User talk:Jarlemag

From 2012.igem.org

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===Useful links===
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=Tasks=
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*Make cloramphenicol stock. Check.
 +
*Make glycerol stocks of important parts. Discard old plates. Check.
 +
*Perform CFU-assay of lysis induced cells. Check. Redo?
 +
*Combine LuxR-HSL and lysis device.
 +
*Combine pBAD and GFP
 +
 
 +
*Research lactate production in E. coli
 +
*Write more for the book chapter
 +
*Research QuikChange
 +
 
 +
 
 +
==Useful links==
http://www.nanodrop.com/Support.aspx?Type=Maintenance&Cat=NanoDrop%201000
http://www.nanodrop.com/Support.aspx?Type=Maintenance&Cat=NanoDrop%201000
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https://2008.igem.org/Team:EPF-Lausanne/2-step_PCR
https://2008.igem.org/Team:EPF-Lausanne/2-step_PCR
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https://2009.igem.org/Team:UNIPV-Pavia/Parts_Characterization#Microplate_reader_experiments
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[http://www.jbioleng.org/content/5/1/17 Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits]
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[http://www.sbkb.org/tt/  Structural Biology Target Registration Database]
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[http://dnasu.asu.edu/DNASU/ DNASU plasmid repository]
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[http://www.addgene.org/ Addgene plasmid repository]
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[http://plasmid.med.harvard.edu/PLASMID/ PlasmID database]
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[http://www.chuq.qc.ca/labomoss/english%20pages/protocols.html Moss lab protocols]
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===Lactate genes and promoters:===
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[http://www.biomedcentral.com/1471-2180/10/321#B24 Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate]
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[http://aem.asm.org/content/71/10/5920.full Characterization of a Corynebacterium glutamicum Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production†]
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[http://www.genome.jp/dbget-bin/www_bget?cgb:cg1027 KEGG: cg1027]
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[http://jb.asm.org/content/191/13/4251.abstract The ldhA Gene, Encoding Fermentative l-Lactate Dehydrogenase of Corynebacterium glutamicum, Is under the Control of Positive Feedback Regulation Mediated by LldR
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[http://mic.sgmjournals.org/content/142/5/1297 Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif]
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[http://www.sciencedirect.com/science/article/pii/S016816560300155X Promoters of Corynebacterium glutamicum]
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[http://www.rcsb.org/pdb/explore/explore.do?structureId=2di3 C. glutamicum lldR crystal structure]
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RNA polymerase:
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[http://www.ncbi.nlm.nih.gov/pubmed/9916034 Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study]
 +
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[http://pubs.acs.org/doi/abs/10.1021/jp9071197 Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner]
 +
 +
[http://www.ncbi.nlm.nih.gov/pubmed/10910724 Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase]
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[http://www.sciencedirect.com/science/article/pii/0092867495903879 Wang et al, 1995: Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex]
==DNA oligo and gene synthesis==
==DNA oligo and gene synthesis==
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[http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.165 Quorum sensing in bacteria - Annu. Rev. Microbiol. 2001. 55:165–99]
[http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.165 Quorum sensing in bacteria - Annu. Rev. Microbiol. 2001. 55:165–99]
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[http://www.ncbi.nlm.nih.gov/pubmed/16487323 N-acyl-L-homoserine lactone signal interception by Escherichia coli.]
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==Other==
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[http://www.bion.no/2011/11/syntetisk-biologi/ Syntetisk biologi: Genmodifisert bakterie drep annan bakterie]
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 +
http://en.wikipedia.org/wiki/DNA_ligase

Latest revision as of 19:04, 24 July 2012

Contents

Tasks

  • Make cloramphenicol stock. Check.
  • Make glycerol stocks of important parts. Discard old plates. Check.
  • Perform CFU-assay of lysis induced cells. Check. Redo?
  • Combine LuxR-HSL and lysis device.
  • Combine pBAD and GFP
  • Research lactate production in E. coli
  • Write more for the book chapter
  • Research QuikChange


Useful links

http://www.nanodrop.com/Support.aspx?Type=Maintenance&Cat=NanoDrop%201000

http://www.troemner.com/pdf/PipetteStandardsHandbook.pdf'

http://www.pipette.com/Support/GuideToPipetting.pdf


https://2008.igem.org/Team:EPF-Lausanne/2-step_PCR

https://2009.igem.org/Team:UNIPV-Pavia/Parts_Characterization#Microplate_reader_experiments

[http://www.jbioleng.org/content/5/1/17 Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits]

[http://www.sbkb.org/tt/ Structural Biology Target Registration Database]

[http://dnasu.asu.edu/DNASU/ DNASU plasmid repository]

[http://www.addgene.org/ Addgene plasmid repository]

[http://plasmid.med.harvard.edu/PLASMID/ PlasmID database]


[http://www.chuq.qc.ca/labomoss/english%20pages/protocols.html Moss lab protocols]

Lactate genes and promoters:

[http://www.biomedcentral.com/1471-2180/10/321#B24 Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate]

[http://aem.asm.org/content/71/10/5920.full Characterization of a Corynebacterium glutamicum Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production†]

[http://www.genome.jp/dbget-bin/www_bget?cgb:cg1027 KEGG: cg1027]

[http://jb.asm.org/content/191/13/4251.abstract The ldhA Gene, Encoding Fermentative l-Lactate Dehydrogenase of Corynebacterium glutamicum, Is under the Control of Positive Feedback Regulation Mediated by LldR

[http://mic.sgmjournals.org/content/142/5/1297 Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif]

[http://www.sciencedirect.com/science/article/pii/S016816560300155X Promoters of Corynebacterium glutamicum]

[http://www.rcsb.org/pdb/explore/explore.do?structureId=2di3 C. glutamicum lldR crystal structure]


RNA polymerase:

[http://www.ncbi.nlm.nih.gov/pubmed/9916034 Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study]

[http://pubs.acs.org/doi/abs/10.1021/jp9071197 Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner]

[http://www.ncbi.nlm.nih.gov/pubmed/10910724 Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase]

[http://www.sciencedirect.com/science/article/pii/0092867495903879 Wang et al, 1995: Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex]

DNA oligo and gene synthesis

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Product-Types/Primers-Oligos-Nucleotides/invitrogen-custom-dna-oligos/Technical-Resources-for-Oligonucleotides/DNA-Oligo-FAQ.html#1

PCR

[http://irc.igd.cornell.edu/Protocols/PCR_principles.htm PCR Principles and Practices]

[http://www.neb.com/nebecomm/products/protocol54.asp New England Biolabs: PCR Guidelines]

http://www.uq.edu.au/vdu/PDU_PCRPrimers.htm

[http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html Premier biosoft: PCR primer design guidelines]

http://www.cybertory.org/exercises/primerDesign/index.html

http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/general_pcr_protocol.html

[http://www.miraibio.com/blog/2008/03/10-tips-for-designing-pcr-primers-that-work/ 10 tips for designing PCR primers that work]

[http://www.ehow.com/how_7242346_make-oligonucleotide-primers-pcr.html How to make oligonucleotide primers for PCR]


Software

http://molbiol-tools.ca/molecular_biology_freeware.htm


quorum sensing

[http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.165 Quorum sensing in bacteria - Annu. Rev. Microbiol. 2001. 55:165–99]

[http://www.ncbi.nlm.nih.gov/pubmed/16487323 N-acyl-L-homoserine lactone signal interception by Escherichia coli.]


Other

[http://www.bion.no/2011/11/syntetisk-biologi/ Syntetisk biologi: Genmodifisert bakterie drep annan bakterie]

http://en.wikipedia.org/wiki/DNA_ligase

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