Team:Northwestern/References

From 2010.igem.org

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<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
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{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"
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{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]
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!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]
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!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]
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!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]
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!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]
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!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]
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!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]
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!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]
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!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]
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!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]
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!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]
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!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]
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!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]
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!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]
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!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]
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!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]
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!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]
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!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]
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!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]
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!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]
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!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]
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!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]
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!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]
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!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]
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!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]
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!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]
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!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]
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!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]
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!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]
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=='''References'''==
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== Lac Operon Control ==
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=== Lac Operon Control ===
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG
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===Chitin===
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Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886
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== Ara Operon Control (pbad promoter)==
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Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]
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http://partsregistry.org/wiki/index.php?title=Part:BBa_R0080
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Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long
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http://partsregistry.org/wiki/index.php/Part:BBa_I0500
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Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html
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arabinose information: http://openwetware.org/wiki/Arabinose
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pbad info: http://openwetware.org/wiki/Titratable_control_of_pBAD_and_lac_promoters_in_individual_E._coli_cells#pBAD_promotersOpenWetWare
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pbad family (only wildtype available) - http://partsregistry.org/PBAD_Promoter_Family
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==Chitin==
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Adding Glucosamine to growth medium boosts chitin production in Yeast (S.C.)- http://ec.asm.org/cgi/reprint/2/5/886
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Chitin synthesis Pathway (image) - [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg] (Figure.1. Biosynthesis of chitin in insects. The pathway starts with trehalose, the main hemolymph sugar in most insects, and ends with the chitin polymer. The diagrammatic representation is based on previously published pathways (Kramer and Koga, 1986; Cohen, 2001).)
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Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production - http://www.jbc.org/content/268/26/19858.long - possible safety issue - "When bacterial cells arelysed by the immune system, fragments of membrane containing lipid A are released into the circulation, causing fever, diarrhea, and possible fatal endotoxic shock (also called septic shock)." - thus spake wikipedia
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Chitin Uses: http://www.gmp-chitosan.com/en/products-services/chitin.html
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=== Chitin Synthesis ===
=== Chitin Synthesis ===
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chitin synthase gene (chs3): http://www.ncbi.nlm.nih.gov/gene/852311
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Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311
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CHS3 does polymerization (Chitin-UDP acetyl-glucosaminyl transferase is just another name for CHS3) - http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465
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http://tools.neb.com/NEBcutter2/cutshow.php?name=cb3c5ddc-
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CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465
===Chitin Staining (Calcofluor)===
===Chitin Staining (Calcofluor)===
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Does not stain E Coli - http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
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Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
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Stains Biofilm Polysaccharides? - http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V73-3YKKH2J-4S-1&_cdi=5831&_user=965532&_pii=0043135494003399&_orig=search&_coverDate=08%2F31%2F1995&_sk=999709991&view=c&wchp=dGLbVzz-zSkzS&md5=fedcb287ed9c9dafca2dbb4f2bc053a4&ie=/sdarticle.pdf
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Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za
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Inhibits Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
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Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
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Data sheet: https://docs.google.com/viewer?url=http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.Par.0001.File.tmp/18909dat.pdf&pli=1
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Data sheet: http://tinyurl.com/283wax2
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html
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== Apoptosis ==
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=== Apoptosis ===
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registry: http://partsregistry.org/Cell_death
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partsregistry: http://partsregistry.org/Cell_death
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===Control===
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*Adjust genetic order
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*RBS of varying strengths
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*OmpR Binding Site (to detect extracellular glucose)
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**http://partsregistry.org/wiki/index.php?title=Part:BBa_I761001
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**http://partsregistry.org/wiki/index.php/Part:BBa_I761011
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*PhoB
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=== Live/Dead Staining aka Viability/Cytotoxicity Assay===
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===
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*http://www.biotium.com/product/product_info/Protocol/30027.pdf
*http://www.biotium.com/product/product_info/Protocol/30027.pdf
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==Keio Collection - KnockOuts==
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===Keio Collection - KnockOuts===
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Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html  
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Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html  
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp
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Method: http://www.pnas.org/content/97/12/6640.full.pdf+html
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html
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Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html
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Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls
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=== ChiA (Chitinase) Knockout ===
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Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
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=== ChiA(Chitinase) Knockout (may not be necessary) ===
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Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837
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summary of e coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
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chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837
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chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300
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===ydgg/tqsA (AI2-Transporter) Knockout===
===ydgg/tqsA (AI2-Transporter) Knockout===
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KO -> ~7000x biofilm thickness, ~500x biomass - http://jb.asm.org/cgi/content/short/188/2/587
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Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593
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http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593
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more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf
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== BIF (Biological Imaging Facility)==
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=== BIF (Biological Imaging Facility)===
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br />
Methods: http://www.northwestern.edu/bioimaging/methods.html
Methods: http://www.northwestern.edu/bioimaging/methods.html

Latest revision as of 01:18, 27 October 2010


Tech Institute
Home Brainstorm Team Acknowledgements Project Human Practices Parts Notebook Calendar Protocol Safety Links References Media Contact

References

Lac Operon Control

Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG

Chitin

Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886

Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]

Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long

Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html

Chitin Synthesis

Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311

CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465

Chitin Staining (Calcofluor)

Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf

Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za

Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/

Data sheet: http://tinyurl.com/283wax2

Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html

Apoptosis

partsregistry: http://partsregistry.org/Cell_death

Live/Dead Staining aka Viability/Cytotoxicity Assay

DMAO(Live), EtD-III(Dead)

  • http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/
  • http://www.biotium.com/product/product_info/Protocol/30027.pdf

Keio Collection - KnockOuts

Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html

Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp

Method: http://www.pnas.org/content/97/12/6640.full.pdf+html

Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html

Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls

ChiA (Chitinase) Knockout

Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts

Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837

chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300

ydgg/tqsA (AI2-Transporter) Knockout

Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593

more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf

BIF (Biological Imaging Facility)

List of Equipment: http://www.northwestern.edu/bioimaging/equip.html
Methods: http://www.northwestern.edu/bioimaging/methods.html


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