific progress that we have an idea of where we are going and why.
A futuristic outlook in my mind permits the creation of organisms that will one day change the face of our planet perhaps for the better, and maybe even the faces of other planets in our solar system or others.
The ecosystems we engineer may improve the conditions of our planet to allow life to continue when it would otherwise fail.
This will of course run the risk of unintended consequences which lead to more harm that benefit. In addition, there will be costs to the natural ecosystems that have developed. Many organisms would be selected out of existance, but this is not new to our planet. Ninety nine percent of all organism that have ever inhabited the earth are now extinct.
We would also like to assume that our cultures will have evolved more mature systems of government that are less chaotic and more unified allowing us to make good decisions about these complicated issues.
We currently have no reason to believe we will come to a point where we will achieve such goals, but in examining the way we procede we should be able to caution ourselves to foresee-ably dangerous technologies we may allow into the hands of others.
On the bright side could engineer more nutritious foods that grow more easily to support our populations, engineer and release organisms that improve the health of our atmosphere and breathable air.. the details of what is possible are unlimited when you understand how complicated ecosystems are and what changes can make them thrive and/or fail.

David Carr

Alexander, Virginia: Is enough understood about synthetic biology to avoid unintended catastrophies?
Related article: '''Synthetics: the Ethics of Synthetic Biology''' [http://www.ethicsandtechnology.eu/images/uploads/Ethics_of_synthetic_biology.pdf]

Philosophy and Ethics of our Project

2012-07-18T17:51:23Z

Dcarr1:

This page is for the Philosophical and Ethical considerations surrounding our project to optimize a metabolic pathway in E. coli.

Eddie Miles- "Do we have the right to engineer living things specifically for our own benefit?" Related Article: '''Synthetic Biology: Drawing a Line in Darwin's Sand''' [http://search.ebscohost.com/login.aspx?direct=true&db=phl&AN=PHL2126216&site=ehost-live] '''Note:''' Some environmental ethicists assert that the evolutionary process serves as a normative foundation for environmental ethics, in other words, an organism's evolutionary history can/should be considered when making "ought" or "ought not" statements regarding these organisms. The main thesis of the above article is that synthetic biology, by separating an organism from its evolutionary history, is upsetting this normative foundation and that on these grounds, synthetic biology should be opposed. Although I haven't yet studied environmental ethics (first-year student here) and am not familiar with the argument for a normative value of evolutionary history, I'm initially skeptical of its relevance due to a few questions that it raises for me. For example, the assertion in the article is that this normative function tells us, at least in the case of synthetic biology, that we shouldn't "create" life due to the fact that we're separating the organism from its evolutionary history but even if the normative value of the evolutionary process can be well demonstrated, could this normative function ever tell us anything other than "don't play god"? If so, what other things can it tell us? If not, of what use is it to begin with?

'''Biology and Art'''- In what ways can synthetic biology be used to create art? What implications might our work have on the accessibility of "bioart"? How does this relate to the ethical questions that we've been considering? [http://en.wikipedia.org/wiki/BioArt]

David, Kamay, and Corinne: What unforeseeable dangers might there be in technology like Gibson Assembly, which allows the possibility of synthetically constructing any existing or new sequences of genes?

**This is a very rough summary of the things I have been thinking about in regards to the following topic. Feel free to add and edit where appropriate.**

Bioethics of Assembling Genomes(Combining the qualities of organisms and or creating new organisms)

The importance of being able to create and control life is paramount to synthetic biologists around the world. However, as be become more technologically advanced in our methods for doing this, it is of concern to our environment and scientific progress that we have an idea of where we are going and why.
A futuristic outlook in my mind permits the creation of organisms that will one day change the face of our planet perhaps for the better, and maybe even the faces of other planets in our solar system or others.
The ecosystems we engineer may improve the conditions of our planet to allow life to continue when it would otherwise fail.
This will of course run the risk of unintended consequences which lead to more harm that benefit. In addition, there will be costs to the natural ecosystems that have developed. Many organisms would be selected out of existance, but this is not new to our planet. Ninety nine percent of all organism that have ever inhabited the earth are now extinct.
We would also like to assume that our cultures will have evolved more mature systems of government that are less chaotic and more unified allowing us to make good decisions about these complicated issues.
We currently have no reason to believe we will come to a point where we will achieve such goals, but in examining the way we procede we should be able to caution ourselves to the foreseeable dangerous technologies we may allow into the hands of others.
On the bright side could engineer more nutritious foods that grow more easily to support our populations, engineer and release organisms that improve the health of our atmosphere and breathable air.. the details of what is possible are unlimited when you understand how complicated ecosystems are and what changes can make them thrive and/or fail.

