Bryan Hernandez: Difference between revisions

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[[Image:bch.jpg|thumb|100px|right|that's me]]
For information on me, see [http://thebryanhernandezgame.wordpress.com/ The Bryan Hernandez Game].
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== Bio ==
== Bio ==


*I am currently a UROP in the [[Endy Lab]] working with [[Jason Kelly]].
*I am currently an undergraduate researcher in the [[Endy Lab]] at MIT.  I am currently building and characterizing orthogonal riboregulators.  Learn more about riboregulators and the work I have done [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain here]
*MIT Class of 2009; Majoring in Mathematics and Biological Engineering.
*MIT Class of 2009; Majoring in [http://math.mit.edu/| Mathematics] and [http://web.mit.edu/be/index.htm| Biological Engineering].
*NorCal=home


== Projects ==
== Projects ==
===[[Sortostat]]===
*We are currently using strain [[Genotypes#MC4100|MC4100]] E.Coli capable of expressing CFP and YFP (Cyan Fluorescent Protein and Yellow Fluorescent Protein, contained on plasmid [http://parts.mit.edu/r/parts/partsdb/view.cgi?part_id=4659 pSB1A2] ) as these are easily distinguished between visually thereby aiding in our descriminitive assortment without relying on chemical selection.  In this way, it is less likely for cells to avoid being sorted by a genetic mutation as one might expect using an antibiotic.       
*[http://www.midgard.liu.se/~b00perst/chemostat.pdf Chemostat Theory]
*[[Sortostat/Experiments]]
*[[Sortostat/Growth Tests]]
...


'''Project Goals'''
===Construction and Characterization of Riboregulators===
A Riboregulator is a post-transcriptional regulator used in bacteria.  Its mechanism for regulation involves the occlusion of the Ribosome via a hairpin on the mRNA transcript in the 'off' state thereby preventing (or 'locking') translation of the ORF.  The 'on' state is recovered by introducing a complementary sequence (or 'key') that disrupts the hairpin on the mRNA transcript allowing the Ribosome to bind and initiate translation.  To learn more, go [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain here].


*[[Bryan Hernandez/UROP Proposal|UROP Proposal]]
*[[Bryan Hernandez/UROP Proposal|UROP Proposal]]


*[[Sortostat]]
===[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 Addressable Conjugation in Bacterial Networks]===
*Our project was to create an addressable cell-to-cell communication mechanism in e. coli.<br>
*[[IGEM:UC Berkeley/2006 | iGEM UC Berkeley]]
*[[IGEM:UC Berkeley/2006/bryans notebook|notebook]]<br>
 
===[[Sortostat]]===
The Sortostat is a microfluidic chemostat integrated with a cell sorter.  My project consists of demonstrating the sortostat's chemostat functionality, a technique rarely seen in microfluidics.


#Debug a microfluidic chemostat ([[Sortostat]]) to improve the time-varying specific selection of cell populations.  
'''Immediate Goals'''
#*Currently troubleshooting problems: i) Cell Death after 3-4 days (presumably due to oxygen depletion,) and ii) Inaccurate cell counts due to poor image processing.
*Debug all engineering-related problems with sortostat.
#Evaluate the response of populations of E.Coli cells containing engineered genetic circuits (http://parts.mit.edu) to particular selective pressures using the Sortostat.
*Demonstrate Sortostat's ability to attain chemostasis in a population of E. Coli.
*Demonstrate Sortostat's ability to sort two phenotypically different populations of E. Coli. In this case, I will be using a mixture of E. Coli expressing CFP and YFP.  
*Demostrate Sortostat's ability to select for an arbitrary population of cells that are phenotypically different from others and maintain this population at a steady state.
*[[Bryan Hernandez/UROP Proposal|UROP Proposal]]
*[http://www.midgard.liu.se/~b00perst/chemostat.pdf Chemostat Theory]
*[[Sortostat/Experiments]]
*[[Sortostat/Growth Tests]]


===Device Longevity Characterization===
-----------
It is known that mutations are more likely to occur with higher cell division rates.  Everytime a cell divides it runs the risk of making a mistake in the replication process and creating a mutant cell.  Evolution is largely in debt to this phenomonon; without mutants an organism's genome would be largely static.  However, beneficial this might be to the survival of a cell species, it poses a problem for our genetically engineered cells.  If a cell divides and mutates in the process it could "break" our engineered genetic device.  The cell will likely go on living, however, it will cease to perform its intended function.  This is an unfortunate reality of biological engineering, and, as such, we must learn the characteristics of our devices and their liklihoods of "breaking."


In order to obtain a quantitative measure of how "fast" our devices break we will first need a controlled environment. By using a chemostat we can control the rate at which cells divide enabling us to calculate the number of cell divisions that have occured over some time. Note that number of divisions is but one variable that can be used to characterize the longevity of a device. One might imagine testing other variables such as temperature or cell cycle position for example, both of which likely have an effect on the "breaking rate." 
[[Bryan Hernandez/20.109|20.109]]<br>
[[IGEM:UC Berkeley/2006/bryans -80 stocks|-80 stocks]]<br>
[[media:oligos.xls|oligos]]


Detecting when a cell's device has broken can be a challenging in it of itself.  We are using a counter selectable marker that will tell us when the cell's device ceases to perform its function.  This marker will allow cells to grow on a plate when the cell has broken.  In other words, by taking a sample of the cells from the chemostat and plating them with the counter selectable marker present, only those whose devices have broken will grow.  If all of the cell's devices are fully functional, however, we expect to see no growth on the plate.  pKSS is capable of providing this type of device in cells.
contact me at bryanh (AT) mit
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Latest revision as of 07:48, 18 May 2010

For information on me, see The Bryan Hernandez Game.

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