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


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'''Badrul Arefin'''
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=Aim=
# 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.
To create a system which responds to ligand binding with a detectable voltage caused by a K<sup>+</sup> flux.
# <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
 
# 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/>
[[IGEM:Cambridge/2008/Notebook/Voltage/Progress | Progress]]
# <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/>
=Background=
# <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/>
[[Media:Voltage_project.ppt | Presentation]]
# <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/>
 
=Experiments=
 
[[IGEM:Cambridge/2008/Notebook/Voltage/Mutant Strains | Mutant Strains]]
 
[[IGEM:Cambridge/2008/Notebook/Voltage/Flame Photometer Calibration|Flame Photometer Calibration]]
 
[[IGEM:Cambridge/2008/Notebook/Voltage/K+ Concentrations|K+ Concentrations]]
 
[[IGEM:Cambridge/2008/Notebook/Voltage/BioBrick Manipulation|BioBrick Manipulation]]
 
[[IGEM:Cambridge/2008/Notebook/Voltage/OD600 Calibration|OD600 Calibration]]
 
=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
 
: Tests for each strain :  plasmid A, plasmid B, plasmid A + plasmid B (so 15 tests)
 
3. Quantify transformation    efficiency (colony counter)
 
4. Quantify promoter    strength (light intensity, expression levels)
 
=Useful Links=
 
[http://expasy.org/tools/ Protein prediction tools]
 
[http://www.uniprot.org/ Uniprot database]
 
=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]
 
[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]
[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]
 
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[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]
 
[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]
 
[http://www.nature.com/nature/journal/v402/n6763/full/402817a0.html 1999 paper on functional characterization of prokaryote Glu Channels]
 
[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]
 
[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi Link to E.coli statistics page (CCDB Database)]
 
 
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Revision as of 11:27, 10 October 2014

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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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