IGEM:MIT/2007/Links for Bioremediation Project

From OpenWetWare

< IGEM:MIT | 2007(Difference between revisions)
Jump to: navigation, search
(New page: ==Protein Surface Display== <biblio> #Wernerus04 pmid=15035661 </biblio> ===OmpX=== <biblio> #Mecsas95 pmid=7836315 #OmpX http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=5596...)
Current revision (17:24, 31 July 2007) (view source)
(Polysterene)
 
(13 intermediate revisions not shown.)
Line 2: Line 2:
<biblio>
<biblio>
#Wernerus04 pmid=15035661
#Wernerus04 pmid=15035661
 +
</biblio>
 +
*OmpA, OmpB, OmpC Surface proteins
 +
<biblio>
 +
#koebnik00 pmid=10931321
</biblio>
</biblio>
Line 28: Line 32:
==Sticky Peptides==
==Sticky Peptides==
-
===Polysterene===
+
===Polystyrene===
====Kenan====
====Kenan====
Line 112: Line 116:
</biblio>
</biblio>
-
==Bioremediation Papers==
+
==pBAD Promoter Info==
-
 
+
*Arabinose PBAD Promoter<cite>pBAD33</cite>
-
===Toxicity of Heavy Metals===
+
<biblio>
<biblio>
-
#Silver05 pmid=16133099
+
#pBAD33 pmid=7608087
</biblio>
</biblio>
-
====Cadmium====
+
==Bioremediation Papers==
-
*Summary: Cd causes damage to cells primarily by the generation of reactive oxygen species (ROS), which causes single-strand DNA damage and disrupts the synthesis of nucleic acids and proteins. Cd is also an inhibitor of the DNA mismatch repair system…Results of this study confirmed that Cd toxicity caused profound changes in gene expression in which several stress response systems were induced simultaneously.
+
-
 
+
-
<biblio>
+
-
#Wang95 pmid=3104315
+
-
</biblio>
+
-
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=986930&dopt=GenBank&WebEnv=00h1mfSbNcrWnt_GeEAeAclSzZ4C1a1RZb7zt6pF-ZLWCiSSMjA-Di7PFSlt0aBL40bjiOJR7ssMw%40264002C567DCA7D0_0078SID&WebEnvRq=1]
+
-
 
+
-
===Heavy Metal Resistance Techniques===
+
-
<biblio>
+
-
#Bruins00 pmid=10702338
+
-
#Hou88 pmid=3056525
+
-
</biblio>
+
-
 
+
-
===Heavy Metal Binding Proteins/Peptides===
+
-
<biblio>
+
-
#Samuelson00 pmid=10698802
+
-
#Biosorbants pmid=9758845
+
-
#Kotrba99 pmid=10049868
+
-
#Mejare01 pmid=11164556
+
-
#Lu01 pmid=11710062
+
-
#Bae00 pmid=11042548
+
-
</biblio>
+
===Pumps===
===Pumps===
Line 153: Line 134:
</biblio>
</biblio>
-
===Promoters===
+
==Heavy Metals (non e.coli systems)==
-
*Cadmium(pCN39, a derivative of pCN37 with a temperature-sensitive replicon)
+
-
<cite> Yao06 </cite>
+
-
*Mercury (Pmer)
+
-
<biblio>
+
-
#Condee92 pmid=1334070
+
-
#Gambill85 pmid=4092936
+
-
#Yao06 pmid=16741231
+
-
#Hansen00 pmid=11094290
+
-
</biblio>
+
-
 
+
-
===Sponges===
+
-
*Mercury [http://www.jstage.jst.go.jp/article/bbb/71/6/1494/_pdf]
+
-
 
+
-
==Miscellaneous==
+
-
*Arabinose PBAD Promoter<cite>pBAD33</cite>
+
-
<biblio>
+
-
#pBAD33 pmid=7608087
+
-
</biblio>
+
-
 
+
-
==Outer Membrane Proteins==
+
-
*OmpA, OmpB, OmpC Surface proteins<cite>koebnik00</cite>
+
-
<biblio>
+
-
#koebnik00 pmid=10931321
+
-
</biblio>
+
-
 
+
-
==Heavy Metals==
+
-
 
+
-
====Review articles====
+
-
<biblio>
+
-
#Paul05 pmid=15734556
+
-
#Valls02 pmid=12413663
+
-
</biblio>
+
-
 
