Sandbox: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(118 intermediate revisions by 43 users not shown)
Line 1: Line 1:
{|cellspacing="5" cellpadding="10" style="background:#000000; width: 820px;"
__TOC__
|-valign="top"
|style="background:#303030"|


[[Image:Xray_logo1.tif]]
'''EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14'''
[[Image:igemlogo.gif | 200px | link=Notebook/Voltage]]




<html>
==Experiment==
<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Voltage"><img border="0" src="http://openwetware.org/images/0/00/Vol_logo.JPG" width="256" height="201"></a></td>
<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Voltage"><img border="0" src="http://openwetware.org/images/d/d1/Mag_logo.JPG" width="210" height="201"></a></td>
<td class="tdboxes"><a href="http://openwetware.org/wiki/iGEM:Cambridge/2008/Notebook/Voltage"><img border="0" src="http://openwetware.org/images/f/fe/Tur_logo.JPG" width="201" height="201"></a></td>
</html>


<hr width="810px">
'''Objective'''
<div id="about">
To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware
{{Cambridge08a}}
'''Procedure'''
</div>
<hr width="810px">
__NOTOC__
{|{{table}} width="810"
|-
|style="background-color: #cdde95;" align="center"|
<!-- ## START calendar column -->
<LNCalendar></LNCalendar>
<!-- ## END calendar column -->
|align="center" style="background-color: #e5edc8;" |
<!-- ## START search column: Place your logo here. Try keep it below 200px in width and 150px in height. ##  -->
[[Image:Untitled-2.jpg‎ |450px]] <sitesearch>title=Search this project</sitesearch>
<!-- ## END search column  ## -->
|-
|colspan="2" style="background-color: #F2F2F2;" align="right"|[[/Entry_Base|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
|-
|colspan="2"|


=Aim=
* Trigeminal nerve bilaterally DiO crystals
To create a system which responds to ligand binding with a detectable voltage caused by a K<sup>+</sup> flux.
* 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)


[[IGEM:Cambridge/2008/Notebook/Voltage/Progress | Progress]]
'''Notes'''
No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.


=Background=
==Files==
[[Media:Voltage_project.ppt | Presentation]]


=Experiments=
*
*
*
*


[[IGEM:Cambridge/2008/Notebook/Voltage/Mutant Strains | Mutant Strains]]
*
**
**


[[IGEM:Cambridge/2008/Notebook/Voltage/Flame Photometer Calibration|Flame Photometer Calibration]]
==Results==


[[IGEM:Cambridge/2008/Notebook/Voltage/K+ Concentrations|K+ Concentrations]]
===Facial===
(Green)


[[IGEM:Cambridge/2008/Notebook/Voltage/BioBrick Manipulation|BioBrick Manipulation]]
* '''''Afferents'''''
 


[[IGEM:Cambridge/2008/Notebook/Voltage/OD600 Calibration|OD600 Calibration]]
* '''''Efferents'''''


=Next Steps=


<u>Characterise promoters</u>


1. Simulate and design    ‘reporter plasmids’ with correct biobricks restriction enzyme sites


2. For each strain:    2 plasmid backbones


::* PSC101 (A) with    OsmY (promoter) + RFP + Stop


::* Another (B), not    yet defined, with Bba_J23100 + YFP + Stop
===VIII ===
(green)


: Tests for each strain :  plasmid A, plasmid B, plasmid A + plasmid B (so 15 tests)
* '''''Afferents'''''


3. Quantify transformation    efficiency (colony counter)


4. Quantify promoter    strength (light intensity, expression levels)


=Useful Links=
* '''''Efferents'''''


[http://expasy.org/tools/ Protein prediction tools]


[http://www.uniprot.org/ Uniprot database]
* '''''Other'''''


=Literature=


[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1214631 Kdp operon diagram]


[http://www.jbc.org/cgi/content/abstract/276/13/9590 Kdp plasmid]
===Basal plate ===
(red)


[http://www.springerlink.com/content/6042632827845551/  The Kdp-ATPase system and its regulation]


Potential Chassis: [http://cgsc.biology.yale.edu/Strain.php?ID=107402 Strain JW1242-1]
==Summary==
[http://cgsc.biology.yale.edu/Strain.php?ID=107065 Strain JW0710-1]


