Team:Northwestern/References

From 2010.igem.org

(Difference between revisions)
 
(40 intermediate revisions not shown)
Line 1: Line 1:
-
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]
+
__NOTOC__
 +
 
 +
 
 +
<html>
 +
<style>
 +
/* Wiki Hacks - START */
 +
#globalWrapper {
 +
    background-color: transparent;
 +
    padding-bottom:0px;
 +
    border: none;
 +
    }
 +
#top-section {
 +
    height: 0px;
 +
    margin-top: 0px;
 +
    margin-left: auto;
 +
    margin-right: auto;
 +
    margin-bottom: 0 !important;
 +
    margin-bottom: 0px;
 +
    padding:0;
 +
    border: 1;
 +
    }
 +
#p-logo {
 +
    height:0px;
 +
    overflow:hidden;
 +
    border:none;
 +
    }
 +
#search-controls {
 +
    overflow:hidden;
 +
    display:none;
 +
    background: none;
 +
    position: absolute;
 +
    top: 100px;
 +
    right: 40px;
 +
    }         
 +
 
 +
 
 +
/* Wiki Hacks - END */
 +
 
 +
 
 +
#content {
 +
    background-color: transparent;
 +
    width:99%;
 +
    position: relative;
 +
    float: center;
 +
    border: 0px;
 +
}
 +
 
 +
#menubar {
 +
background-color:transparent;
 +
font-size:85%;
 +
line-height:1em;
 +
position:absolute;
 +
top:10px;
 +
white-space:nowrap;
 +
width:50%;
 +
z-index:5;
 +
height:25px;
 +
overflow:hidden;
 +
}
 +
 
 +
#menubar li a {
 +
color:#000000;
 +
}
 +
 
 +
.left-menu {
 +
left:0;
 +
padding-left:13px;
 +
}
 +
.right-menu  {
 +
right:0;
 +
}
 +
 
 +
.firstHeading { display:none; }
 +
}
 +
 
 +
 
 +
 
 +
 
 +
#footer-box {
 +
background-color: transparent;
 +
color: #000000;
 +
border: 0px;
 +
margin:0 auto;
 +
padding:13px 5px;
 +
width:auto;
 +
margin-top:-1px;
 +
}
 +
 
 +
#footer-box a {
 +
        background-color: transparent;
 +
color: #000000;
 +
font-size:90%;
 +
 
 +
}
 +
/* Wiki Hacks - END */
 +
</style>
 +
</html>
 +
 
<html>
<html>
<head>
<head>
<style>
<style>
body {
body {
-
   background: white url(https://static.igem.org/mediawiki/2010/3/38/NUbackground.jpg) repeat-x;
+
   background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; -->
}
}
</style>
</style>
</head>
</head>
</html>
</html>
 +
 +
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]
 +
<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
-
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"
+
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"
-
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]
+
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]
-
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]
+
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]
-
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]
+
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]
-
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]
+
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]
-
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]
+
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]
-
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]
+
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]
-
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]
+
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]
-
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]
+
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]
-
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]
+
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]
-
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]
+
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]
-
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]
+
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]
-
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]
+
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]
-
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]
+
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]
-
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]
+
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]
-
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]
+
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]
|}
|}
 +
{| align="center" border="0" width="75%"
 +
|
 +
=='''References'''==
-
== Lac Operon Control ==
+
=== Lac Operon Control ===
-
http://openwetware.org/wiki/IPTG
+
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG
-
==Chitin==
+
===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 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
-
====Chitin Staining (Calcofluor)====
+
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465
-
Does not stain E Coli - http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
+
===Chitin Staining (Calcofluor)===
-
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
+
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf
-
Inhibits Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
+
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za
-
== Apoptosis ==
+
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/
-
registry: http://partsregistry.org/Cell_death
+
Data sheet: http://tinyurl.com/283wax2
-
==== Live/Dead Staining aka Viability/Cytotoxicity Assay
+
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html
-
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
+
=== Apoptosis ===
 +
partsregistry: http://partsregistry.org/Cell_death
-
==Keio Collection - KnockOuts==
+
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===
-
http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp
+
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
-
=== ChiA(Chitinase) Knockout (may not be necessary) ===
+
===Keio Collection - KnockOuts===
-
summary of e coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts
+
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html
-
chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837
+
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
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300
Line 70: Line 196:
===ydgg/tqsA (AI2-Transporter) Knockout===
===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
 +
 
 +
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 <br />
 +
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


Retrieved from "http://2010.igem.org/Team:Northwestern/References"