Team:Washington/Bibliography

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=Works Cited=
=Works Cited=
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'''Include references'''
 
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Play [http://files.agame.com/mirror/flash/p/puzzle_bobble.swf Puzzle Bobble]!
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Angelo Scorpio, Donald J. Chabot, William A. Day, David K. O'Brien, Nicholas J. Vietri, Yoshifumi Itoh, Mansour Mohamadzadeh, and Arthur M. Friedlander.  Poly-gamma-Glutamate Capsule-Degrading Enzyme Treatment Enhances Phagocytosis and Killing of Encapsulated Bacillus anthracis Antimicrobial Agents and Chemotherapy, January 2007, p. 215-222,Vol. 51, No. 1.  PMCID: PMC1797643
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Play [http://www.thepcmanwebsite.com/media/pacman_flash/pacman-flash.swf Pac Man]!
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Angelo Scorpio, Donald J Chabot, William A Day, Timothy A Hoover, and Arthur M Friedlander
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Capsule depolymerase overexpression reduces Bacillus anthracis virulence
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Microbiology 2010 : mic.0.035857-0v1-mic.0.035857-0.
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Candela T, Fouet A.  Bacillus anthracis CapD, belonging to the gamma-glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan.
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Mol Microbiol. 2005 Aug;57(3):717-26.  PMID: 16045616
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'''will include intro image, idea is currently being fleshed out from sketch into image'''
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Chandran D. [http://www.jbioleng.org/content/3/1/19 TinkerCell: modular CAD tool for synthetic biology].
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Journal of Biological Engineering 2009, 3:19.
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=21st century antibiotics GENERAL STORYLINE FLOW=
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Filloux, Alain, Hachani, Abderrahman, Bleves, Sophie
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'''The bullet points are the key images that need to be generated. They should be very general and easy to understand!  The text will basically be explaning the pictures and telling the story.... think of this as a comic book!
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[http://mic.sgmjournals.org/cgi/content/full/154/6/1570#SEC7 The bacterial type VI secretion machine: yet another player for protein transport across membranes]
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'''
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Microbiology 2008 154: 1570-1583
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==gram(+)==
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Hood RD, Singh P, Hsu F, Güvener T, Carl MA, Trinidad RR, Silverman JM, Ohlson BB, Hicks KG, Plemel RL, Li M, Schwarz S, Wang WY, Merz AJ, Goodlett DR, Mougous JD. [http://www.cell.com/cell-host-microbe/abstract/S1931-3128%2809%2900417-X#Summary A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria].
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===summary===
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Cell Host Microbe. 2010 Jan 21;7(1):25-37. PMID: 20114026
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*why anthrax is bad
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*proteins fighting anthrax
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===design===
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*circular permutation
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*computational design
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===build===
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*How we made mutants
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*How we made protiein
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===Test===
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*gel/mass spec cp vs D
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*activity cp vs D
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*catalytic KO of CP vs CP
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*CP mutations
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*Specificity switch
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===Future Directions===
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*Just some bullet points, no figures needed
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==gram(-)==
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T.A. KUNKEL, P NATL ACAD SCI USA 82, 488 (JANUARY 1985, 1985)
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puzzle bobble with evil bacteria as bubbles?
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===summary (bugs vs bugs)===
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*type 6 secretion (spear) done-Matthew Harger
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*Toxin/Antitoxin produced in prescence of XXX (poison) done
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===design===
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Lucey DR, Anthrax. In: Goldman L, Ausiello D, eds. Cecil Medicine. 23rd ed. Philadelphia, Pa: Saunders Elsevier; 2007:chap 317.
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*operon in Pseudomonas —> operon in e coli ( fosmid image)
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**what parts of this operon are needed? justin has this
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*sensor —produces—> toxin/antitoxin (classic tinkercell picture) done
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===build===
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Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID: 19535342
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*exporter —> recombineering to promoter  image already made
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*sensor/toxin: —> PCR —> HSL biobrick vector made by Matthew Harger
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===Test===
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[[Image: Washington Get away.jpg]]
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*Exporter:  Still under construction
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*Sensor/Toxin
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**Toxin is toxic in ecoli: (Rachael hood,2010) paper;  Sensor works and produces tse2 as expected ( include image of western blot with annotations)
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Antidote still works in e.coli indirect evidence, state lack of mutations, may not need image.;
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===Future Directions===
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*Just some quick Bullet Points
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[[Image:Washington_T6SS_diagram.png]]
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[[Image:Washington T7-PCR.jpg|200px|thumb|right|T7 recombinant cassette insertion]]
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=PCR testing for insertion=
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We want to test for gene insertions and recombinations at several steps of our project.  PCR is the easiest and fastest way to determine the success of Recombineering.
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Using a set of primers flanking the intragenic promoter region, we tested the insertion on our recombinants.  ''galK'' is around 1200 base pairs in size. The T7 double promoter cassette not only deletes ''galK'' but around a hundred base pairs of the original sequence.  Therefore, we would expect the ''galK'' recombinant PCR to be about 1200 bp larger than the non-recombinant, and the T7 recombinant to be about 100 bp smaller than the non-recombinant. Indeed, this is exactly what we saw.
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[[Image:Washington_2010_vector9.jpg|400px|]]
