Team:Penn/Notebook

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                  <a href="https://2013.igem.org/Team:Penn/HumanPractices"><li>human practices</li></a>
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<div class = "textwrap">
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<a href="https://2013.igem.org/Team:Penn/Notebook"><li  class="active" style="background-color: rgb(200,200,215);">notebook</li></a>
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    <div class="section-title">notebook</div>
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        <li>Week 1</li>
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        <li>Week 2</li>
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        <li>Week 3</li>
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        <li>Week 4</li>
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        <li>Week 5</li>
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        <li>Week 6</li>
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        <li>Week 7</li>
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        <li>Week 8</li>
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        <li>Week 9</li>
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        <li>Week 10</li>
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        <li>Week 11</li>
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        <li>Week 12</li>
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        <li>Week 13</li>
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        <li>Week 14</li>
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        <li>Week 15</li>
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        <li>Week 16</li>
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        <li>Week 17</li>
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        <li>Week 18</li>
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         <h2>WEEK 1</h2>
         <h2>WEEK 1</h2>
         <div class="box">
         <div class="box">
         <h2>June 4 2013 - June 11 2013</h2>
         <h2>June 4 2013 - June 11 2013</h2>
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         <img src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/APrj2Se2i-/Lynch%20Labs%20PGFI/BE_LynchLabGroup_DSC2811.jpg?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg" class="image"/><li>4-Jun
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         <img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg"  width = "600px" class="image"/>
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             <ol>
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             <p><b>Goals:<br></b>
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            <li>Learned how to make competent cells, growing up two strains for tomorrow</li>
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<p>   This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br>
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            <li>Transformed 8 plasmids</li>
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<p><b>Achievements:<br></b>
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            <li>Determined EL222 fusion is risky but still going ahead with it</li>
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<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br>
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            <li>Linkers are totally setlled</li>
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</div>
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            <li>Found zinc finger plasmid and updated target sequence</li>
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            <li>Learned how to make tetr- mcherry fusion</li>
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            <li>Settled on 5 promoters</li>
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      </ol></li>
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      <br/>
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        <li>5-Jun
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      <ol>
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            <li>Learned how to make competent cells, testing them and then making more tomorrow</li>
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            <li>Transformed 8 plasmids again</li>
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            <li>Made primers to clone the TET-GFP reporter system, the mCherry promoter strength system,
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ready to order</li>
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            <li>Made ultramers for variable promoter blocks (and no target neg controls) – ready to order</li>
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            <li>Spilled a lot of iced tea outside, bummer</li>
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            <li>Started primers for dna binding machines</li>
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            <li>Got a handle on cas9 fusions (pun intended).</li>
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            <li>Put awesome pics in dropbox</li>
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      </ol></li>
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      <br/>
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      <li>6-Jun
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            <ol>
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            <li>Clean up dropbox</li>
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            <li>Update budget sheet with addgene and cell center orders</li>
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            <li>Finish primers for fusion</li>
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            <li>Set up plate reader for GFP and mCherry assays</li>
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            <li>run minipreps on pdawn, pdawn-mcherry, pet26b</li>
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            <li>Grow up mCherry stock</li>
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            <li>Wrote Penn iGEM on our plasmid</li>       
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      </ol></li>
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      <br/>
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          <li>7-Jun
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      <ol>
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            <li>Transform</li>
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            <ol>
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                <li>C0012 –amp/chlor (do both)</li>
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                <li>M11307 – amp/chlor (do both)</li>
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                <li>I13458 – amp/chlor (do both)</li>
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                <li>R0010 – amp/chlor (do both)</li>
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                <li>R0051 – amp</li>
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                <li>K206000 –chlor</li>
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            </ol>
