IGEM:MIT/2007/Links for Bioremediation Project

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(Promoters)
Current revision (17:24, 31 July 2007) (view source)
(Polysterene)
 
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<biblio>
<biblio>
#Wernerus04 pmid=15035661
#Wernerus04 pmid=15035661
 +
</biblio>
 +
*OmpA, OmpB, OmpC Surface proteins
 +
<biblio>
 +
#koebnik00 pmid=10931321
</biblio>
</biblio>
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==Sticky Peptides==
==Sticky Peptides==
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===Polysterene===
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===Polystyrene===
====Kenan====
====Kenan====
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</biblio>
</biblio>
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==Bioremediation Papers==
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==pBAD Promoter Info==
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*Arabinose PBAD Promoter<cite>pBAD33</cite>
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===Toxicity of Heavy Metals===
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<biblio>
<biblio>
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#Silver05 pmid=16133099
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#pBAD33 pmid=7608087
</biblio>
</biblio>
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====Cadmium====
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==Bioremediation Papers==
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*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.
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<biblio>
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#Wang95 pmid=3104315
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</biblio>
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[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]
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===Heavy Metal Resistance Techniques===
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<biblio>
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#Bruins00 pmid=10702338
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#Hou88 pmid=3056525
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</biblio>
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===Heavy Metal Binding Proteins/Peptides===
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<biblio>
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#Samuelson00 pmid=10698802
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#Biosorbants pmid=9758845
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#Kotrba99 pmid=10049868
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#Mejare01 pmid=11164556
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#Lu01 pmid=11710062
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#Bae00 pmid=11042548
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</biblio>
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===Pumps===
===Pumps===
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</biblio>
</biblio>
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===Promoters===
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==Heavy Metals (non e.coli systems)==
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*Cadmium(pCN39, a derivative of pCN37 with a temperature-sensitive replicon)
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<cite> Yao06 </cite>
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#[[http://aem.asm.org/cgi/content/full/67/4/1437 Two Good Cadmium Promoters]]
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*Mercury (Pmer)
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<biblio
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#Hamlett92 pmid=1328156
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#Park92 pmid=1312997
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#Condee92 pmid=1334070
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#Gambill85 pmid=4092936
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#Yao06 pmid=16741231
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#Hansen00 pmid=11094290
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</biblio>
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===Sponges===
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*Mercury [http://www.jstage.jst.go.jp/article/bbb/71/6/1494/_pdf]
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==Miscellaneous==
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*Arabinose PBAD Promoter<cite>pBAD33</cite>
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<biblio>
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#pBAD33 pmid=7608087
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</biblio>
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==Outer Membrane Proteins==
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*OmpA, OmpB, OmpC Surface proteins<cite>koebnik00</cite>
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<biblio>
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#koebnik00 pmid=10931321
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</biblio>
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==Heavy Metals==
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====Review articles====
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<biblio>
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#Paul05 pmid=15734556
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#Valls02 pmid=12413663
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</biblio>
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====Other Bacteria====
====Other Bacteria====
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#Clemes02 pmid=12119168
#Clemes02 pmid=12119168
#Tripathi07 pmid=17306392
#Tripathi07 pmid=17306392
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</biblio>
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#Tripathi07 pmid=17306392
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#ick00 pmid=11092618
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===Heavy Metals and E. coli===
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#Weinberg89 pmid=2530602
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====Heavy Metal Resistance====
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<biblio>
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#Nakajima95 pmid=7793951
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</biblio>
</biblio>
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<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
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</biblio>
 
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====Absorption of Heavy Metals====
 
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<biblio>
 
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#Gutn
 
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#Tripathi07 pmid=17306392ick00 pmid=11092618
 
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#Weinberg89 pmid=2530602
 
</biblio>
</biblio>

Current revision

Contents

Protein Surface Display

Error fetching PMID 15035661:
  1. Error fetching PMID 15035661: [Wernerus04]
  • OmpA, OmpB, OmpC Surface proteins
Error fetching PMID 10931321:
  1. Error fetching PMID 10931321: [koebnik00]

OmpX

Error fetching PMID 7836315:
  1. Error fetching PMID 7836315: [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

Error fetching PMID 10543834:
  1. Error fetching PMID 10543834: [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

Error fetching PMID 9048419:
Error fetching PMID 16873017:
Error fetching PMID 7737512:
Error fetching PMID 15620878:
  1. Error fetching PMID 7737512: [Adey95]
  2. Error fetching PMID 9048419: [Gebhart96]
  3. Error fetching PMID 16873017: [Kenan06]
  4. Error fetching PMID 15620878: [Menendez05]
All Medline abstracts: PubMed HubMed

Polypyrrole

T59: THRTSTLDYFVI
[11]
Error fetching PMID 15895095:
  1. Error fetching PMID 15895095: [Sanhvi05]

pBAD Promoter Info

  • Arabinose PBAD Promoter[12]
Error fetching PMID 7608087:
  1. Error fetching PMID 7608087: [pBAD33]

Bioremediation Papers

Pumps

  • Cadmium(Plasmid pI258 (from S.aureus) cadmium resistance (cadA) gene, complete cds) [13]
  • ZntA(Divalent Metal Transporter)
Error fetching PMID 17326661:
Error fetching PMID 16890908:
Error fetching PMID 12746428:
Error fetching PMID 10660539:
  1. Error fetching PMID 17326661: [Dutta07]
  2. Error fetching PMID 16890908: [Okkeri06]
  3. Error fetching PMID 12746428: [Hou03]
  4. Error fetching PMID 10660539: [Sharma00]
All Medline abstracts: PubMed HubMed

Heavy Metals (non e.coli systems)

Other Bacteria

Error fetching PMID 12829276:
Error fetching PMID 17475501:
Error fetching PMID 16294830:
Error fetching PMID 16307789:
  1. Error fetching PMID 12829276: [Mergeay03]
  2. Error fetching PMID 17475501: [Mizuno07]
  3. Error fetching PMID 16294830: [Mehta05]
  4. Error fetching PMID 16307789: [Munoz06]
  5. http://water.usgs.gov/wid/html/bioremed.html [USGS]
All Medline abstracts: PubMed HubMed

Phytoremediation

Error fetching PMID 16028496:
Error fetching PMID 11:
  1. Error fetching PMID 16028496: [Yang05]
  2. Error fetching PMID 11: [Kamnev00]
All Medline abstracts: PubMed HubMed


Heavy Metal Absorption in Plants and Soil

Error fetching PMID 15109722:
Error fetching PMID 14663492:
Error fetching PMID 12119168:
Error fetching PMID 17306392:
Error fetching PMID 17306392:
Error fetching PMID 11092618:
Error fetching PMID 2530602:
  1. Error fetching PMID 15109722: [DeMarco04]
  2. Error fetching PMID 14663492: [Vivas03]
  3. Error fetching PMID 12119168: [Clemes02]
  4. Error fetching PMID 17306392: [Tripathi07]
  5. Error fetching PMID 17306392: [Tripathi07]
  6. Error fetching PMID 11092618: [ick00]
  7. Error fetching PMID 2530602: [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]
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