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Team:Northwestern/References
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Lac Operon Control
http://openwetware.org/wiki/IPTG
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
PhoB Promoter
http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00053
Chitin
Adding Glucosamine to growth medium boosts chitin production in Yeast (S.C.)- 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 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 Synthesis
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
Chitin Staining (Calcofluor)
Does not stain 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
Inhibits Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
Apoptosis
registry: 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
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
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
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 (may not be necessary)
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
KO -> ~7000x biofilm thickness, ~500x biomass - 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
