Team:Baskent-Meds

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<li><a href="2012.igem.org/Team:Baskent-Meds" title="BaskentMeds main page">Home</a></li>
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<li><a href="/Team:Baskent-Meds" title="BaskentMeds main page">Home</a></li>
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<li><a href="/Team:Baskent-Meds/Notebook" title="Our Beloved Notebook!">Notebook</a></li>
<li><a href="/Team:Baskent-Meds/Notebook" title="Our Beloved Notebook!">Notebook</a></li>
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<li><a href="/Team:Baskent-Meds/Results" title="Still Working on this">Results</a></li>
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<li><a href="" title="Still Working on this">Results</a></li>
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   <p class="style8">Brainstorming Part </p>
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   <p align="center" class="style10"><strong> Transformation of <em>Escherichia coli</em> In Order To Develop </strong></p>
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  <p class="style9"> December 15th 2011, Thursday </p>
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   <p align="center" class="style10"><strong><em> Legionella pneumophila</em> Sensing Bacteria </strong></p>
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  <p>In our very first meeting, we were excited as hell. Almost none of us know how to work in the lab we didn&rsquo;t know the lab rules. We began to learn about practicing in lab and lab rules. We are not so great on the theoric basis so , we&rsquo;re gonna have to work hard and learn all about molecular genetics, bacteria and iGEM. </p>
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   <p align="center"><strong> &nbsp;</strong></p>
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   <p class="style9">22.12 .11 December 22nd 2011, Thursday</p>
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   <p> Our aim, as the team &ldquo;Baskent_Meds&rdquo;, is developing bacteria which can recognize <em>Legionella pneumophila</em> specifically at species level by legionella quorum sensing (lqs), and respond to that recognition by producing anti-Legionella peptide which is produced by some <em>Staphylococcus</em> strains. <em>lqs</em> gene locus is responsible for quorum sensing mechanism in<em> Legionella pneumophila</em>. On the <em>lqs</em> locus there are three genes; <em>lqsA</em> (encoding autoinducer synthase), <em>lqsR</em> (encoding response regulator), and <em>lqsS</em> (encoding a sensor kinase). LqsA is a pyridoxal-5&prime;-phosphate-dependent enzyme that catalyses the production of the signaling molecule 3-hydroxypentadecane-4-one (LAI-1; Legionella autoinduer-1), a novel member of &alpha;-hydroxyketone signalling molecules (Spirig et al., 2008). In this comprehensive and long-termed project, our initial objectives were; generating competent <em>E. coli</em> cells in which we are planning to clone <em>lqs</em> gene locus (the gene locus responsible for quorum sensing mechanism in<em> Legionella pneumophila</em>), and optimizing transformation procedures. pNT-1 (Tiaden et al., 2007), a pUCBM20-derivative, bearing full <em>lqs</em> gene cluster, and pTS-2 (Spirig et al., 2008), a pMMB207C-derivative expression vector, bearing <em>LqsA</em> gene were kindly provided by Prof. Dr. Hubert Hilbi. </p>
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  <p>We realized that it&rsquo;s a long road to walk. We are learning new stuff almost every day about bioengineering and it&rsquo;s exciting. We began our brainstorming meetings. Every member of our team thinks about what we can do to save the world every week! J After a week, we have lots of new ideas and we spend the rest of our time to search about if it&rsquo;s possible to carry them to the benchtop and then to real life! </p>
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   <p> Initially, <em>E. coli</em> competent cell groups (JM109, DH5&alpha; and XL1-Blue) were formed by exerting calcium chloride precipitation. pNT-1 and pTS-2 were transferred into competent <em>E. coli</em> cells using heat shock transformation method, and clones were selected with ampicillin and chloramphenicol, respectively. Plasmid isolations were performed from transformants by QIAprep Spin Miniprep Kit (Qiagen), and visualized by agarose gel electrophoresis. Our recent studies are designing our construct with BioBricks, and amplifying <em>LqsR</em> and <em>LqsS</em> by gene specific primers having restriction enzyme cut sites as small adaptors. We are going to clone these genes by digesting with these restriction enzymes followed by ligation to one of the iGEM vectors. After cloning these genes, we are planning to clone anti-Legionella peptide nucleotide sequence under <em>lqs</em> control. In order to check response of transformant <em>E. coli</em> we are planning to clone pTS-2 to BL21(DE3) <em>E. coli</em> for the constitutive expression and production of the LAI-1 without the handling of the pathogen strains in our laboratory. </p>
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   <p class="style9">December 29th 2011, Sunday </p>
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   <p> By the end of our experiments, we aim to obtain sensor <em>E. coli</em> cells which respond to <em>Legionella pneumophila </em>quorum sensing by recognizing LAI-1. Our expression construct will also enable production of the anti-Legionella peptide in response to LAI-1. Since the peptide has specific antibacterial activity on <em>Legionella</em> spp., the achievement of the project is the destruction of <em>Legionella pneumophila </em>by transformant <em>E. coli</em> sensor cells. </p>
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   <p>We were discussing about &ldquo;detecting methane gas in the air&rdquo; and we were so hopeful about it but while we were searching online we saw that another Turkish team already performed it for last year&rsquo;s iGEM competition. We were so frustrated that we felt that we would never gonna find an original, bright idea.Anyway, it looks like our brainstorming meetings will be beginning again! </p>
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  <p class="style9">05.01.12 January 5th 2011, </p>
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  <p>Happy new year! Here is some exciting and impossible ideas from our last meeting: </p>
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    <p>- Human epithelial cells making photosynthesis resulting in green men!!! (So weard) </p>
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    <p> - Bacteria sensing an approaching subject to be used in cars as a park sensor </p>