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            <li>Start the LIMS and file all the strains and DNA we have made/ ordered</li>
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      </ol></li>
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      <br/>
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          <li>8-Jun</li> <ol>
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            <li>Miniprep Addgene stuff + transformations that worked</li>
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            <li>Growing up low copy plasmids in 40mLs</li>
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      </ol>          <li>Mini-prepped</li><ol>
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                <li>I9002</li>
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                <li>I13458</li>
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                <li>C0051</li>
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                <li>Pdawn-mcherry</li>
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                <li>Pdawn</li>
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                            <li>Dhsa mcherry</li>
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                <li>Pdawn dhsa</li>
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                <li>Psb1a3</li>
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                <li>JM mcherry</li>
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                <li>Pet26b</li>
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            </ol>    </div>
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             <h2>June 11 2013 - June 18 2013</h2>
             <h2>June 11 2013 - June 18 2013</h2>
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         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/-ZtRJ7Gu1U/photo-8.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
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            <li>17-Jun <ol>
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              <p><b>Goals:<br></b>
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            <li>Grow up luxI culture and grow up tetR culture </li>
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<p>   This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br>
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            <li>Sequence all of the minipreps</li>
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<p><b>Achievements:<br></b>
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            <li>Transform t9002 in psb1A3 in NEB10</li>
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<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div>
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            <li>Retransform ptetGFP to see if BL21DE3 cells are competent </li>
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            <li>Transform r0079, k081015, r0063 in NEB10 </li>
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            <li>Miniprep psb1k3</li>
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            <li>Redo dam gel with more dna </li>
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            <li>Figure out second control zfp from addgene </li>
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            <li>Figure out how to add luxR binding site to target region </li>
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            <li>Order sequencing primers for all addgene minipreps </li>
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            <li>Bisulfite converted msssi methylated c0051</li>
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      </ol></li>
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      <br/>
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      <li>18-Jun<ol>
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            <li>The bisulfite conversion was missing a negative control (bisulfite converted but unmethylated c0051) we'll need this to interperet results</li>
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            <li> Miniprep c0078, c0079 + make glycerol stocks check same plasmid with our kit </li>
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            <li>Order 13420 (second zfp)</li>
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<li>Design a way to make variable promoters more easily varied (for a biobrick so teams can use the reporter plasmid for their own nefarious reasons)</li>
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      </ol></li>
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      <li>19-Jun  <ol>
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            <li>Transform failed transformation</li>
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            <li>  Make competent DH5a && Dam- </li>
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            <li>Figure out methylation assays for promoters</li>
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            <li>Miniprep psb1A3 && all the 40mL cultures</li>
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            <li>Picked many colonies</li>
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            <li>Check pTet-gfp under blue light</li>
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      </ol></li> </div></div>
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         <h2>WEEK 3</h2>
         <h2>WEEK 3</h2>
         <div class="box"> <h2>June 18 2013 - June 25 2013</h2>
         <div class="box"> <h2>June 18 2013 - June 25 2013</h2>
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         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
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         <img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px">
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<p><b>Goals:<br></b>
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<li>21-Jun<ol>
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<p>   It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br>
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        <li>troubleshoot plux-luxI pcr</li>
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<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div>
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        <li>roubleshoot pdawn-luxI pcr</li>
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        <li>made pDawn-tetR pcr work</li>
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        <li>troubleshoot pet26b-tetR pcr</li>
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        <li>troubleshoot pDawn-GFP pcr</li>
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        <li>troubleshoot pDawn-mCherry-secretion tag pcr </li>
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        <li>miniprep growing cultures, be sure to pick only the glowing ligations </li>
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        <li>ransform the correct t9002 amp ligation - determined from gel</li>
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        <li>digested t9002 in amp and ptet gfp in amp to identify the correct ligation</li>
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        <li>all of the chosen ptet gfp ligations worked, but let's not use 5 || 13 12. troubleshoot t9002 digest</li>
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        <li>troubleshoot t9002 digest</li><ol>
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            <li>check for contamination of something (run uncut sample, sample + buffer, sample + 1
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enzyme, sample + other enzyme, sample + both enzymes)</li>
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      <br/>
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      <li>24-Jun<ol>
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        <li>Dam-/dh5a v dam methylation + dpnI && dpnII digest</li>
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        <li>Digested/ligated/transformed t9002 in amp</li>
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        <li>Get methylated biobrick sequenced</li>
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        <li>get chlor backbones sequenced</li>
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        <li>culture t9002 transformations in liquid media with i751250</li>
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        <li>mini prep stuff in the incubator</li>
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        <li>figure out the primer issues 8</li>
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        <li> Pick t9002 colonies for miniprep </li>
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      </ol></li></div>
+
     </div>
     </div>
    
    
Line 338: Line 68:
         <h2>WEEK 4</h2>
         <h2>WEEK 4</h2>
         <div class="box"> <h2>June 25 2013 - July 2 2013</h2>
         <div class="box"> <h2>June 25 2013 - July 2 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/1LlS0hsVIZ/Screen%20shot%202013-05-29%20at%2016.22.13.png?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b>
-
<ul><li>26-Jun<ol>
+
<p>   This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p>
-
        <li>Dam-/dh5a v dam methylation + dpnI && dpnII digest</li>
+
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box-->
-
        <li>Digested/ligated/transformed t9002 in amp </li>
+
-
        <li>get chlor backbones sequenced</li>
+
-
        <li>culture t9002 transformations in liquid media with i751250 </li>
+
-
        <li>mini prep stuff in the incubator</li>
+
-
        <li>figure out the primer issues</li>
+
-
        <li> Pick t9002 colonies for miniprep</li>
+
-
        <li>USER Cloning reporter plasmid </li>
+
-
      </ol></li>
+
-
<br/>
+
-
   
+
-
        <li>1-Jul<ol>
+
-
            <li>Beautiful Brady Bunch photoshoot</li>
+
-
            <li>Troubleshooted and Re-tred PCR for user ends for reporter plasmid</li>
+
-
            <li>Called IDT about pcr assembly – they said Gibson tends to work better, no mutations, all in one tub. If we must PCR assembly – add DMSO, hotstart reaction, anneal at 68-70C (we did this).</li>
+
-
            <li>Get methylated biobrick sequenced </li>
+
-
            <li>Only sequence ptet GFP 11, if verified make sure to note on LIMS that we are only using ptet GFP 11 </li>
+
-
            <li> Check if plux/luxI system is working in liquid cultures – this failed</li> <ol style =""margin-left: 50px;"">
+
-
                <li>a. Might be strain competition, need to know growth rates</li>
+
-
            </ol>
+
-
            <li>Re-suspend primers for lux amplifier </li>
+
-
            <li>Mini-prep: e0040, psb1a3, r0062</li>    
+
-
        </ol></li>
+
-
        <br/>
+
-
       
+
-
        <li>2-Jul <ol><br>
+
-
            <li>Think about application of mathylation project in e.coli</li>
+
-
            <li>Ceck if plux/GFP-psb1C3 system is working in liquid cultures
+
-
            <ol>
+
-
                <li>+/- AHL induction at 100nM</li>
+
-
                <li>Compare with ptetGFP fluorescence, normal LB fluorescence</li>
+
-
            </ol></li>
+
-
            <li>Streak zinc finger 2</li>
+
-
            <li>Grow up 44251</li>
+
-
            <li>Transform up R0062</li>
+
-
            <li>When BstuI arrives<ol>
+
-
                <li>Assay BstuI working</li>
+
-
                <li>Assay the bvluc and tale1 minipreps in dh5a, dam-, and bl21 cells with msssi and bstuI </li>
+
-
                <li>Results: BstUI is blocked by methylation, and cells don’t normally methylate</li>
+
-
            </ol></li>
+
-
            <li>Growing up t9002 in chlor and i751250 in amp for fluorescence study</li>
+
-
            <li>Investigate CHIP or other ways of determining DNA binding domain specificity </li>
+
-
        </ol></li></ul></div><!--/box-->
+
     </div>
     </div>
      
      
Line 388: Line 76:
         <h2>WEEK 5</h2>
         <h2>WEEK 5</h2>
         <div class="box"> <h2>July 2 2013 - July 9 2013</h2>
         <div class="box"> <h2>July 2 2013 - July 9 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Y5d0PLu26o/photo-7.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px">
-
             <ul><li>3-Jul<ol>
+
             <p><b>Goals:<br></b>
-
            <li>Streak zinc finger 2 </li>
+
<p>   We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project.  We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br>
-
            <li>Grow up 44251 </li>
+
<p><b>Achievements:<br></b>
-
            <li>Look into lux box being light sensitive </li>
+
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div>
-
        </ol></li>
+
-
       
+
-
        <li>4-Jul<ol>
+
-
            <li>Mini prep 44251 </li>
+
-
            <li>Pick ZFP2 colonies to grow up, throw out liquid culture in fridge </li>
+
-
        </ol></li>
+
-
       
+
-
        <li>5-Jul<ol>
+
-
            <li>Repeat BstUI assay, taking into account new controls</li>
+
-
            <li>Suspend the primers in the freezer </li>
+
-
            <li>We need to check if the origin of replications are compatible before co transformation</li>
+
-
            <li>Characterize pDawn-mcherry </li>
+
-
            <li>Practice measuring fluorescence</li>
+
-
        </ol></li>
+
-
       
+
-
       
+
-
        <li>6-Jul
+
-
      <ol>
+
-
            <li>troubleshoot ptetGFP user PCR - band was visible but too small to extract</li>
+
-
            <li>gel extract promoter fragments from USER PCR</li>
+
-
            <li>re-do USER PCR for: TetR, pTetGFP</li>
+
-
            <li>Design/check/order (Tale,Cas,ZFP)-flex-REV primers - check fwd primers</li>
+
-
        </ol></li>
+
-
 
+
-
 
+
-
      <li>8-Jul<ol>
+
-
            <li>pick up minigenes and primers from the cell center</li>
+
-
            <li>pick many colonies, colony PCR, and run results on a gel</li>
+
-
            <li>Restriction digest sgRNA with RFP for cotransformation with cas9 </li>
+
-
            <li>Find/make/buy TBE for use in TBE gels (hi-resolution)</li>
+
-
            <li>PCR assemble MsssI with USER primers</li>
+
-
            <li>get pTetGfp from pcr box and run gel</li>
+
-
            <li>PCR purify pTetGFP in eppendorf and LIMs it </li>
+
-
            <li>Fab device(s) and begin fiddling with them</li>
+
-
            <li>get t9002 seq</li>
+
-
            <li>pcr luxI, gel verify, pcr purify, restriction digest, ligate into pDawn (remember NIC), transform</li>
+
-
            <li>redo fluorescence experiment using the new cultures as well - report fluorescence per OD.  
