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  1. Frost LS, Ippen-Ihler K, and Skurray RA. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 1994 Jun;58(2):162-210. PubMed ID:7915817 | HubMed [Frost]
  2. Jaenecke S, de Lorenzo V, Timmis KN, and Díaz E. A stringently controlled expression system for analysing lateral gene transfer between bacteria. Mol Microbiol. 1996 Jul;21(2):293-300. PubMed ID:8858584 | HubMed [Jaenecke]
  3. Lawley TD, Klimke WA, Gubbins MJ, and Frost LS. F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett. 2003 Jul 15;224(1):1-15. PubMed ID:12855161 | HubMed [Lawley]
  4. Lessl M, Balzer D, Weyrauch K, and Lanka E. The mating pair formation system of plasmid RP4 defined by RSF1010 mobilization and donor-specific phage propagation. J Bacteriol. 1993 Oct;175(20):6415-25. PubMed ID:8407818 | HubMed [Lessl]
  5. Miller JF, Lanka E, and Malamy MH. F factor inhibition of conjugal transfer of broad-host-range plasmid RP4: requirement for the protein product of pif operon regulatory gene pifC. J Bacteriol. 1985 Sep;163(3):1067-73. PubMed ID:2993231 | HubMed [Miller]
  6. Martinez-Morales F, Borges AC, Martinez A, Shanmugam KT, and Ingram LO. Chromosomal integration of heterologous DNA in Escherichia coli with precise removal of markers and replicons used during construction. J Bacteriol. 1999 Nov;181(22):7143-8. PubMed ID:10559184 | HubMed [Martinez-Morales]
  7. Wilkins BM. Plasmid promiscuity: meeting the challenge of DNA immigration control. Environ Microbiol. 2002 Sep;4(9):495-500. PubMed ID:12220405 | HubMed [Wilkins]
  8. Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, and Settleman J. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell. 2010 Apr 2;141(1):69-80. DOI:10.1016/j.cell.2010.02.027 | PubMed ID:20371346 | HubMed [Paper39]
  9. Walsh CT and Fischbach MA. Natural products version 2.0: connecting genes to molecules. J Am Chem Soc. 2010 Mar 3;132(8):2469-93. DOI:10.1021/ja909118a | PubMed ID:20121095 | HubMed [Paper38]
  10. Dawlaty J, Zhang X, Fischbach MA, and Clardy J. Dapdiamides, tripeptide antibiotics formed by unconventional amide ligases. J Nat Prod. 2010 Mar 26;73(3):441-6. DOI:10.1021/np900685z | PubMed ID:20041689 | HubMed [Paper37]
  11. Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, and Nusbaum C. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009 Sep 17;461(7262):393-8. DOI:10.1038/nature08358 | PubMed ID:19741609 | HubMed [Paper36]
  12. Fischbach MA and Walsh CT. Antibiotics for emerging pathogens. Science. 2009 Aug 28;325(5944):1089-93. DOI:10.1126/science.1176667 | PubMed ID:19713519 | HubMed [Paper35]
  13. Fischbach MA. Antibiotics from microbes: converging to kill. Curr Opin Microbiol. 2009 Oct;12(5):520-7. DOI:10.1016/j.mib.2009.07.002 | PubMed ID:19695947 | HubMed [Paper34]
  14. Walsh CT and Fischbach MA. New ways to squash superbugs. Sci Am. 2009 Jul;301(1):44-51. PubMed ID:19555023 | HubMed [Paper33]
  15. Clardy J, Fischbach MA, and Currie CR. The natural history of antibiotics. Curr Biol. 2009 Jun 9;19(11):R437-41. DOI:10.1016/j.cub.2009.04.001 | PubMed ID:19515346 | HubMed [Paper32]
  16. Wieland Brown LC, Acker MG, Clardy J, Walsh CT, and Fischbach MA. Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2549-53. DOI:10.1073/pnas.0900008106 | PubMed ID:19196969 | HubMed [Paper31]
  17. Walsh CT and Fischbach MA. Repurposing libraries of eukaryotic protein kinase inhibitors for antibiotic discovery. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1689-90. DOI:10.1073/pnas.0813405106 | PubMed ID:19193851 | HubMed [Paper30]
  18. López D, Fischbach MA, Chu F, Losick R, and Kolter R. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):280-5. DOI:10.1073/pnas.0810940106 | PubMed ID:19114652 | HubMed [Paper29]
  19. Sattely ES, Fischbach MA, and Walsh CT. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep. 2008 Aug;25(4):757-93. DOI:10.1039/b801747f | PubMed ID:18663394 | HubMed [Paper28]
  20. Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C, Clarke K, Cronin A, Davis P, Goodhead I, Holroyd N, Jagels K, Lord A, Moule S, Mungall K, Norbertczak H, Quail MA, Rabbinowitsch E, Walker D, White B, Whitehead S, Small PL, Brosch R, Ramakrishnan L, Fischbach MA, Parkhill J, and Cole ST. Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res. 2008 May;18(5):729-41. DOI:10.1101/gr.075069.107 | PubMed ID:18403782 | HubMed [Paper27]
  21. Fischbach MA, Walsh CT, and Clardy J. The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4601-8. DOI:10.1073/pnas.0709132105 | PubMed ID:18216259 | HubMed [Paper26]
  22. Walsh CT and Fischbach MA. Inhibitors of sterol biosynthesis as Staphylococcus aureus antibiotics. Angew Chem Int Ed Engl. 2008;47(31):5700-2. DOI:10.1002/anie.200801801 | PubMed ID:18576462 | HubMed [Paper25]
  23. Nolan EM, Fischbach MA, Koglin A, and Walsh CT. Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate. J Am Chem Soc. 2007 Nov 21;129(46):14336-47. DOI:10.1021/ja074650f | PubMed ID:17973380 | HubMed [Paper24]
  24. Fischbach MA, Lai JR, Roche ED, Walsh CT, and Liu DR. Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11951-6. DOI:10.1073/pnas.0705348104 | PubMed ID:17620609 | HubMed [Paper23]