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=='''Analyzing CapD_CP'''==
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[[Image:Washington_CapD_CP_Trans_Hydro_Kinectic_Table_full.jpg|thumb|400px|right|Figure 4 shows the kinetic constants of CapD_CP's transpeptidation and hydrolysis capability]]
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[[Image:Washington_CapD_CP_Michaelis_Curve.jpg|thumb|300px|right|]]
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<br style="clear: both" />
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The two abilities of CapD_CP are transpeptidation and hydrolysis. Based on the Kcat and Km (see figure 4)
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values of the two, we conclude that CapD_CP is a weak binder and efficient catalyst for the transpeptidation reaction. In terms of  hydrolysis, it shows strong binding but slow catalysis, thus our mutant designs focus on increasing the catalytic efficiency.
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=='''Test: Enzyme Assay'''==
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[[Image:Washington_Assay_Scheme_revised2.jpg|thumb|400px|left|The general scheme of our fluorescence-based [https://2010.igem.org/Team:Washington/Protocols/EnzymeAssayCapD enzyme assay]]]
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After we have the CapD_CP mutants, we tested our mutants for their catalytic activity using our fluorescence-based enzyme assay scheme. Fluorescence-based enzyme assay measures the rate at which fluorescence in the testing media is released and the amount fluorescence depends on the rate at which fluorophore-quencher linkage is disrupted. Our substrate PDGA contains a linked fluorophore-quencher component. The faster fluorophore-quencher component is cleaved, the higher the amount of fluorescence is released and thus the greater the enzymatic activity observed.
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[[Image:CapDCP_MassSpecNoMethionine.png|thumb|780px|right| Expected weight of CapD_CP without Methionine=55285Da, with Methionine=55417Da. Our mass spec detected a peak at 55274.8Da (no Methionine) well within the 0.02% error limit for our mass spec]]
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[[Image:WashingtonCapDToCapDCP.png|thumb|950px|left|]]
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=Using Recombineering to create a constitutive T6SS=
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[[Image:Washington Recombineering.jpg|400px|thumb|right|Insertion of T7 promoters]]
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The process for using homologous recombination to replace the T6SS native promoters is simple.  We begin with a previously characterised fosmid (a large, single-copy plasmid based on the F' plasmid) which contains all the genes in our T6SS.  Of particular interest is the ''fha1-tssA1'' intergenic region containing the promoters.  We transform this fosmid into recombineering strain ''E. coli'' SW102, which contains heat-inducible lambda phage recombinases and lacks the galactose metabolism gene ''galK''.
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Using PCR, we create a cassette containing the ''galK'' gene flanked by 50 bp of homology to the intergenic region.  The lambda recombinases integrate the cassette into the fosmid.  The transformants are plated on minimal galactose media to select for the recombinants.
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A second cassette is created via PCR, this time containing our new promoters.  In this case, we chose to use T7 phage promoters due to their constitutive expression and small size, making them easier to synthesize.  The promoters are again flanked with homologous regions, and integrated into the fosmid.  This cassette displaces the ''galK'' cassette.  The transformants are this time plated on 2-deoxy-galactose (DOG), which is a toxic homolog to galactose.  Cells which can metabolize galactose (that is, those with a functioning ''galK'' gene) are killed, while those without the gene are unharmed.
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The final step is to transform the recombinant plasmid into a T7 polymerase expression strain, to allow T6SS constitutive expression.
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=Overall Objective:Using Type VI Secretion as an Antibacterial Agent=
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Our overall goal is to clone the Type 6 secretion system and the Tse2/Tsi2 toxin/antitoxin system from ''Pseudomonas aeruginosa'' into ''E. coli'' to make a strain of ''E. coli'' that could be used to kill off gram negative pathogens present in the human gut. Ideally, this system would be regulated in such a way that the strain of ''E. coli'' would only be able to kill gram negative bacteria when a gram negative pathogen is present. This strain could (ideally) be introduced into the gut either as a preventive measure or as a treatment after a known infection. Ideally, the probiotic would only kill of gram negative bacteria in the area of infection.
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==Cool Picture goes here==
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==Designing the T6SS for a ''E. coli'' probiotic==
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'''Justin and or Laura, please write this section'''
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short intro, basic plan:
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-molecular schematic of T6SS (Jesa send to Matthew)
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-include map of, describe T6SS  putative operon ( there is a map color coded to diagram
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<br>
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-mention that it is in pao1 and state objective overall:  transfer into ecoli so that it functions constitutively ,  what genes
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===Objectives:
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====1. figure out which genes are necessary====
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Mention not all genes in operon neccessarily needed for T6SS, preferable to be smaller
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====2. physically transfer genes into ''E. coli'' ====
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mention large size makes it difficult, mention/explain fosmid, include fosmid map ( Laura should have This)
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====3. optimize regulation====
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mention that fosmid contains natural promoter, may not be trascribed from at all, or at right amount for a plasmid ( more than 1 copy of plasmid)
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<br>
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<br>
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<br>
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In order to create a probiotic application for this system, we first attempt to express it heterologously in non-pathogenic ''E. Coli''.  Starting from a Fosmid containing our T6SS, we are using [http://web.ncifcrf.gov/research/brb/recombineeringInformation.aspx Recombineering] to replace the strict native regulation with robust T7 promoters to create strong expression of the T6SS. 
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All the essential genes for our T6SS are contained within two putative operons, encoded in opposite directions.  The native promoters for both operons are found in the same intergenic region, between ''fha1'' and ''tssA1''.  Therefore, we can easily replace the promoter regions for both operons in one step.
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'''&larr; [[Team:Washington/Accomplishments|Accomplishments and Submitted Parts]] &rarr;'''
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'''&larr; [[Team:Washington/Notebook|Lab Notebook]]'''
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Latest revision as of 20:21, 27 October 2010

