Shehla

Hello, I'm Shehla (pronounced shell-uh, not Sheila).
====I am fifteen years old and I'm from Dyersburg, Tennessee. I came across this program by accident; an academic coach suggested I take part in a research-based summer program and we settled on this one. I'm a rising junior and science has always been my favorite subject, probably because science isn't very heavily stressed at my school and I've ended up doing a lot of learning for standardized tests and such outside of the classroom, which I guess ultimately heightened my appreciation for science. Unfortunately, I've never taken a biology class (I take my first this upcoming school year), so this will be a very new experience. I hope to attend college and end up in some sort of science-based career. I am heavily involved in all things theatre, and I've tried my hand at several different jobs, on and offstage, in productions both at my high school and at the local college. I'm looking forward to learning from everyone over these next three weeks!====

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Engineers at MIT have discovered way to make bacteria remember the results of basic logical functions they are programmed to carry out. These results are encoded into the cell's DNA and are eventually carried on for generations. The basis of these genetic circuits is that after the original stimulus, the circuit irreversibly alters itself in order to keep a record of the event. In order to make this happen engineers had to use enzymes known as recombinases. These recombinases can cut out lengths of DNA, and then flip and/or insert them. By sequentially activating the recombinases, the cell can count certain events. ======

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There are two known ways for bacteria to keep a record of all the events. The first is Ribo-regulated Transcription Cascase (RTC). RTC functions by starting and stopping transcription and translation -- the process by which cells read gene and produce proteins. After the second interruption (or third, depending on how the circuit was programmed), green fluorescent protein is made. =====

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As shown in the diagram, when the chemical arabinose is introduced to the circuit, the promoter P-BAD is turned on. This transcribes the taRNA polymerase. Originally, the // cis // -repressor (cr) inhibits the ribosome binding site (RBS), and ultimately, the T7 RNAP. However, when the P-BAD is turned on the taRNA binds to the cr, and relieves it so that the P-Ltet0-1 can bind to the RBS and the T7 RNAP produces its protein. Before the T7 RNAP can turn on the P-T7, the arabinose pulse is over and the gate (the P-BAD) that repressed the cr closes. A second pulse of cr is required to activate the taRNA and relieve the cr gates again. The previously produced T7 RNAP is used to active the P-T7, which eventually produces GFP. This is called bacterial "counting" because the bacteria can only produce GFP after two arabinose pulses. =====

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The second method of bacterial counting is DNA Invertase Cascade (DIC). Essentially, when a key chemical is present, a portion of the gene cuts itself out, flips itself, and then reinserts itself back into the genetic circuit. The protein-making process continues after each flip. After the second (or third) flip, GFP is produced.=====



The box in the diagram indicates the first section of the gene that will be flipped by the introduction of arabinose to the circuit. After the first pulse of arabinose, the first section flips itself over and reinserts itself into the circuit. The second pulse flips the second portion, and so on. As shown in the diagram, when ever a portion is flipped, the promoter (P-BAD) is turned on top, meaning it can be used, and the terminator (Term) is flipped upside, voiding its usefulness. By the third pulse of arabinose, the third portion is flipped and GFP is produced.

Scientists hope to be able to use this technology in environmental sensors, and even to better control what sort of cells stem cells will develop into.

__Bibliography__

Trafton, Anne. "Cell Circuits Remember Their History." MIT's News Office. MITnews, 10 Feb. 2013. Web. 05 July 2013.

Friedland, Ari E., Timothy K. Lu, Xiao Wang, David Shi, George Church, and James J. Collins. "Synthetic Gene Networks That Count." Ncbi.nlm.nih.gov. NCBI, 29 May 2009. Web. 5 July 2013.

Design: Air-freshening Bacteria
The main component of the air freshener Febreze is a compound called hydroxypropyl beta cyclodextrin. Cyclodextrin is an 8-sugar ringed molecule that is created as the result of an enzyma tic conversion of starch. The water released when the Febreze is sprayed partially dissolves the odor. The odor is then able to form a complex in the hole in the center of the cyclodextrin. This new complex can not bind to the smell-receptors in the nose, so the odor becomes undetectable.

However, the problem with Febreze is that each individual spray can only trap a limited number of the odor molecules. Because of this, Febreze is often over-sprayed and wasted, because people would rather spray air freshener with abandon than wait for the cyclodextrin to do its job. Not only does this mean that people are wasting Febreze and their money in vain, but this much air freshener being sprayed into the air without any odor to latch onto is bad for the environment.