+
-
                  do it in replicate, also use minimal media</li>
+
-
            <li>Do I751250(in pDAWN) + T9002 (in psb1a3) co-transformation</li>
+
-
            <li>MoveT9002 into psb1k3 to be compatible with pdawn - first re-transform psb1k3 then digest/ligate/transform/miniprep</li>
+
-
        </ol></li>
+
-
 
+
-
      <li>9-Jul<ol>
+
-
            <li>Make clear media for lux stuff hold on this until device</li>
+
-
            <li>Run gel to confirm MsssI PCR assembly/ before meeting-then gel extract the correct band </li>
+
-
            <li>nanodrop pTetGFPUSER/ TetR USER/ promoters (pcr products) </li>
+
-
            <li>Run gel to confirm tetR/ 4 promoters PCR</li>
+
-
            <li>Troubleshoot these USER PCR's (msssI,tetR,4 promoters): msssi</li>
+
-
            <li>Label gel and send out images and analysis (tetr/promoters)</li>
+
-
            <li>1st round DBD pcr's add his tag and flex user site</li>
+
-
            <li>grow up c0040 (TetR) glycerol stock and miniprep and then sequence</li>
+
-
            <li>redo TetR sequencing of our current miniprep just to be sure</li>
+
-
            <li>transform C0179 (lasR without LVA degradation tag) in DH5a, pick colonies, miniprep/glycerol stock</li>
+
-
            <li>miniprep T9002/amp from glyc at H10 and C0079 (grow overnight on Thurs to miniprep at same time as C0179)</li>
+
-
            <li>Redesign LuxI into pDAWN primers (NdeI, BamHI)</li>
+
-
        </ol></li></ul></div>
+
     </div>
     </div>
Line 454: Line 86:
         <h2>WEEK 6</h2>
         <h2>WEEK 6</h2>
         <div class="box"> <h2>July 10 2013 - July 17 2013</h2>
         <div class="box"> <h2>July 10 2013 - July 17 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px">
-
         <li>11-July<ol>
+
         <p><b>Goals:<br></b>
-
        <li>when we have purified pcr USER product of petgfp/tetR/ promoters - USER fuse the reporter plasmids - note: if there is only one band, then you don't even need to pcr purify</li>
+
<p>   As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br>
-
        <li>Trouble shoot 1st round DBD pcr's add his tag and flex user site</li>
+
<p><b>Achievements:<br></b>
-
        <li>We've grown up c0040 (TetR): make a glycerol stock and miniprep and then sequence-it grew in the wrong culture, currently waiting for it to regrow</li>
+
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br>
-
        <li>redo TetR sequencing of our current miniprep just to be sure</li>
+
-
        <li>redo 1st round DBD pcr's - add his tag and flex site</li>
+
-
        <li>miniprep T9002/amp from glyc at H10 and C0079 (grow overnight on Thurs)</li>
+
-
        <li>Redesign LuxI into pDAWN primers (NdeI, BamHI)</li>
+
-
        <li>use linearized psb1k3, go ahead and do the digest/ligation t9002 </li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>13-July<ol>
+
-
        <li>add in primers to MsssI PCR</li>
+
-
        <li>redo Step 1 of plan - pcr assembly MsssIwith new primers - pfu. do we have enough msssi to bother with taq?</li>
+
-
        <li>do step 7 simultaneously - ie. take some of Part 1 pot into new reaction pot with (7) primers</li>
+
-
        <li>PCR purify pfu version of 1st round DBD pcr</li>
+
-
        <li>step 3 - 2nd Round dbd PCR </li>
+
-
        <li>Step 5 of plan - PCR pet26b (50ul rxn) (ie. go ahead with zf/tale even though we need to wait up for cas9 backbone)</li>
+
-
        <li>streak lawned user fusions of reporter plasmid, grow in SOC for an hour, dilute and use new plates to get single colonies</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>14-July<ol>
+
-
        <li>trouble shoot gels of step (4) and (3) and (5). figure out which PCR to redo. which to go ahead and digest etc</li>
+
-
        <li>run tae gel with both msssi pcrs, re-run pet26b pcr, re-run cas9rd2, re-run sgRNA1 pcr, run all of TALE1rd2 for gel extraction</li>
+
-
        <li>image/analyze big TAE gel. Gel extract TALE 2.5kb</li>
+
-
        <li>step (5) - redo pet26b PCR with lower annealing temp, troubleshoot more</li>
+
-
        <li>step (3) - redo cas and TALE PCR for cleaner result. troubleshoot somehow.</li>
+
-
        <li>Gel image redo of cas, Tale, sgrna1, and pet26b. </li>
+
-
        <li>step 4 - redo sgRNA1 PCR, maybe lower annealing temp?</li>
+
-
        <li>Digest 44251 with EcoRI and XbaI</li>
+
-
        <li>Gel extract 44251 digest</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>15-July<ol>
+
-
        <li>3rd try cas9/TALE rd2 and pET26b PCR.</li>
+
-
        <li>salvage/Redo MsssI pcr</li>
+
-
        <li>redo TetR PCR from biobrick and from Mo's new miniprep</li>
+
-
        <li>grow up pet26b glycerol stock for miniprep</li>
+
-
        <li>Write Protocol: Check rep plasmids fluorescence, if there are no NIC colonies: pick 3 colonies of each to grow,</li>
+
-
        <li> Rep Plasmids: take dilutions and see if they fluoresce with tetracycine induction, use this to choose clones for glycerol stock, miniprep, and seq. </li>
+
-
        <li>grow up R0071 colony for miniprep</li>
+
-
        <li>redo the standard curve - measure tomorrow</li>
+
-
        <li>test sender receiver in M9 - growing up, need to induce tomorrow (maybe)</li>
+
-
        <li>redo testing spent media - growing up, need to induce tomorrow </li>
+
-
        <li>troubleshoot kan tranformations - WE CANT LET THE KANAMYCIN WIN!</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>16-July<ol>
+
-
        <li>run Gel of Cas/Tale rd 2 & pET26b</li>
+
-
        <li>Miniprep pet26b then continue with step (4)</li>
+
-
        <li>step4- digest/ligate (NIC)/ transform sgrna1 w/ pet26b. do simultaneously with (7)</li>
+
-
        <li>Check RP's colonies fluorescence/ NIC colonies, pick 5 to grow.</li>
+
-
        <li>Since NIC (no insert control) grew, we need to colony PCR these guys</li>
+
-
        <li> Order internal primers for MsssI</li>
+
-
        <li>Redo Cas9 and Tale rd 2 with PFU turbo cx </li>
+
-
        <li>do we need new reverse primers for Cas9 and Tale rd 2?</li>
+
-
        <li>Figure out western/SDS page to see if fusions are being expressed - send protocol. Note we have his-tagged our fusions, if that helps at all</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>17-July<ol>
+
-
        <li>run pET26b gel</li>
+
-
        <li>continue (4) - colony pcr, grow 3 correct cultures (pet26b+sgrna)</li>
+
-
        <li>Check Rep. Plasmid's fluorescence, pick 3 colonies for colony PCR if NIC is empty, 5 if NIC is small growth, start over if NIC grows well</li>
+
-
        <li>Plan tetracycline induction expt</li>
+
-
        <li>grow up T9002 chlor for miniprep</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 528: Line 98:
<h2>WEEK 7</h2>
<h2>WEEK 7</h2>
         <div class="box"> <h2>July 18 2013 - July 24 2013</h2>
         <div class="box"> <h2>July 18 2013 - July 24 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px">
-
         <li>18-July<ol>
+
         <p><b>Goals:<br></b>
-
        <li>Redo pET26b USER PCR with pfu</li>
+
<p>   This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br>
-
        <li>Call taq/Pfu company about 5.5 kb amplicon</li>
+
<p><b>Achievements:<br></b>
-
        <li>redo pTetGFP w taq/ Pfu</li>
+
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br>
-
        <li>Miniprep pet26b+sgRNA1 and send for sequencing with primers from positions E1 and E2</li>
+
-
        <li>Save pET26b+USER pcr product in 1.5 ml in misc box. Save 2 best pTetGFP+USER pcr products in 1.5ml in misc box. type up PCR protocol and send (we have to repeat this PCR for the modified pET26b+sgRNA1 now) </li>
+
-
        <li> USER Fuse new pTetGFP+TetR+5varpromoters and transform</li>
+
-
        <li>Get sgRNA in psb1A3 sequenced - use vf vr</li>
+
-
        <li>do co transformation of dcas and sgrna in psb1a3 </li>
+
-
        <li>Call NEB about M.Sssi</li>
