Team:Northwestern/References

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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

@@ Line 137: / Line 137: @@
-== Ara Operon Control (pbad promoter)==
-http://partsregistry.org/wiki/index.php?title=Part:BBa_R0080
-http://partsregistry.org/wiki/index.php/Part:BBa_I0500
-arabinose information: http://openwetware.org/wiki/Arabinose
-pbad info: http://openwetware.org/wiki/Titratable_control_of_pBAD_and_lac_promoters_in_individual_E._coli_cells#pBAD_promotersOpenWetWare
-pbad family (only wildtype available) - http://partsregistry.org/PBAD_Promoter_Family
 ==Chitin==
-Adding Glucosamine to growth medium boosts chitin production in Yeast (S.C.)- http://ec.asm.org/cgi/reprint/2/5/886
+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] (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).)
+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 - 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
+Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long
-Chitin Uses: http://www.gmp-chitosan.com/en/products-services/chitin.html
+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
+Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311
-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
+CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465
-http://tools.neb.com/NEBcutter2/cutshow.php?name=cb3c5ddc-
 ===Chitin Staining (Calcofluor)===
-Does not stain E Coli - http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
+Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
-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
+Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za
-Inhibits Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
+Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
-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
+Data sheet: http://tinyurl.com/283wax2
 Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html
@@ Line 182: / Line 170: @@
 == Apoptosis ==
-registry: http://partsregistry.org/Cell_death
+partsregistry: http://partsregistry.org/Cell_death
-===Control===
-*Adjust genetic order
-*RBS of varying strengths
-*OmpR Binding Site (to detect extracellular glucose)
-**http://partsregistry.org/wiki/index.php?title=Part:BBa_I761001
-**http://partsregistry.org/wiki/index.php/Part:BBa_I761011
-*PhoB
 === Live/Dead Staining aka Viability/Cytotoxicity Assay===
@@ Line 202: / Line 181: @@
 ==Keio Collection - KnockOuts==
-Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html
+Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html
 Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp
@@ Line 208: / Line 187: @@
 Method: http://www.pnas.org/content/97/12/6640.full.pdf+html
-Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.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
@@ Line 214: / Line 193: @@
-=== ChiA(Chitinase) Knockout (may not be necessary) ===
+=== ChiA (Chitinase) Knockout ===
-summary of e coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
+Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
-chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837
+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
@@ Line 224: / Line 203: @@
 ===ydgg/tqsA (AI2-Transporter) Knockout===
-KO -> ~7000x biofilm thickness, ~500x biomass - http://jb.asm.org/cgi/content/short/188/2/587
+Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593
-http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593
 more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf