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{{clickpic|iGEM:Cambridge/2008/Notebook/Voltage|igemlogo.gif}}
__TOC__


[[Image:igemlogo.gif | 200px | link=Notebook/Voltage]]


----


<html>
== My Test of OpenWetWare Editing ==
<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>
I would like to try the following editing tasks:
<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>
* Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
<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>
** For example: Link to the paper can be found HERE[http://www.nature.com/nature/journal/v403/n6767/pdf/403339a0.pdf].
</html>
* Add a document or Dropbox link:
** Addition of document: [[Image:Example.jpg]]
** Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
* Cite a paper.
** Hopefully see the list of references at the bottom of the page.
** This is a really interesting study <ref>Reference goes here</ref>
* Add a picture.


{| {{table}}
== References ==
| align="center" style="background:#f0f0f0;"|width="30%"|''' '''
{{Reflist}}
| align="center" style="background:#f0f0f0;"|''' '''
 
| align="center" style="background:#f0f0f0;"|'''Personnel'''
----
| align="center" style="background:#f0f0f0;"|'''Progress'''
 
|-
'''EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14'''
| '''Research'''|| || ||
 
|-
 
| ||Potassium intake || ||
==Experiment==
|-
 
| ||Preventing K+ efflux || ||
'''Objective'''
|-
To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware
| ||Bacterial tolerance for high K+ and turgor
'''Procedure'''
:*Osmolites (“inert” sugars)
 
|| ||
* 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)
| ||Ligand gated channels|| ||
 
|-
'''Notes'''
| ||Media || ||
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.
|-
 
|'''Preliminary wet work ''' || || ||
==Files==
|-
 
| ||Extract promoter, RBS and terminator BioBricks from registry
*
:*Refine protocol for paper-bound DNA extraction
*
:*Use PCR and transformations to confirm presence of DNA
*
|| ||
*
|-
 
|'''Internal K+ build-up''' || || ||
*
|-
**
| ||PCR Kdp K+ pump gene from E.coli MG1655
**
:*Design and order primers, including BioBrick prefix and suffix
 
|| ||
==Results==
|-
 
| ||Put Kdp gene under control of stationary phase promoter (osmY, used by MIT 2006 team)
===Facial===
:* Obtain primer sequences and order, for PCR from BioBricks containing osmY (J45992)
(Green)
:* Ligate to RBS, Kdp gene and terminators in plasmid
 
|| ||
* '''''Afferents'''''
|-
 
| ||Transform into wildtype and mutant E.coli strains || ||
 
|-
* '''''Efferents'''''
| ||Test
 
:*Measure internal K+ concentration using flame photometry
 
|| ||
 
|-
 
| '''Chassis'''|| || ||
 
|-
 
| ||Order from Yale
===VIII ===
:*Kch- mutant, preventing uncontrolled K+ efflux
(green)
:*Kef- mutants, preventing uncontrolled K+ efflux
 
:*Kdp- mutants, preventing regulation of K+ intake|| ||
* '''''Afferents'''''
|-
 
| ||Test
 
:*Check competence using YFP BioBrick plasmid
 
:*Measure internal K+ concentration using flame photometry
* '''''Efferents'''''
:*Quantify growth relative to wildtype E.coli strain || ||
 
|-
 
|'''Controlled K+ efflux''' || || ||
* '''''Other'''''
|-
 
| ||Design sequence based on GluR0 glutamate-gated K+ channel from Synechocystis PCC 6803 || ||
 
|-
 
| ||Send to DNA 2.0 for synthesis || ||
===Basal plate ===
|-
(red)
| ||Backup
 
:* Obtain Synechocystis PCC 6803 strain (from Imperial College London)
 
:*Design and order primers for GluR0, PCR
==Summary==
:*Include rare tRNA plasmid in transformation|| ||
 
|-
'''Questions'''
| ||Ligate gene into BioBrick plasmid || ||
 
|-
'''Future'''
| ||Transform into chosen chassis || ||
 
|-
 
| ||Test
<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">
:* Measure internal K+ concentration with and without presence of glutamate, using flame photometry
 
|| ||
 
|-
Mary {pad|4em} had a little lamb.
|'''Measuring voltage''' || || ||
 
|-
'''Badrul Arefin'''
| ||Quantify output using oxygen electrode or glass capillary microelectrode || ||
 
|-
 
|'''Medium optimisation''' || || ||
# 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
| ||Vary K+ concentrations, using KCl || ||
# 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/>
| ||Vary nutrient levels || ||
# <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/>
|'''Output optimisation''' || || ||
# <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/>
|-
| ||Vary strength of promoters/RBS || ||
|-
|}

Revision as of 09:23, 6 October 2015


My Test of OpenWetWare Editing

I would like to try the following editing tasks:

  • Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
    • For example: Link to the paper can be found HERE[1].
  • Add a document or Dropbox link:
    • Addition of document:
    • Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
  • Cite a paper.
    • Hopefully see the list of references at the bottom of the page.
    • This is a really interesting study [1]
  • Add a picture.

References

  1. ↑ Reference goes here

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.

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