Team:Toronto/Team

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<img src="https://static.igem.org/mediawiki/2013/7/77/PAPERRRRR.png" alt="paper" width="1100" height="1941" /></div>
 
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<h6><font color="#edebcc"><p style = "text-align:center; font-size:35px;"><b>BIOFILM ENGINEERING</b></p><br/>
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<p style = "font-size:17px;"><b><u>What are biofilms?</u></b><br/>
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<th><img src="https://static.igem.org/mediawiki/2013/4/46/Boris.png"align=center></th>
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Biofilms are communities of microbes where the cells aggregate onto a surface, and are bound together by secreted extramembranous materials made of a mixture of specialised carbohydrates and extramembrane proteins. The special environment in the biofilm allows cells to survive harsher environments.<br/><br/>
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<th><p style = "font-size:17px;"><b><u>Boris Dyakov</u></b><br/>Boris is a 3rd year student studying cell and molecular biology. He was our lab manager this summer and was too busy doing work to really put much thought into this section. His hobbies include cooking and repairing bikes.  
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<b><u>What is the “biofilm response”?</u></b><br/>
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Bacterial cells can exist in multiple physiological states, switching between them as a direct consequence of environmental factors. Common ones include heat shock, nutrient (carbohydrate or amino acid) starvation, metal micronutrient starvation, etc.<br/>
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Fun fact: he has his pilots license!</th>
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Gene expression in each of these physiological states is mediated by the changing the sigma (<tt>σ</tt>) factor involved in transcript synthesis. Each <tt>σ</tt> factor has its own consensus sequence; the <tt>σ</tt> factor on the RNA polymerase recognises and binds to promoter regions. When a <tt>σ</tt> factor is active, its effect is to shift which fractions of the genome are preferably expressed, because of the different promoter recognition consensus sequences. The sigma factor that is involved in the stationary phase (i.e. no motility, no reproduction) of E. coli strains is the <tt>σ<sub>s</sub></tt> factor. It directs the expression of genes necessary to induce biofilm and aggregation behaviour are a subset of those genes whose promoters are recognised by the <tt>σ<sub>s</sub></tt> factor.<br/><br/>
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<b><u>Modulating and Measuring the Biofilm Response</u></b><br/>
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The focus of our project is to characterise the physical and chemical manifestations of the biofilm response for cells in which key genes for both structural and regulatory aspects of the biofilm response  have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardised battery of assays, so that the cell can be studied as an entire system, as opposed to the methods used in past literature that only measured the effects of genetic engineering on just one manifestation of the biofilm response. </br><br/>
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<b><u>Defect in the BioBrick Paradigm</u></b><br/>
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Due to the mechanics of the BioBrick Assembly method, the BioBrick paradigm lends itself to the construction of gene parts that are necessarily additive. Consequently, apart from using “additive” exotic methods such as RNAi to disrupt gene expression to achieve functional gene silencing, gene deletions from a genome (negative “additive” modifications) simply cannot be submitted to the Gene Parts Registry.
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The spectacular success of the metabolic engineering field eminently shows the defect in this paradigm. Successful engineering of model organisms is based on using chemical kinetics and metabolic networks, where metabolite flux is directed by both gene up-regulation and deletion. (Insert examples here...)
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Since deletions from a cell's genome is another means to engineering the cell as a system, we have also characterised the biofilm response of a set of knockout E. coli. Unfortunately, these systems cannot be submitted to the BioBrick registry because they do not conform to the BioBrick paradigm, an issue we hope that the iGEM competition can address.
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<td><p style = "font-size:17px;"><b><u>Adam Komorowski</u></b><br/>Adam is currently completing his third year; he is a double major in Immunology, as well as Molecular Genetics and Microbiology. This is Adam's second year with the UofT iGEM team, in which he filled the role of President.</td>
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<td><img src="https://static.igem.org/mediawiki/2013/c/c4/Adamtoronto.png" align="right" width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/4/47/Micheal.png" width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Michael Yu</u></b><br/>In biological sciences I am interested in <i>ab initio</i> protein structure prediction, because it is a hard problem that hasn’t been fully solved and I like hard problems. At home I like to cook and not do the dishes afterwards, because the first is tasty and the second is boring so I procrastinate. When I get bored I either read a book, or go on my computer to build ahistorical countries in the historical game Europa Universalis 4, or just go buy beer.</td>
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<td><p style = "font-size:17px;"><b><u>Monica Akula</u></b><br/>I am a neuroscience major with a 4.3 GPA. My interests include mathematics and genetics. In my barely existent spare time I do slave labour for others.</td>
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<td><img src="https://static.igem.org/mediawiki/2013/c/c8/Monica.png"width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/d/de/AL.png"width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Alejandro Duque</u></b><br/>Third year undergraduate majoring in both Biotechnology and Molecular Genetics & Microbiology. First year involved in the iGEM Toronto team. Focused on the risk assessment and biosafety of our biofilm project.</td>
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<td><p style = "font-size:17px;"><b><u>Cathy Su</u></b><br/>I am a biophysics specialist who is especially interested in working on epigenetics. I'd like to cure myopia within the next quarter century.</td>
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<td><img src="https://static.igem.org/mediawiki/2013/0/01/Cathy.png"width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/c/ca/Seemi.png"width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Seemi </u></b><br/>Seemi is completing her second year as a Global Health and Molecular Genetics and Microbiology major, as well as a Psychology minor.</td>
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<td><p style = "font-size:17px;"><b><u>Abdiwahab Moalim</u></b><br/>I am a third year undergraduate student in Cell Biology and Physiology. In science, my interests lie in many fields but especially in the spaces between them. In fact I have just reached a breakthrough in my super top secret research bridging all fields that will change the world and I can't wait to tell you! But hey, look over there - fourth sentence!</td>
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<td><img src="https://static.igem.org/mediawiki/2013/1/14/Abdiiiiii.png"width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/7/71/Samantha.png"width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Samantha Chow</u></b><br/>¯\_(ツ)_/¯</td>
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<td><p style = "font-size:17px;"><b><u>Julianne Lee</u></b><br/>¯\_(ツ)_/¯</td>
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<td><img src="https://static.igem.org/mediawiki/2013/3/3d/Julianneeee.png"width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/a/a3/Li_Ke.png"width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Li Ke Liu</u></b><br/>¯\_(ツ)_/¯</td>
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<td><p style = "font-size:17px;"><b><u>Bowen Le</u></b><br/>¯\_(ツ)_/¯</td>
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<td><img src="https://static.igem.org/mediawiki/2013/a/a6/Bowwen.png"width="430px" height="432px"></td>
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<td><img src="https://static.igem.org/mediawiki/2013/b/ba/BorisS.png"width="430px" height="432px"></td>
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<td><p style = "font-size:17px;"><b><u>Boris Steipe</u></b><br/>Boris Steipe has been the principal UofT iGEM Faculty Advisor since 2011. He is an Associate Professor at the University of Toronto, and is cross-appointed to the Departments of Biochemistry and Molecular Genetics and Microbiology. He serves as the director of the Specialist programme in Bioinformatics and Computational Biology. Boris completed both his MD and PhD at the Ludwig-Maximilians-Universität in München (Munich), Germany. Boris' post-doctoral work was completed under Nobel laureate Robert Huber at the Max-Planck-Institut für Biochemie in Martinsreid, Germany.
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<td><p style = "font-size:17px;"><b><u>Kristina Han</u></b><br/>Kristina Han is the principal graduate student advisor for the UofT iGEM team. Kristina is completing her PhD at the University of Toronto in the lab of Prof. James Rini at the Department of Biochemistry. The award for Outstanding TA was given to Kristina by the Department of Biochemistry in 2012.</td>
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<td><img src="https://static.igem.org/mediawiki/2013/0/0d/Kristinnna.png"width="430px" height="432px"></td>
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Latest revision as of 00:00, 31 January 2014