+
-
        <li>Grow up T9002 in chlor</li>
+
-
        <li>Miniprep T9002 in chlor</li>
+
-
        <li>co transform T9002 in chlor and I751250 in AMP - waiting on t9002 miniprep</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>19-July<ol>
+
-
        <li>MsssI PCRs with new internal primers</li>
+
-
        <li>redo cas9/tale with 7.17 new (F) and (R) and pfu</li>
+
-
        <li>skype with Stef @ 3:00</li>
+
-
        <li>Order seq primers for reporter plasmids</li>
+
-
        <li>run C2,T2,Z2 gel (thermocycler count dracula)</li>
+
-
        <li>mp dcas, dcas-sgrna</li>
+
-
        <li>Design primers for M.SssI from NEB - waiting on dude from NEB on sequence</li>
+
-
        <li>PCR M.SssI from NEB  - waiting on primers</li>
+
-
        <li>PCR luxI out of v. fischeri, digest it and ligate it into pDAWN then transform ----- waiting for primers</li>
+
-
        <li>tranform rhl system (c0070, c0071, r0071)</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>22-July<ol>
+
-
        <li>grow NEB mSssI in chlor/kan,kan,chlor, and no AB LB culture tubes</li>
+
-
        <li>Re-transform ZF fusion, pET26b-MsssI ligation</li>
+
-
        <li>Order seq primers for fusion plasmids</li>
+
-
        <li>Set up time to work out bisulfite seq primers with chris asap</li>
+
-
        <li>Redo Cas9 and Tale Round 2 PCR</li>
+
-
        <li> check on pET26b/sgRNA sequencing</li>
+
-
        <li>digest, gel extract digested fragments of pEt26b and sgRNA1</li>
+
-
        <li>grow up pTETGFP for positive control for fluorescence expt</li>
+
-
        <li>grow up pET26b to replenish miniprep stock</li>
+
-
        <li>grow up r0071 (amp)</li>
+
-
        <li>digest T9002 and pSB1K3, gel extract</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>23-July<ol>
+
-
        <li>MPs: first, glycerol stock MsssI, pBAD3, R0071. then miniprep all 3 and pET26b. LIMS. Check ~7:00</li>
+
-
        <li>Miniprep/glycerol stock/send for seq: pBAD reporter plasmid. NOTE: aliquot some off first for fluorescence induction experiment. (dilute back to .05 and induce at 0.1)</li>
+
-
        <li>Miniprep pET26b to replace miniprep in spot D9</li>
+
-
        <li>Check on reporter plasmid re-transformations. Troubleshoot. Re-do transformations as necessary</li>
+
-
        <li>minprep/glycy/make competent NEB M.SssI cells depending on DC's results</li>
+
-
        <li> Troubleshoot gel extraction w Spence. Re-do digestion/gel extraction of pET26b and sgRNA1.</li>
+
-
        <li>ligate, transform pET26b and sgRNA</li>
+
-
        <li>Colony PCR ZF fusion plasmid (1 PET seq primer, 1 fusion primer) and MsssI-pet26b plasmid (1 pet seq primer, 1 MsssI primer) then grow up for miniprep/seq/glycerol stocking</li>
+
-
        <li>Digest verify pBAD miniprep</li>
+
-
        <li>Transform pBAD miniprep into DF's newly competent MsssI strain (use amp + resistance that worked best last night). and test transformation to see that competent cells work ok (psb1a3)</li>
+
-
        <li>Order Primers for COBRA</li>
+
-
        <li>Refine ATC induction protocol with Spencer</li>
+
-
        <li>inoculate M9 cultures with pBAD and with pTetGFP and begin tetracycline/ATC induction experiment. compelling data</li>
+
-
        <li>Watch SAAST demo of SDS Page ~ 1:30pm</li>
+
-
        <li>Transform last night's USER reporter plasmids </li>
+
-
        <li>Digest/Ligate/Transform pET26b with MsssI</li>
+
-
        <li>LIMS minipreps</li>
+
-
        <li>Grow up MsssI in correct antibiotics</li>
+
-
        <li>grow up more T9002 in chlor from glycyrol stock</li>
+
-
        <li>get T9002 from Brad (or re-digest), ligate reporter plasmid, transform</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>24-July<ol>
+
-
        <li>Miniprep ZF fusion plasmid , glycerol stock, send for sequencing</li>
+
-
        <li>Miniprep pET26b alongside</li>
+
-
        <li>Send pBAD3 reporter plasmid for sequencing (4 primers)</li>