Works Cited

Angelo Scorpio, Donald J. Chabot, William A. Day, David K. O'Brien, Nicholas J. Vietri, Yoshifumi Itoh, Mansour Mohamadzadeh, and Arthur M. Friedlander. Poly-gamma-Glutamate Capsule-Degrading Enzyme Treatment Enhances Phagocytosis and Killing of Encapsulated Bacillus anthracis Antimicrobial Agents and Chemotherapy, January 2007, p. 215-222,Vol. 51, No. 1. PMCID: PMC1797643

Angelo Scorpio, Donald J Chabot, William A Day, Timothy A Hoover, and Arthur M Friedlander Capsule depolymerase overexpression reduces Bacillus anthracis virulence Microbiology 2010 : mic.0.035857-0v1-mic.0.035857-0.

Candela T, Fouet A. Bacillus anthracis CapD, belonging to the gamma-glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan. Mol Microbiol. 2005 Aug;57(3):717-26. PMID: 16045616

Chandran D. [http://www.jbioleng.org/content/3/1/19 TinkerCell: modular CAD tool for synthetic biology]. Journal of Biological Engineering 2009, 3:19.

Filloux, Alain, Hachani, Abderrahman, Bleves, Sophie [http://mic.sgmjournals.org/cgi/content/full/154/6/1570#SEC7 The bacterial type VI secretion machine: yet another player for protein transport across membranes] Microbiology 2008 154: 1570-1583

Hood RD, Singh P, Hsu F, Güvener T, Carl MA, Trinidad RR, Silverman JM, Ohlson BB, Hicks KG, Plemel RL, Li M, Schwarz S, Wang WY, Merz AJ, Goodlett DR, Mougous JD. [http://www.cell.com/cell-host-microbe/abstract/S1931-3128%2809%2900417-X#Summary A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria]. Cell Host Microbe. 2010 Jan 21;7(1):25-37. PMID: 20114026

T.A. KUNKEL, P NATL ACAD SCI USA 82, 488 (JANUARY 1985, 1985)

Lucey DR, Anthrax. In: Goldman L, Ausiello D, eds. Cecil Medicine. 23rd ed. Philadelphia, Pa: Saunders Elsevier; 2007:chap 317.

Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID: 19535342

Washington Get away.jpg

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