+
====Other Bacteria====
====Other Bacteria====
Line 211: Line 159:
#Clemes02 pmid=12119168
#Clemes02 pmid=12119168
#Tripathi07 pmid=17306392
#Tripathi07 pmid=17306392
-
</biblio>
+
#Tripathi07 pmid=17306392
-
 
+
#ick00 pmid=11092618
-
===Heavy Metals and E. coli===
+
#Weinberg89 pmid=2530602
-
 
+
-
====Heavy Metal Resistance====
+
-
<biblio>
+
-
#Nakajima95 pmid=7793951
+
</biblio>
</biblio>
Line 225: Line 169:
<biblio>
<biblio>
#Bontidean98 http://pubs.acs.org/cgi-bin/article.cgi/ancham/1998/70/i19/html/ac9803636.html
#Bontidean98 http://pubs.acs.org/cgi-bin/article.cgi/ancham/1998/70/i19/html/ac9803636.html
-
</biblio>
 
-
 
-
====Absorption of Heavy Metals====
 
-
<biblio>
 
-
#Gutn
 
-
#Tripathi07 pmid=17306392ick00 pmid=11092618
 
-
#Weinberg89 pmid=2530602
 
</biblio>
</biblio>

Current revision

Contents

Protein Surface Display

  1. Wernérus H and Ståhl S. . pmid:15035661. PubMed HubMed [Wernerus04]
  • OmpA, OmpB, OmpC Surface proteins
  1. Koebnik R, Locher KP, and Van Gelder P. . pmid:10931321. PubMed HubMed [koebnik00]

OmpX

  1. Mecsas J, Welch R, Erickson JW, and Gross CA. . pmid:7836315. PubMed HubMed [Mecsas95]
  2. http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=559693 [OmpX]

CPX

  • Total length is 558 bp + length of passenger peptide
  1. Native SS - 69 bp
     MKKIACLSALAAVLAFTAGTSVA 
  2. Embedded SfiI restriction site - 15 bp
     GQSGQ 
  3. Passenger Peptide
     XXXXXXXXXXXXXX 
  4. Sequence - 18 bp
     GGQSGQ  
  5. S54-F148 - 285 bp
     SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 
  6. Join native C and N - 12 bp
     GGSG 
  7. A1-S53 - 159 bp
     ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS 

OmpC

  1. Xu Z and Lee SY. . pmid:10543834. PubMed HubMed [Xu99]
  2. http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=15832358 OmpC Sequence [OmpC]

Sticky Peptides

Polystyrene

Kenan

  • Strong Binders >150
    • 17 FFPSSWYSHLGVL
    • 18 FFSFFFPASAWGS

Menendez

  • YTGWETWYSFDPFTHYGGPGSRFDFVHDKSEDPIDRSY [7]
  • QDLDHWSYWSMYSTYPTSPGLVPYSWGYGSPNSHTDKL
  • PWWWVSWVDAGGGSLALPTQPSD
  • WGWPTWWGWTGGDARHPSAPEAH
  • WWDPDIWFGWGGAHPPNLIQPIS
  • GWQSGWEWWIGGGNWTSNTTH
  • IYYPFFVWGNYANGGLLSPGHVYSSNFIPLYMQREVSP
  • SSRLAYDHYFPSWRSYIFPGSNSSYYNNSWPTITMETN
  • RPYLYDPNEWHRYYSYLLPGHSYNVQSWPDGLGKSASR
  • LGFSGWYWQGLYGLGSHDPGFIHEQSPAEVAMEDTEQS
  • QTLIDFHDLHYWGAYYGWPGIYDAESGSQAVRHNMTHT
  • DSWPLRIYSGLSNYYHYFPGSLVYNMMYPSLSRLPKGD
  • HHGAMNRYYTWLWDNSRFPGRSYLLSAPATQPEASISQ
  • TYDYTYDWSGLFWSPFTHPGAHMTTHSPWAGHKPHAET
  • EIHGNLYNWSPLLGYSYFPGISPKHISGEVPPRPSTKV
  • PYWMFYGFDWRGGFPPSHQIMDQ
  • WMQSWYYHWGGGETFPIRRDSGG

  • SRTWVLWIRY [8]
  • LSAWARWGSS
  • SRGFWLVWEQ
  • TWTLWFASMS
  • VDWVGWGASW
  • WVEWRRGWLS
  • PWNAWGRTWV
  • GGWAMWGRVW
  • WMRWGRSWGR
  • GSWKEWGGAW
  • SAWVRWGRVW
  • WSAWVGDWAL
  • GVIHWRAWGGDW
  • LNWRGGWNWF
  • WRLGFARWIG
  • WGYVFHGWNL
  • CCWGYGGSLV
  • VYRVIWFVGR
  • FHAFHAWSAA
  • GSVWWQAHVDR
  • LWGGLYGIWM
  • MWGMHWAEGW
  • FLPYARWFSR
  • VIYYFLVMFM
  • VCFVMFSMCR
  • RPVAGDHPGS

