Matt Gethers: Difference between revisions

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I'm currently a sophomore in course 20. When I'm behaving myself, I'm allowed to work in the [[Endy Lab]] at [http://mit.edu MIT]. I will be documenting my UROP projects [[Endy:Translation demand | here]]. I will put my 20.109 work directly below.
I'm currently a sophomore in course 20. When I'm behaving myself, I'm allowed to work in the [[Endy Lab]] at [http://mit.edu MIT]. I have links to my UROP projects and 20.109 work directly below.
 
 
==UROP Projects==
 
[[/20.380 HIV Project|20.380 HIV Project]]
 
[[/Articles of General Interest| Articles of General Interest]]
 
[[/Articles to Read|Articles to Read]]
 
[[Endy:Translation demand | Translation Demand]]
 
[http://bcanton.private.openwetware.org/wiki/Lab_Notebook/Matt/Mitochondria_Project Mitochondrial Engineering]
 
[[/CRI, Thailand| CRI Thailand]]
 
[[/Matt's Stanford Freezer Stocks|Matt's Stanford Freezer Stocks]]
 
[[/OWW Syntax| OWW Syntax]]
 
[[/Eloranta Ideas|Eloranta Ideas]]


==20.109 Work==
==20.109 Work==


===M13 Engineering Ideas===
*[[User:Mgethers/M13 Engineering Ideas|M13 Engineering Ideas]]
 
*[[User:Mgethers/2.27.06 Ligation and Transformation Data|2.27.06 Ligation and Transformation Data]]
 
*[[User:Mgethers/2.27.09 Refactoring Work|2.27.09 Refactoring Work]]
 
*[[:Image:4.3.07_Primer_Design_Team_Purple.doc|4.3.07_Primer_Design_Team_Purple.doc]]
 
*[[User:Mgethers/Research Proposal|Research Proposal]]


{| {{table}}
==Class projects==
| align="center" style="background:#f0f0f0;"|'''Gene'''
[[/20.310 Term Paper| 20.310 Term Paper]]
| align="center" style="background:#f0f0f0;"|'''Modification'''
|-
| X||Extract from gene II
|-
| II||Extract gene X
|-
| V||
|-
| VII||Separate from gene IX
|-
| III||Change the GTG to ATG Start?
|-
| VI||
|-
| I||Separate from genes IV and XI
|-
| XI||Separate from genes I and IV
|-
| IV||Separate from genes I and XI
|-
| M13 ORI 1 & 2|| Are two ORIs necessary? If so, can they be consolidated?
|-
| KanR||
|-}


==20.310 Project==


Extractions, separations, etc. include ensuring that each gene has its own promoter, RBS, terminator, and any other pertinent regulatory sequences.
<biblio>
#Galkin pmid=17449671
#Carragher pmid=3351926
#Carragher2 pmid=3351927
#Carragher3 pmid=3351930
#Turner pmid=12638863
#Wang pmid=11812133
</biblio>


In addition to separating the genes, it would also be wise to develop or utilize/modify an existing system like [[ ||Biobricks]] to build the genome so that convenient restriction sites exist between the genes so they can be easily removed or replaced.
Treatments exist for preventive and palliative treatment of sickle cell episodes, but no treatment has yet been developed to mitigate the effects of an attack once it has started. We need a way of dealing with Hbs fibers once they have polymerized. We feel we can develop a treatment for an ongoing attack by addressing the biomechanical basis of the pathology.

Latest revision as of 05:22, 18 February 2009

I'm currently a sophomore in course 20. When I'm behaving myself, I'm allowed to work in the Endy Lab at MIT. I have links to my UROP projects and 20.109 work directly below.


UROP Projects

20.380 HIV Project

Articles of General Interest

Articles to Read

Translation Demand

Mitochondrial Engineering

CRI Thailand

Matt's Stanford Freezer Stocks

OWW Syntax

Eloranta Ideas

20.109 Work

Class projects

20.310 Term Paper

20.310 Project

  1. Galkin O, Pan W, Filobelo L, Hirsch RE, Nagel RL, and Vekilov PG. Two-step mechanism of homogeneous nucleation of sickle cell hemoglobin polymers. Biophys J. 2007 Aug 1;93(3):902-13. DOI:10.1529/biophysj.106.103705 | PubMed ID:17449671 | HubMed [Galkin]
  2. Carragher B, Bluemke DA, Gabriel B, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. I. Sickle hemoglobin fibers. J Mol Biol. 1988 Jan 20;199(2):315-31. DOI:10.1016/0022-2836(88)90316-6 | PubMed ID:3351926 | HubMed [Carragher]
  3. Bluemke DA, Carragher B, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. II. Sickle hemoglobin macrofibers. J Mol Biol. 1988 Jan 20;199(2):333-48. DOI:10.1016/0022-2836(88)90317-8 | PubMed ID:3351927 | HubMed [Carragher2]
  4. Carragher B, Bluemke DA, Becker M, McDade WA, Potel MJ, and Josephs R. Structural analysis of polymers of sickle cell hemoglobin. III. Fibers within fascicles. J Mol Biol. 1988 Jan 20;199(2):383-8. DOI:10.1016/0022-2836(88)90322-1 | PubMed ID:3351930 | HubMed [Carragher3]
  5. Jones CW, Wang JC, Ferrone FA, Briehl RW, and Turner MS. Interactions between sickle hemoglobin fibers. Faraday Discuss. 2003;123:221-36; discussion 303-22, 419-21. DOI:10.1039/b207388a | PubMed ID:12638863 | HubMed [Turner]
  6. Wang JC, Turner MS, Agarwal G, Kwong S, Josephs R, Ferrone FA, and Briehl RW. Micromechanics of isolated sickle cell hemoglobin fibers: bending moduli and persistence lengths. J Mol Biol. 2002 Jan 25;315(4):601-12. DOI:10.1006/jmbi.2001.5130 | PubMed ID:11812133 | HubMed [Wang]

All Medline abstracts: PubMed | HubMed

Treatments exist for preventive and palliative treatment of sickle cell episodes, but no treatment has yet been developed to mitigate the effects of an attack once it has started. We need a way of dealing with Hbs fibers once they have polymerized. We feel we can develop a treatment for an ongoing attack by addressing the biomechanical basis of the pathology.

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