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    <p> - Dancing bacteria- we thought it as it is without a utility </p>
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    <p> - Bacteria sensing earthquake with a gene sensing pressure changes </p>
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  <p><em> &nbsp;</em>Some of them just for fun of course but we liked the other ones and we&rsquo;re gonna spend the rest of the week about making a search for them. </p>
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  <p class="style9">12.01.12 </p>
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  <p>It turns out it&rsquo;s really not that possible to create those last weeks&rsquo; ideas and some of them had already had been done by other iGEM teams. So we didn&rsquo;t stop our brainstorming and come up with even crazier ideas to our meeting! </p>
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    <p><em> &nbsp;</em>- Bacteria detecting the purity of gold and silver </p>
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    <p> - Bacteria changing color with daytime accorsding to the light spectrum from the sun, used as a sun clock </p>
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    <p> - Bacteria produced to change the irresistable smell of waste water with a rose flavour ! </p>
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  <p class="style9">19.01.12 </p>
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  <p> We spent the week by thinking about last week&rsquo;s ideas and trying to find new ones. Two people came with the same idea to this week&rsquo;s meeting; lightning moment! We decided to work with detection and destruction of legionella pnomophilia, by using its quorum sensing gene parts! That legionella disease is still killing so many people every year and it&rsquo;s especially common in our country. We couldn&rsquo;t find a an IGEM team that worked with it before but we&rsquo;re gonna look around more and more. Of course we wouldn&rsquo;t wanna do the same project . </p>
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   <p class="style9">24.01.12 </p>
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  <p>So let&rsquo;s begin to work in our lovely lab, finally! We are officially gonna study about creating an E. coli that&rsquo;s gonna find and kill legionella pnomophilia in every place it could hide. We can&rsquo;t wait to get to work and do some real experiments! </p>
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  <p class="style9">30.01.12 </p>
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  <p> Today, in our first real lab experience we created competent cells that can take our plasmids by using JM109, DH5&alpha;, XL-1Blue E. coli strains. We used calcium chloride (CaCl2) treatment while forming it. </p>
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  <p> It&rsquo;s just like building a home for our plasmids to live in happily ever after. By the way, we need to start thinking about our application to the big competition, we have big exams every month as med students, we can even forget the last date of sign in to iGEM! We need to accomplish every mission we have, and we need to do it well. </p>
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  <p class="style9">09.02.12 </p>
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  <p>This week we began with transformation experiments. We don&rsquo;t know how to do them, we are not experienced and we need to learn a lot. These first transformation experiments are very informative for every member of our group. We started with E. Coli JM109 strain. We used pUCBM20 (pNT-1) (includes <em>lqs </em>locus), pMMB207C-RBS (pTS-2) (expression vector which includes <em>lqsA</em> gene), pUSEamp(+) (includes <em>luc </em>gene), and pGEM-3Z (control) for transformation. It was very fun to do it as a group, team spirit is rising! Heat shock transformation sounds very kicka**. Our instructor told us that we may have to do it until transformation became successful. </p>
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  <p class="style9">16.02.12 </p>
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  <p>YAY! pGEM-3Z and pUSEamp(+) was successfully transformated to our E. coli strains. It took a month to have successfully transformated cells. But it turns out our plasmids that include lqs gene locus are not very likely to be transformed. </p>
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  <p>We learned so many things. We can prepare LB medium, and our component cells stays alive thanks to us, and we transform plasmids into them! What a success, even for now! </p>
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  <p class="style9">23.02.12 </p>
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   <p>We came back from our semester break and we are now officially an iGEM team. We paid our registration fee. There are so much to do, like preparing a wiki page for our team, It&rsquo;s so important and we checked out some old wikis, we should create a better one, actually why can&rsquo;t we create the best wiki page ever?</p>
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  <p class="style9"> 01.03 .12 </p>
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  <p> We now continue to do experiments. Preparing compotent cells, plasmid transformation, pcr, plasmid isolation&hellip; We&rsquo;re going pretty well. Rise and shine, Baskent_Meds! (It&rsquo;s our official team name. We loved it.) </p>
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  <p class="style9">15.06.12 </p>
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  <p>Hard and stressful times. This year&rsquo;s last comitee exam was today and now we&rsquo;re gonna have our final exam, if we couldn&rsquo;t get enough notes to pass, we&rsquo;re gonna have to repeat this year. We have to study all the time for two weeks because if we couldn&rsquo;t finish this year our project will crash down L that was our deal with our mentors for starting this in the beginning. See you in two weeks little lovely bacteria families. </p>
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  <p class="style9">04.07.12 </p>
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  <p>We had our final exam and started to work in our lab while waiting our exam results. Excitiment still goes on but we really missed that place. There are so much to do so we made a &ldquo;to do list&rdquo; and we&rsquo;re gonna finish everything we need to do by the end of july. Yeah we will! Everything goes on according to plan. </p>
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Revision as of 23:47, 7 July 2012