+
-
        <li>send minipreps of 44249,27969, and 12612 from positions A2, G5, C10 for complete sequence verification ASAP. These are the exact minipreps used for our fusion plasmids- we ran out of the dCas miniprep, so we need more of that before it can be sentin for sequencing</li>
+
-
        <li>Transform MsssI(+) kan and its NIC - these are in Attila the HUn. Ligations, so use 3 uL and plate all of it undiluted</li>
+
-
        <li>Transform your redo of pET26b+sgRNA1, and NIC. plate all, undiluted </li>
+
-
        <li>grow up more pET26b</li>
+
-
        <li>Continue taking time points of ATC induction (ie 16 hours etc)</li>
+
-
        <li>Redo TALE round 1, then redo TALEround 2</li>
+
-
        <li>More colony PCR of ZF fusion plasmid to try to get more clones</li>
+
-
        <li>Pick Rep Plas colonies for colony PCR/ grow</li>
+
-
        <li>Re-do digestion, gel extraction, ligation of pET26b+sgRNA1 and NIC</li>
+
-
        <li>If you have more sample - re run meth diagnostic in 1.5% TBE Gel (load all!). </li>
+
-
        <li>grow up dcas9 44249 for miniprep</li>
+
-
        <li>test pBAD reporter with arabinose </li>
+
-
        <li>SDS page the zfp</li>
+
-
        <li> order miniprep columns</li>
+
-
        <li>grow up zf 4, 11 in kan. grow up pLci 10 in amp</li>
+
-
        <li>grow up pdawn</li>
+
-
        <li>miniprep T9002 in chlor</li>
+
-
        <li>redo digestion, gel extraction, ligation of T9002 and pSB1K3 and NIC</li>
+
-
        <li>redo transformation of T9002/pSB1K3 and NIC</li>
+
-
        <li>Take reading of sender experiment @ 7</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 626: Line 110:
<h2>WEEK 8</h2>
<h2>WEEK 8</h2>
         <div class="box"> <h2>July 25 2013 - July 31 2013</h2>
         <div class="box"> <h2>July 25 2013 - July 31 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px">
-
         <li>25-July<ol>
+
         <p><b>Goals:<br></b>
-
        <li>First thing, miniprep  glyc stock ZF Fusion plasmid for better yield and ASAP send out for seq again so we can have seq before meeting</li>
+
<p>   We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br>
-
        <li>miniprep dcas9 44249</li>
+
<p><b>Achievements:<br></b>
-
        <li>Miniprep/ glycerol stock ZFP4, ZFP11, and pLcI10. send for sequencing (fusion plasmids and rep plasmid)</li>
+
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br>
-
        <li>Send pBAD3 reporter plasmid for sequencing (4 primers)</li>
+
-
        <li>Transform Reporter plasmid ligations (pcr tubes in freezer) (6)</li>
+
-
        <li> Transform 3 ZF fusion plasmid into BL21 for protein expression and SDS page, also cotransform with pBAD3 </li>
+
-
        <li>PCR purify sgRNA PCR product, digest, gel extract, ligate to pET26b, transform again</li>
+
-
        <li>Redo Pet26b + MsssI Digestion / ligation with new NdeI</li>
+
-
        <li>figures from atc induction</li>
+
-
        <li>Redo dcas round 1, then redo dcas round 2</li>
+
-
        <li>confirm/order BL21 (DE3) cells ~ 7:20</li>
+
-
        <li>Design primers to amplify dCas9 in one round. design first round primers for phusion polymerase. </li>
+
-
        <li>check if other methylation sensitive enyzmes are in target sequence</li>
+
-
        <li>Design primers to add BstUI site before promoter in reporter (site directed mutagenesis)</li>
+
-
        <li>User fuse and transform new TALE with msssi and pet26b</li>
+
-
        <li>Repeat ATC induction experiment @ 1 time point (media, ptet, reporter induced at 0-1280)</li>
+
-
        <li>BstUI assay/verification for pLcI 10 </li>
+
-
        <li>try dCas9 in one round with new primers when they come in</li>
+
-
        <li>transform ab's pet26 b msssi ligation and NIC marked L in the fridge</li>
+
-
        <li>Transform Barry Canton's part</li>
+
-
        <li>redo AHL experiment with new AHL </li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>29-July<ol>