  25. Fischbach MA and Clardy J. One pathway, many products. Nat Chem Biol. 2007 Jul;3(7):353-5. DOI:10.1038/nchembio0707-353 | PubMed ID:17576415 | HubMed [Paper22]
  26. Butcher RA, Schroeder FC, Fischbach MA, Straight PD, Kolter R, Walsh CT, and Clardy J. The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1506-9. DOI:10.1073/pnas.0610503104 | PubMed ID:17234808 | HubMed [Paper21]
  27. Straight PD, Fischbach MA, Walsh CT, Rudner DZ, and Kolter R. A singular enzymatic megacomplex from Bacillus subtilis. Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):305-10. DOI:10.1073/pnas.0609073103 | PubMed ID:17190806 | HubMed [Paper20]
  28. Clardy J, Fischbach MA, and Walsh CT. New antibiotics from bacterial natural products. Nat Biotechnol. 2006 Dec;24(12):1541-50. DOI:10.1038/nbt1266 | PubMed ID:17160060 | HubMed [Paper19]
  29. Fischbach MA, Lin H, Zhou L, Yu Y, Abergel RJ, Liu DR, Raymond KN, Wanner BL, Strong RK, Walsh CT, Aderem A, and Smith KD. The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16502-7. DOI:10.1073/pnas.0604636103 | PubMed ID:17060628 | HubMed [Paper18]
  30. Fischbach MA and Walsh CT. Biochemistry. Directing biosynthesis. Science. 2006 Oct 27;314(5799):603-5. DOI:10.1126/science.1132692 | PubMed ID:17068249 | HubMed [Paper17]
  31. Lai JR, Fischbach MA, Liu DR, and Walsh CT. Localized protein interaction surfaces on the EntB carrier protein revealed by combinatorial mutagenesis and selection. J Am Chem Soc. 2006 Aug 30;128(34):11002-3. DOI:10.1021/ja063238h | PubMed ID:16925399 | HubMed [Paper16]
  32. Larsen NA, Lin H, Wei R, Fischbach MA, and Walsh CT. Structural characterization of enterobactin hydrolase IroE. Biochemistry. 2006 Aug 29;45(34):10184-90. DOI:10.1021/bi060950i | PubMed ID:16922493 | HubMed [Paper15]
  33. Jin M, Fischbach MA, and Clardy J. A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid. J Am Chem Soc. 2006 Aug 23;128(33):10660-1. DOI:10.1021/ja063194c | PubMed ID:16910643 | HubMed [Paper14]
  34. Fischbach MA and Walsh CT. Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem Rev. 2006 Aug;106(8):3468-96. DOI:10.1021/cr0503097 | PubMed ID:16895337 | HubMed [Paper13]
  35. Lin H, Fischbach MA, Gatto GJ Jr, Liu DR, and Walsh CT. Bromoenterobactins as potent inhibitors of a pathogen-associated, siderophore-modifying C-glycosyltransferase. J Am Chem Soc. 2006 Jul 26;128(29):9324-5. DOI:10.1021/ja063236x | PubMed ID:16848455 | HubMed [Paper12]
  36. Sharma SV, Fischbach MA, Haber DA, and Settleman J. "Oncogenic shock": explaining oncogene addiction through differential signal attenuation. Clin Cancer Res. 2006 Jul 15;12(14 Pt 2):4392s-4395s. DOI:10.1158/1078-0432.CCR-06-0096 | PubMed ID:16857816 | HubMed [Paper11]
  37. Lai JR, Fischbach MA, Liu DR, and Walsh CT. A protein interaction surface in nonribosomal peptide synthesis mapped by combinatorial mutagenesis and selection. Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5314-9. DOI:10.1073/pnas.0601038103 | PubMed ID:16567620 | HubMed [Paper10]
  38. Fischbach MA, Lin H, Liu DR, and Walsh CT. How pathogenic bacteria evade mammalian sabotage in the battle for iron. Nat Chem Biol. 2006 Mar;2(3):132-8. DOI:10.1038/nchembio771 | PubMed ID:16485005 | HubMed [Paper9]
  39. Luo M, Lin H, Fischbach MA, Liu DR, Walsh CT, and Groves JT. Enzymatic tailoring of enterobactin alters membrane partitioning and iron acquisition. ACS Chem Biol. 2006 Feb 17;1(1):29-32. DOI:10.1021/cb0500034 | PubMed ID:17163637 | HubMed [Paper8]
  40. Dorrestein PC, Blackhall J, Straight PD, Fischbach MA, Garneau-Tsodikova S, Edwards DJ, McLaughlin S, Lin M, Gerwick WH, Kolter R, Walsh CT, and Kelleher NL. Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry. Biochemistry. 2006 Feb 14;45(6):1537-46. DOI:10.1021/bi052333k | PubMed ID:16460000 | HubMed [Paper7]
  41. Garstecki P, J Fuerstman M, Fischbach MA, Sia SK, and Whitesides GM. Mixing with bubbles: a practical technology for use with portable microfluidic devices. Lab Chip. 2006 Feb;6(2):207-12. DOI:10.1039/b510843h | PubMed ID:16450029 | HubMed [Paper6]
  42. Fischbach MA and Settleman J. Regulation of the nucleotide state of oncogenic ras proteins by nucleoside diphosphate kinase. Methods Enzymol. 2006;407:33-45. DOI:10.1016/S0076-6879(05)07004-7 | PubMed ID:16757312 | HubMed [Paper5]
  43. Lin H, Fischbach MA, Liu DR, and Walsh CT. In vitro characterization of salmochelin and enterobactin trilactone hydrolases IroD, IroE, and Fes. J Am Chem Soc. 2005 Aug 10;127(31):11075-84. DOI:10.1021/ja0522027 | PubMed ID:16076215 | HubMed [Paper4]
  44. Fischbach MA, Lin H, Liu DR, and Walsh CT. In vitro characterization of IroB, a pathogen-associated C-glycosyltransferase. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):571-6. DOI:10.1073/pnas.0408463102 | PubMed ID:15598734 | HubMed [Paper3]
  45. Wolfe DB, Conroy RS, Garstecki P, Mayers BT, Fischbach MA, Paul KE, Prentiss M, and Whitesides GM. Dynamic control of liquid-core/liquid-cladding optical waveguides. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12434-8. DOI:10.1073/pnas.0404423101 | PubMed ID:15314232 | HubMed [Paper2]
  46. Fischbach MA and Settleman J. Specific biochemical inactivation of oncogenic Ras proteins by nucleoside diphosphate kinase. Cancer Res. 2003 Jul 15;63(14):4089-94. PubMed ID:12874011 | HubMed [Paper1]
All Medline abstracts: PubMed | HubMed