Boris Dyakov
Boris is a 3rd year student studying cell and molecular biology. He was our lab manager this summer and was too busy doing work to really put much thought into this section. His hobbies include cooking and repairing bikes.
Fun fact: he has his pilots license!

Adam Komorowski
Adam is currently completing his third year; he is a double major in Immunology, as well as Molecular Genetics and Microbiology. This is Adam's second year with the UofT iGEM team, in which he filled the role of President.

Michael Yu
In biological sciences I am interested in ab initio protein structure prediction, because it is a hard problem that hasn’t been fully solved and I like hard problems. At home I like to cook and not do the dishes afterwards, because the first is tasty and the second is boring so I procrastinate. When I get bored I either read a book, or go on my computer to build ahistorical countries in the historical game Europa Universalis 4, or just go buy beer.

Monica Akula
I am a neuroscience major with a 4.3 GPA. My interests include mathematics and genetics. In my barely existent spare time I do slave labour for others.

Alejandro Duque
Third year undergraduate majoring in both Biotechnology and Molecular Genetics & Microbiology. First year involved in the iGEM Toronto team. Focused on the risk assessment and biosafety of our biofilm project.

Cathy Su
I am a biophysics specialist who is especially interested in working on epigenetics. I'd like to cure myopia within the next quarter century.

Seemi
Seemi is completing her second year as a Global Health and Molecular Genetics and Microbiology major, as well as a Psychology minor.

Abdiwahab Moalim
I am a third year undergraduate student in Cell Biology and Physiology. In science, my interests lie in many fields but especially in the spaces between them. In fact I have just reached a breakthrough in my super top secret research bridging all fields that will change the world and I can't wait to tell you! But hey, look over there - fourth sentence!

Samantha Chow
¯\_(ツ)_/¯

Julianne Lee
¯\_(ツ)_/¯

Li Ke Liu
¯\_(ツ)_/¯

Bowen Le
¯\_(ツ)_/¯

Boris Steipe
Boris Steipe has been the principal UofT iGEM Faculty Advisor since 2011. He is an Associate Professor at the University of Toronto, and is cross-appointed to the Departments of Biochemistry and Molecular Genetics and Microbiology. He serves as the director of the Specialist programme in Bioinformatics and Computational Biology. Boris completed both his MD and PhD at the Ludwig-Maximilians-Universität in München (Munich), Germany. Boris' post-doctoral work was completed under Nobel laureate Robert Huber at the Max-Planck-Institut für Biochemie in Martinsreid, Germany.

Kristina Han
Kristina Han is the principal graduate student advisor for the UofT iGEM team. Kristina is completing her PhD at the University of Toronto in the lab of Prof. James Rini at the Department of Biochemistry. The award for Outstanding TA was given to Kristina by the Department of Biochemistry in 2012.



















































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