Team:Toronto/Team

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<th><img src="https://static.igem.org/mediawiki/2013/4/46/Boris.png"align=center></th>
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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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Fun fact: he has his pilots license!</th>
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<h7><font color=black><p style = "text-align:center; font-size:35px;"><b>BIOFILM ENGINEERING</b></p><br/>
 
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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><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><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/2013/7/71/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/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/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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<p style = "font-size:17px;"><b><u>What are biofilms?</u></b><br/>
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Biofilms are communities of microbes where the cells are in an aggregate on a surface, bound together by extra-membrane material made of a mixture of specialized carbohydrates and extra-membrane proteins. The special environment in the biofilm allows cells to survive harsher environments.<br/><br/>
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<b><u>What is the “biofilm response”?</u></b><br/>
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Bacteria cells can exist in multiple physiological states, which are caused by environmental factors. Common ones include heat shock, nutrient (carbohydrate or amino acid) starvation, metal micronutrient starvation, etc.<br/>
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Gene expression in each of these physiological states is mediated by the changing the sigma factor involved in transcript synthesis. Each sigma factor has its own consensus sequence; the sigma factor on the RNA polymerase recognizes and binds to promoter regions. When a sigma 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 σS factor. It directs the expression of genes necessary to induce biofilm and aggregation behavior are a subset of those genes whose promoters are recognized by the σSfactor.<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 characterize the physical and chemical manifestations of the biofilm response in cells where key genes in the biofilm response (for both structural and regulatory aspects) have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardized 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. </br><br/>
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<b><u>Defect in the Biobrick Paradigm</u></b><br/>
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The Biobrick paradigm is that gene parts are necessarily additive, due to the mechanics of the Biobrick Assembly method. Consequently, apart from by 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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<b><u>Modulating and Measuring the Biofilm Response</u></b><br/>
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The focus of our project is to characterize the physical and chemical manifestations of the biofilm response in cells where key genes in the biofilm response (for both structural and regulatory aspects) have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardized 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. </br><br/>
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<b><u>Defect in the Biobrick Paradigm</u></b><br/>
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The Biobrick paradigm is that gene parts are necessarily additive, due to the mechanics of the Biobrick Assembly method. Consequently, apart from by 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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<b><u>Modulating and Measuring the Biofilm Response</u></b><br/>
+
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The focus of our project is to characterize the physical and chemical manifestations of the biofilm response in cells where key genes in the biofilm response (for both structural and regulatory aspects) have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardized 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. </br><br/>
+
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<b><u>Defect in the Biobrick Paradigm</u></b><br/>
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The Biobrick paradigm is that gene parts are necessarily additive, due to the mechanics of the Biobrick Assembly method. Consequently, apart from by 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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<b><u>Modulating and Measuring the Biofilm Response</u></b><br/>
+
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The focus of our project is to characterize the physical and chemical manifestations of the biofilm response in cells where key genes in the biofilm response (for both structural and regulatory aspects) have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardized 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. </br><br/>
+
-
<b><u>Defect in the Biobrick Paradigm</u></b><br/>
+
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The Biobrick paradigm is that gene parts are necessarily additive, due to the mechanics of the Biobrick Assembly method. Consequently, apart from by 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.
+
-
<b><u>Modulating and Measuring the Biofilm Response</u></b><br/>
+
-
The focus of our project is to characterize the physical and chemical manifestations of the biofilm response in cells where key genes in the biofilm response (for both structural and regulatory aspects) have been either overexpressed or deleted. The numerous assays that need to be done drove us to develop a standardized 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. </br><br/>
+
-
<b><u>Defect in the Biobrick Paradigm</u></b><br/>
+
-
The Biobrick paradigm is that gene parts are necessarily additive, due to the mechanics of the Biobrick Assembly method. Consequently, apart from by 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 characterized 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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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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