[http://www.ncbi.nlm.nih.gov/pubmed/4942756 Kdp mutant - paper from 1971]
'''Questions'''


|-
'''Future'''
|style="background-color: #F2F2F3;"|


[http://www.shigen.nig.ac.jp/WGR/link/link_E.coli_e.html Worldwide E.coli Databases]


[http://jb.asm.org/cgi/content/abstract/188/5/1950 Characterisation of kdpD - 2005]
<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">


[http://jb.asm.org/cgi/content/full/180/19/5102 Investigations on Kdp Operon exp. & flux]


[http://dx.doi.org/10.1006/jmbi.2001.4884 Very interesting 2001 paper concerning Glutamate Channels]
Mary {pad|4em} had a little lamb.


[http://www.nature.com/nature/journal/v402/n6763/full/402817a0.html 1999 paper on functional characterization of prokaryote Glu Channels]
'''Badrul Arefin'''


[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=BA000022 Sequenced Synechocystis PCC 6803 genome]


[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=47118304&from=1401809&to=1403002&view=gbwithparts Glutamate-gated K+ channel GluR0]
# Jeong M^, {{spaces|7}} <u>Sun D^</u>, Luo M^, Huang Y, Challen GA, <u>Rodriguez B</u>, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, <u>Li W*</u>, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a. <br/> '''''          Nature Genetics''''' . Accepted.
 
# <u>Akdemir KC</u>, Jain AK, Alton K, Arronow B, J. CA, ..., <u>Li W*</u>, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells. <br/>'''''Nucleic Acids Res.''''' Accepted
[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi Link to E.coli statistics page (CCDB Database)]
# Klein JB, Piao L, …, <u>Li W</u>, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.<br/>''Cell Reports''. Accepted. <br/><br/>'''2013''' <br/><br/>
 
# <u>Chen K</u>, <u>Xi Y</u>, Pan X, Dent S, He X, <u>Li W*</u>: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. <br/>'''''Genome Res.''''' 23 (2013) 341-351. [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News];  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline]  <br/><br/>
 
# <u>Wang L</u>, <u>Park JH</u>, Wang S, Kocher JP, <u>Li W*</u>: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model. <br/>'''''Nucleic Acids Res.''''' 41 (2013) e74.<br/><br/>
|}
# <u>Lin X</u>, <u>Sun D</u>, <u>Rodriguez B</u>, Zhao Q, Sun H, Zhang Y, <u>Li W*</u>: BseQC: Quality Control of bisulfite sequencing experiments. <br/>'''''Bioinformatics''''' 29 (2013) 3227-3229. PMCID: PMC3842756 .<br/><br/>
# <u>Chen K^</u>, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, <u>Li W*</u>, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. <br/>'''''Genome Res.''''' 23 (2013) 312-322. <br/><br/>

Revision as of 11:51, 25 March 2015

EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14


Experiment

Objective To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware Procedure

  • Trigeminal nerve bilaterally DiO crystals
  • 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)

Notes No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.

Files

Results

Facial

(Green)

  • Afferents


  • Efferents




VIII

(green)

  • Afferents


  • Efferents


  • Other


Basal plate

(red)


Summary

Questions

Future


<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">


Mary {pad|4em} had a little lamb.

Badrul Arefin


  1. Jeong M^, Template:Spaces Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a.
    Nature Genetics . Accepted.
  2. Akdemir KC, Jain AK, Alton K, Arronow B, J. CA, ..., Li W*, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells.
    Nucleic Acids Res. Accepted
  3. Klein JB, Piao L, …, Li W, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.
    Cell Reports. Accepted.

    2013

  4. Chen K, Xi Y, Pan X, Dent S, He X, Li W*: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
    Genome Res. 23 (2013) 341-351. BCM News; Epigenie Headline

  5. Wang L, Park JH, Wang S, Kocher JP, Li W*: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model.
    Nucleic Acids Res. 41 (2013) e74.

  6. Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W*: BseQC: Quality Control of bisulfite sequencing experiments.
    Bioinformatics 29 (2013) 3227-3229. PMCID: PMC3842756 .

  7. Chen K^, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, Li W*, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
    Genome Res. 23 (2013) 312-322.

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Sandbox&oldid=875145"