Team:Northwestern/References

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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]
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<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
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{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"
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{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"
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!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]
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!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]
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!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]
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!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]
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!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]
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!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]
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!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]
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!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]
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!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]
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!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]
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!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]
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!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]
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!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]
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!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]
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!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]
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!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]
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!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]
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!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]
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!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]
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!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]
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!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]
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!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]
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!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]
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!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]
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!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]
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!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]
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!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]
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!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]
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!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]
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!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]
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{| align="center" border="0" width="75%"
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|
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=='''References'''==
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== Lac Operon Control ==
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=== Lac Operon Control ===
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http://openwetware.org/wiki/IPTG
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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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== Vary RBS ==
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Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]
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http://partsregistry.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Community_Collection
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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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Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html
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=== Chitin Synthesis ===
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==Chitin==
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Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311
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=== Chitin Synthesis ===
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chitin synthase gene (chs3): http://www.ncbi.nlm.nih.gov/gene/852311
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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: http://tinyurl.com/283wax2
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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
=== 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 Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html
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==Keio Collection - KnockOuts==
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Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp
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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
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=== ChiA(Chitinase) Knockout (may not be necessary) ===
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Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html
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summary of e coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
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Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls
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chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837
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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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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
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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more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf
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=== BIF (Biological Imaging Facility)===
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List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br />
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Methods: http://www.northwestern.edu/bioimaging/methods.html
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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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