There are three types of cyclodextrins, as shown above. The smallest has only 6 glucose units, and the largest -- the one used in Febreze -- has 8 glucose units. There are different enzymes, called CGTases, that degrade starch in order to produce the different cyclodextrins. To regulate which cyclodextrin is made when a CGTase degrades starch, scientists specified the different enzymes that create different cyclodextrin. The one used in Febreze is y-CGTase.

This design project would allow bacteria to create y-CGTase, the enzyme that is needed to be present to degrade starch in order to produce cyclodextrin. However, the y-CGTase would only be produced in the presence of benzylamine. This would mean that even if the air freshener was sprayed randomly, no cyclodextrin would be produced and no chemicals would be released unless an actual odor was present. Also, rather than spraying several times, a user could spray the air freshener once, and as long as benzylamine was present in the air, the bacteria would keep producing y-CGTase that would keep degrading the starch until all the benzylamine was gone. This saves both money and the environment.

As shown in the diagram, the benzylamine activates the promoter for cgtA, which in turn activates the cgtA gene. This results in the production of y-CGTase, which degrades starch to produce cyclodextrin.



The table indicates that when benzylamine is present, y-CGTase will also be prese nt, and when benzylamine is not present CGTase will not be produced.

However, there are potential problems with the device. For instance, if there are copious amounts of benzylamine in the environment, the bacteria will keep creating the CGTase enzyme. However, the starch may run out before all the benzylamine is trapped. In this case there will be CGTase in the environment as well as the benzylamine. Testing the effectiveness of the system would be relatively simple: if the device was sprayed in the presence of benzylamine and the benzylamine was gone in a rational amount of time, it could be reasonably assumed that the device worked as it was intended to.

__Bibliography__

"Benzylamine." Wikipedia. Wikimedia Foundation, 29 May 2013. Web. 10 July 2013. Biwer, A. "Enzymatic Production of Cyclodextrins - Springer." Enzymatic Production of Cyclodextrins - Springer. Springer Link, 01 Sept. 2002. Web. 10 July 2013. CL, Jeang. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, 10 Aug. 2005. Web. 10 July 2013. "Cyclodextrin Glycosyltransferase." Wikipedia. Wikimedia Foundation, 30 June 2013. Web. 10 July 2013. "Cyclodextrin." Wikipedia. Wikimedia Foundation, 07 Oct. 2013. Web. 10 July 2013. Edwards, Lin. "Bacteria Shown to 'smell' Ammonia." Bacteria Shown to 'smell' Ammonia. PhysOrg, 18 Aug. 2010. Web. 10 July 2013. Georgia, Georganto. "Expression of the CGTase Gene of Alkalophilic Bacillus No. 38-2 in Various Hosts." Onlinelibrary.wiley.com. Wiley Online Library, 1991. Web. 10 July 2013. Helmenstine, Anne M., Ph.D. "How Does Febreze Work?" About.com Chemistry. About.com, n.d. Web. 10 July 2013. Ide, Takahiro. "Patent EP1284293A2 - Gene Coding for Cyclodextrin Glucanotransferase Chiefly Producing Gamma ... - Google Patents." Google Books. Google, 19 Feb. 2003. Web. 10 July 2013. Jonathan B. "Good Question: Green Alternative to Febreze?" Apartment Therapy. Apartment Therapy, 28 Apr. 2008. Web. 10 July 2013. S., Fujiwara. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, Dec. 1992. Web. 10 July 2013. Schmid, Gerhard. "Cyclodextrin Glycosyltransferase Production: Yield Enhancement by Overexpression of Cloned Genes." Cyclodextrin Glycosyltransferase Production: Yield Enhancement by Overexpression of Cloned Genes. SciVerse, Sept. 2002. Web. 10 July 2013. T., Kaneko. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, Jan. 1990. Web. 10 July 2013. Tausch, M. W. "Sachinfo - Herstellung." Sachinfo - Herstellung. Wuppertal University, n.d. Web. 10 July 2013. Uitedehaag, Joost C.M. "The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (CGTase) as Revealed by a γ-Cyclodextrin-CGTase Complex at 1.8-Å Resolution*." The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (CGTase) as Revealed by a γ-Cyclodextrin-CGTase Complex at 1.8-Å Resolution. The Journal of Biological Chemistry, n.d. Web. 10 July 2013. "What Are Cyclodextrins?" CTD Holdings, Inc. (CTDH). CTD Holdings, Inc., n.d. Web. 10 July 2013.