User:ShLo

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[[shlo/notebook]]
[[shlo/notebook]]
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NanoDrop results (6/20) performed by Ellenor and Stephanie:<br>
 
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(1.5 uL used out of a 30uL elution with nuclease free water)<br>
 
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S: 10.9 ng/uL<br>
 
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S2: 15.4 ng/uL<br>
 
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B: 59.1 ng/uL<br>
 
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B1: 25.1 ng/uL<br>
 
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<br><br><br>
 
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Brainstorming for the two-component systems (really for my own use for now - not expected to be coherent)<br>
 
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[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10653699&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Structural comparison of the PhoB and OmpR DNA binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box]<br>
 
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-NMR used to determine 3DE structure of PhoB DNA-binding/transactivation domain. Very similar to OmpR DNA-binding/transactivation domain, except for conformation of the long turn region of PhoB (interaction site for sigma subunit, rather than interaction with alpha subunit for OmpR)
 
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<br><br>
 
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[http://jb.asm.org.ezp1.harvard.edu/cgi/content/full/185/1/317?view=long&pmid=12486069 Interdomain linkers of homologous response regulators determine their mechanism of action]<br>
 
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Focuses on OmpR and PhoB and, as the title suggests, supports that phosphorylation of sites (particularly N-terminus of both proteins) improves affinity to bind DNA. Isolated C terminus of OmpR is insufficient to productively interact with RNA polymerase. <br>
 
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I've been told by some of the lab members that OmpR is an inner-membrane protein and therefore cannot be used for our assays. It seems that we'll have to find another protein ...<br>
 
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<br>
 
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[http://www.ncbi.nlm.nih.gov.ezp1.harvard.edu/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11325944&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA]
 
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<br> UhpB = histidine kinase protein that controls production of sugar phosphate transporter UhpT<br>
 
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UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.
 
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<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>
 
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... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I've found that UhpA resides in the cytoplasm, whereas UhpB is an inner-membrane protein. Boo.<br>
 
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More thoughts: we could potentially try to target some of these inner-membrane proteins to the outer-membrane. I don't know if this is really feasible - while we can attach the appropriate signal sequence, I'm not sure the environment would allow for correct conformation and activity of said proteins.
 
[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]
[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]

Revision as of 18:43, 20 June 2007

Stephanie Lo
Harvard College 2010

c/o Harvard College PRISE
Leverett Mail Center
28 DeWolfe Street
Cambridge, MA 02138

I have always had a passion for sciences, particularly chemistry, and hope to pursue a joint concentration in Molecular and Cellular Biology and Economics. Eventually, I plan to apply for an MD/PhD program and specialize in digestive disorders.

shlo/notebook



Harvard iGEM

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