<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext">08/20/2009,01/29/2010,10/25/2010</div><div style="display:none;" id="page">Sandbox</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

EXPANDING A TEMPLATE

BASED ON TEMPLATE:FILEDESCRIPTION: {{FILEDESCRIPTION | NAME=NAME | DATE=20081012 | DESCRIPTION=HELLO I'M A DESCRIPTION | COMMENT=HELLO I'M A COMMENT }}

RESULT

Template:FILEDESCRIPTION

THIS 17 3.44
IS 29 2.33
A 39 5.31
TEST 44 45.3

--LINDENB 10:01, 8 DECEMBER 2008 (EST)

VOLUNTEER: JULIE NORVILLE DATE: (SIGNED UP) JANUARY 26, 2009-(EXPECTS TO BE ACTIVE TILL) 2010 BIO: A GRADUATE STUDENT AT MIT CONTACT: DIYOUTREACH AT GMAIL DOT COM (IF YOU DO NOT WANT THIS LISTED, YOU MAY PUT CONFIDENTIAL-CONTACT DIYOUTREACH AND SEND YOUR CONTACT INFO TO DIYOUTREACH AT GMAIL DOT COM) INTERESTS: DEVELOPING CHEAP BIOLOGICAL TOOLS AND TEACHING MATERIALS UNIVERSITY AFFILIATIONS: MIT (CURRENT), CALTECH (ALUMNA) GEOGRAPHICAL LOCATION: BOSTON AREA

BELOW IS ONE IMAGE.

LINK TO BIOTEST

File:WELLESLEY-QUAD.JPEG

File:ABSTRACT.PDF


TESTING WIKED

X2

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