David Carr

Alexander, Virginia: Is enough understood about synthetic biology to avoid unintended catastrophies?
Related article: '''Synthetics: the Ethics of Synthetic Biology''' [http://www.ethicsandtechnology.eu/images/uploads/Ethics_of_synthetic_biology.pdf]

Gibson Assembly

2012-07-12T16:44:54Z

Dcarr1:

Assembly Recipe and Methods

2ul NEB Gibson MM

_ul Vector (Always 20ng)

_ul Insert (Calculate insert amount below)

_ul dH2O

4ul Total Volume

Incubate at 50 degrees Celcius for approximately 1 hour.
Transform 1ul w/ 40ul Cells diluted to no more that 8 fold

Insert Size; Insert:Vector

25-300 bp; 5:1

300-1000 bp; 3:1

1000-3000 bp; 1:1

Insert Calculation

Insert (ng)=(ng of vector) (Insert bp/Vector bp)(1 or 3 or 5)

e.g. (20)(75/2900)(5)= 2.6 ng

Gibson Assembly

2012-07-12T16:44:00Z

Dcarr1:

Assembly Recipe and Methods

2ul NEB Gibson MM

_ul Vector (Always 20ng)

_ul Insert (Calculate insert amount below)

_ul dH2O

4ul Total Volume

Incubate at 50 degrees Celcius for approximately 1 hour.
Transform 1ul w/ 40ul Cells diluted to no more that 8 fold

Insert Size Insert:Vector

25-300 bp 5:1

300-1000 bp 3:1

1000-3000 bp 1:1

Insert Calculation

Insert (ng)=(ng of vector) (Insert bp/Vector bp)(1 or 3 or 5)

e.g. (20)(75/2900)(5)= 2.6 ng

Gibson Assembly

2012-07-12T16:43:03Z

Dcarr1:

Assembly Recipe and Methods

2ul NEB Gibson MM

_ul Vector (Always 20ng)

_ul Insert (Calculate insert amount below)

_ul dH2O

4ul Total Volume

Incubate at 50 degrees Celcius for approximately 1 hour.
Transform 1ul w/ 40ul Cells diluted to no more that 8 fold

Insert Size Insert:Vector

25-300 bp 5:1

300-1000 bp 3:1

1000-3000 bp 1:1

Insert Calculation

Insert (ng)=(ng of vector) (Insert bp/Vector bp)(1 or 3 or 5)

e.g. (20)(75/2900)(5)= 2.6 ng

Gibson Assembly

2012-07-12T16:42:46Z

Dcarr1:

Assembly Recipe and Methods

2ul NEB Gibson MM

_ul Vector (Always 20ng)

_ul Insert (Calculate insert amount below)

_ul dH2O

4ul Total Volume

Incubate at 50 degrees Celcius for approximately 1 hour.
Transform 1 ul w/ 40ul Cells diluted to no more that 8 fold

Insert Size Insert:Vector

25-300 bp 5:1

300-1000 bp 3:1

1000-3000 bp 1:1

Insert Calculation

Insert (ng)=(ng of vector) (Insert bp/Vector bp)(1 or 3 or 5)

e.g. (20)(75/2900)(5)= 2.6 ng

Gibson Assembly

2012-07-12T16:41:19Z

Dcarr1: Created page with 'Assembly Recipe and Methods 2ul NEB Gibson MM _ul Vector (Always 20ng) _ul Insert (Calculate insert amount below) _ul dH2O 4ul Total Volume Incubate at 50 degre…'

Assembly Recipe and Methods

2ul NEB Gibson MM
_ul Vector (Always 20ng)
_ul Insert (Calculate insert amount below)
_ul dH2O

4ul Total Volume

Incubate at 50 degrees Celcius for approximately 1 hour.
Transform 1 ul w/ 40ul Cells diluted to no more that 8 fold