  • FHENWPS

  • FHWTWYW

  • WHRWPWLVSG
  • WHWWYWALDR

  • APFYYSWFPSYMAEGLPSPSPLDPVQDNLY
  • Notes:
    • Fixed residues at the N and C terminus of the peptides are not shown, fixed amino acids within the sequences are double-underlined.
    • Unpublished results, plate binding confirmed by ELISA.

Bibliography

  1. Adey NB, Mataragnon AH, Rider JE, Carter JM, and Kay BK. . pmid:7737512. PubMed HubMed [Adey95]
  2. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. . pmid:9048419. PubMed HubMed [Gebhart96]
  3. Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. . pmid:16873017. PubMed HubMed [Kenan06]
  4. Menendez A and Scott JK. . pmid:15620878. PubMed HubMed [Menendez05]
All Medline abstracts: PubMed HubMed

Polypyrrole

T59: THRTSTLDYFVI
[11]
  1. Sanghvi AB, Miller KP, Belcher AM, and Schmidt CE. . pmid:15895095. PubMed HubMed [Sanhvi05]

pBAD Promoter Info

  • Arabinose PBAD Promoter[12]
  1. Guzman LM, Belin D, Carson MJ, and Beckwith J. . pmid:7608087. PubMed HubMed [pBAD33]

Bioremediation Papers

Pumps

  • Cadmium(Plasmid pI258 (from S.aureus) cadmium resistance (cadA) gene, complete cds) [13]
  • ZntA(Divalent Metal Transporter)
  1. Dutta SJ, Liu J, Stemmler AJ, and Mitra B. . pmid:17326661. PubMed HubMed [Dutta07]
  2. Okkeri J and Haltia T. . pmid:16890908. PubMed HubMed [Okkeri06]
  3. Hou Z and Mitra B. . pmid:12746428. PubMed HubMed [Hou03]
  4. Sharma R, Rensing C, Rosen BP, and Mitra B. . pmid:10660539. PubMed HubMed [Sharma00]
All Medline abstracts: PubMed HubMed

Heavy Metals (non e.coli systems)

Other Bacteria

  1. Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, and Wattiez R. . pmid:12829276. PubMed HubMed [Mergeay03]
  2. Mizuno T, Usui K, Nishida S, Unno T, and Obata H. . pmid:17475501. PubMed HubMed [Mizuno07]
  3. Mehta SK and Gaur JP. . pmid:16294830. PubMed HubMed [Mehta05]
  4. Muñoz R, Alvarez MT, Muñoz A, Terrazas E, Guieysse B, and Mattiasson B. . pmid:16307789. PubMed HubMed [Munoz06]
  5. http://water.usgs.gov/wid/html/bioremed.html [USGS]
All Medline abstracts: PubMed HubMed

Phytoremediation

  1. Yang X, Feng Y, He Z, and Stoffella PJ. . pmid:16028496. PubMed HubMed [Yang05]
  2. Lefkowitz RJ. . pmid:11. PubMed HubMed [Kamnev00]
All Medline abstracts: PubMed HubMed


Heavy Metal Absorption in Plants and Soil

  1. De Marco P, Pacheco CC, Figueiredo AR, and Moradas-Ferreira P. . pmid:15109722. PubMed HubMed [DeMarco04]
  2. Vivas A, Azcón R, Biró B, Barea JM, and Ruiz-Lozano JM. . pmid:14663492. PubMed HubMed [Vivas03]
  3. Clemens S, Palmgren MG, and Krämer U. . pmid:12119168. PubMed HubMed [Clemes02]
  4. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392. PubMed HubMed [Tripathi07]
  5. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392. PubMed HubMed [Tripathi07]
  6. Gutnick DL and Bach H. . pmid:11092618. PubMed HubMed [ick00]
  7. Weinberg ED. . pmid:2530602. PubMed HubMed [Weinberg89]
All Medline abstracts: PubMed HubMed

Biosensors

  1. Paul05 pmid=15734556
  • Using overexpression and purification of proteins for biosensor
  1. http://pubs.acs.org/cgi-bin/article.cgi/ancham/1998/70/i19/html/ac9803636.html [Bontidean98]
Personal tools