Team:Washington/Bibliography

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=Works Cited=
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'''Include references'''
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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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[[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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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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[[Image:WashingtonCapDToCapDCP.png|thumb|950px|left|]]
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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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=Using Recombineering to create a constitutive T6SS=
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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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[[Image:Washington Recombineering.jpg|400px|thumb|right|Insertion of T7 promoters]]
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Journal of Biological Engineering 2009, 3:19.
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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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Filloux, Alain, Hachani, Abderrahman, Bleves, Sophie
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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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Microbiology 2008 154: 1570-1583
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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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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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Cell Host Microbe. 2010 Jan 21;7(1):25-37. PMID: 20114026
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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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T.A. KUNKEL, P NATL ACAD SCI USA 82, 488 (JANUARY 1985, 1985)
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=Overall Objective:Using Type VI Secretion as an Antibacterial Agent=
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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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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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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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====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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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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[[Image: Washington Get away.jpg]]
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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

← Lab Notebook

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