Insert Size Insert:Vector
25-300 bp 5:1
300-1000 bp 3:1
1000-3000 bp 1:1

Insert Calculation

Insert (ng)=(ng of vector) (Insert bp/Vector bp)(1 or 3 or 5)
e.g. (20)(75/2900)(5)= 2.6 ng

MWSU protocols

2012-07-12T16:38:17Z

Dcarr1:

'''Purification of DNA'''

[[Isolation of Genomic DNA from Bacteria]]

'''PCR'''

[[Standard PCR]]

[[Resuspending Oligos]]

[[Davidson_Missouri_W/colony_PCR | Colony PCR]]

'''Recombinant DNA Production'''

[[Pouring an Agarose Gel]]

[[BioBrick Digestions for Fragment and Vector Preparation]]

[[Fragment Purification]]

[[Gibson Assembly]]

[[Direct Synthesis with Overlapping Oligos]]

[[Annealing Oligos for Cloning]]

[[Ethanol Precipitation of Vector DNA]]

[[Reducing Background from Double Digested Vector]]

'''Ligation and Transformation'''

[[BioBrick Ligations]]

[[Ligation and Transformation]]

[[Bacterial Media]]

'''Screening Clones'''

[[Diagnostic RP Digestion for Checking Insert Size]]

[[DNA Sequencing at Iowa State University]]

[[What to do with a new clone]]

'''Measuring Phenotypes'''

[[Measuring Fluorescence in Bacteria]]

Philosophy and Ethics of our Project

2012-07-05T18:00:35Z

Dcarr1:

This page is for the Philosophical and Ethical considerations surrounding our project to optimize a metabolic pathway in E. coli.

Eddie Miles- "Do we have the right to engineer living things specifically for our own benefit?"

David, Kamay, and Corinne: What unforeseeable dangers might there be in technology like Gibson Assembly, which allows the possibility of synthetically constructing any existing or new sequences of genes?

Philosophy and Ethics of our Project

2012-07-05T18:00:14Z

Dcarr1:

This page is for the Philosophical and Ethical considerations surrounding our project to optimize a metabolic pathway in E. coli.

Eddie Miles- "Do we have the right to engineer living things specifically for our own benefit?"

David, Kamay, and Corinne: What unforeseeable dangers might there be in the technology like Gibson Assembly, which allows the possibility of synthetically constructing any existing or new sequences of genes?

File:Gibson Control Oligos Final.docx

2012-06-11T17:36:59Z

Dcarr1: Oligo designs for Gibson Size Control Experiment

Oligo designs for Gibson Size Control Experiment

File:Gibson Assembly Size Control.pptx

2012-06-11T17:33:11Z

Dcarr1: uploaded a new version of "File:Gibson Assembly Size Control.pptx": Experiment proposal: At Missouri Western we have designed and order primers that will allow us to test Gibson Assembly in our own lab and to see if it will work for our purposes.

Experiment proposal:
At Missouri Western we have designed and order primers that will allow us to test Gibson Assembly in our own lab and to see if it will work for our purposes.
Using J119022 (a promoter in psb1a2) and J119044 (a terminator-Cdog-RFP construct in psb1a2 BR) we have designed 10 primers that will allow us to try and put J119022 in place of the terminator in J119044. This experiment includes 4 variations on the size of J119022 by using extra sequence in front of the promoter that goes into the vector.

File:Gibson Assembly Size Control.pptx

2012-06-11T17:30:37Z

Dcarr1: Experiment proposal: At Missouri Western we have designed and order primers that will allow us to test Gibson Assembly in our own lab and to see if it will work for our purposes. Using J119022 (a promoter in psb1a2) and J119044 (a terminator-Cdog-RFP cons

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-31T15:17:42Z

Dcarr1: /* Assembly */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC454214/] '''gene-specific promoter element is required for optimal expression of the histone H1 gene in S-phase.'''

*[http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.57.030502.090913] '''Multiple Sigma Factors'''

'''Promoters Section'''

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)'''

*http://partsregistry.org/PBAD_Promoter_Family

'''C-Dog Section'''

*

*

'''Degradation Tag Section'''

*

*

==Selection Modules==
'''Bad-ish genes/proteins'''
*[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
*[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
*[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
*[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
*[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
*[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
*[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
*[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
*[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
'''Good genes/proteins'''
*[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
*[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Background on CRISPR and steps in adaptation process''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
*[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]

{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']

*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
*[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
*[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T17:53:55Z