Baskent-Meds IGEMwiki



Transformation of Escherichia coli In Order To Develop

Legionella pneumophila Sensing Bacteria

 

Our aim, as the team “Baskent_Meds”, is developing bacteria which can recognize Legionella pneumophila specifically at species level by legionella quorum sensing (lqs), and respond to that recognition by producing anti-Legionella peptide which is produced by some Staphylococcus strains. lqs gene locus is responsible for quorum sensing mechanism in Legionella pneumophila. On the lqs locus there are three genes; lqsA (encoding autoinducer synthase), lqsR (encoding response regulator), and lqsS (encoding a sensor kinase). LqsA is a pyridoxal-5′-phosphate-dependent enzyme that catalyses the production of the signaling molecule 3-hydroxypentadecane-4-one (LAI-1; Legionella autoinduer-1), a novel member of α-hydroxyketone signalling molecules (Spirig et al., 2008). In this comprehensive and long-termed project, our initial objectives were; generating competent E. coli cells in which we are planning to clone lqs gene locus (the gene locus responsible for quorum sensing mechanism in Legionella pneumophila), and optimizing transformation procedures. pNT-1 (Tiaden et al., 2007), a pUCBM20-derivative, bearing full lqs gene cluster, and pTS-2 (Spirig et al., 2008), a pMMB207C-derivative expression vector, bearing LqsA gene were kindly provided by Prof. Dr. Hubert Hilbi.

Initially, E. coli competent cell groups (JM109, DH5α and XL1-Blue) were formed by exerting calcium chloride precipitation. pNT-1 and pTS-2 were transferred into competent E. coli cells using heat shock transformation method, and clones were selected with ampicillin and chloramphenicol, respectively. Plasmid isolations were performed from transformants by QIAprep Spin Miniprep Kit (Qiagen), and visualized by agarose gel electrophoresis. Our recent studies are designing our construct with BioBricks, and amplifying LqsR and LqsS by gene specific primers having restriction enzyme cut sites as small adaptors. We are going to clone these genes by digesting with these restriction enzymes followed by ligation to one of the iGEM vectors. After cloning these genes, we are planning to clone anti-Legionella peptide nucleotide sequence under lqs control. In order to check response of transformant E. coli we are planning to clone pTS-2 to BL21(DE3) E. coli for the constitutive expression and production of the LAI-1 without the handling of the pathogen strains in our laboratory.

By the end of our experiments, we aim to obtain sensor E. coli cells which respond to Legionella pneumophila quorum sensing by recognizing LAI-1. Our expression construct will also enable production of the anti-Legionella peptide in response to LAI-1. Since the peptide has specific antibacterial activity on Legionella spp., the achievement of the project is the destruction of Legionella pneumophila by transformant E. coli sensor cells.