+
-
        <li>colony PCR on cultures of pet26b+sgrna & NIC using (R)sgRNA1-XhoI from H2 and pet26b(+) Fwd seq from E2 = exp band 414bp</li>
+
-
        <li>glycerol stock ZF fusion 11 in BL21 and dilute and keep culture going to use for protein expression and SDS page</li>
+
-
        <li>colony PCR on cultures 5 reporter plasmids & NIC with primers VF2 and (R) RepPlasSeq1 from i9 = exp band 1650bp</li>
+
-
        <li>Colony PCR on TALE Fusion plasmid with pET26b(+) Fwd seq from E2 and (R)MsssI2 from H8= exp band 3.5kb</li>
+
-
        <li>Glycerol stock / Miniprep the verified cultures/glycerol stock / miniprep I13202 (Canton's sender)</li>
+
-
        <li>PCR user ends onto pet26b+sgRNA1 </li>
+
-
        <li>redo colony PCR for tale, pLac, pDNAa (run gel Tuesday morning then grow up successful colonies ASAP)</li>
+
-
        <li>grow up sender/receiver cotransformation </li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>30-July<ol>
+
-
        <li>AM: Run Gel on Colony PCRS</li>
+
-
        <li>2pm: Grow cultures of 5 biobricks, NEB</li>
+
-
        <li>Dilute to .1, then induce with aTc</li>
+
-
        <li>Figure out what went wrong with TetR Sequencing - fix map</li>
+
-
        <li>BEFORE 5PM: Send new reporters, TALE, pet26b+sgrna for sequencing</li>
+
-
        <li> AM : Run Gel on pet26b+sgRNA1 PCR </li>
+
-
        <li>USER fuse and transfrom dCas9+msssi+pet26b+sgRNA, and its (NIC) - ask spencer for cannons</li>
+
-
        <li>Write protocol for protein expression based on spencers</li>
+
-
        <li>Before 5 pm: Acquire from Chow Lab / Cell center all materials for Protein Expression and SDS PAGE</li>
+
-
        <li>minprep pBAD3 (3:30 PM Tuesday)</li>
+
-
        <li>run gels of col pcr of TALE and MsssI, grow up the right clones</li>
+
-
        <li>update lims with seq results; send out type up</li>
+
-
        <li>co-transform zinc finger w pbad3 - commercial bl21. consider doing single transformations on double antibiotic plates as controls</li>
+
-
        <li>transform MsssI ligation and NIC. Transform NEB MsssI - dh5@ max eff</li>
+
-
        <li>try canton sender's media with receiver</li>
+
-
        <li>start cultures in AM</li>
+
-
        <li> Gantt Chart</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>31-July<ol>
+
-
        <li>glycerol stock and miniprep k325259, k325219, k577893, k145279</li>
+
-
        <li>re-do MsssI colony PCR - there were no bands</li>
+
-
        <li>grow up culture of NEB cells</li>
+
-
        <li>look into choosing McrA-, McrB- cells : figure out whats up with NEB's cells</li>
+
-
        <li>Co-transform ZFP11 with pBAD1 in BL21 ~500ng each. Transform just ZFP11 and just pBAD1 in BL21. Transform dcas9 fusions and NIC in DH5@max. Transform NEB Plasmid in DH5@max. </li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 696: Line 122:
<h2>WEEK 9</h2>
<h2>WEEK 9</h2>
         <div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2>
         <div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px">
-
         <li>4-Aug<ol>
+
         <p><b>Goals:<br></b>
-
        <li>glycerol stock and miniprep k206500 and Tale18+pBAD1 BL21 cotransformation</li>
+
<p>   We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br>
-
        <li>send out co trans growth curve </li>
+
<p><b>Achievements:<br></b>
-
        <li>Induction and SDS PAGE on ZF11, TALE 18, and MsssIPET12</li>
+
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br>
-
        <li>-80c lims missing coordinates</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>5-Aug<ol>
+
-
        <li>Induce M12,T + B1,L4 co trans with .1mM</li>
+
-
        <li>miniprep MsssiPet12Dh5a, ZF11dh5a, pLci4NEb10, TALE18Dh5a</li>
+
-
        <li>Grow up Glycerol Stocks of NEB+pBad1, NEB+pLcI4 for induction Experiment</li>
+
-
        <li>ZF11+pBad1 in DH5@ - use 15 uL</li>
+
-
        <li>ZF11+pBad1 in T7 express - use 20 uL</li>
+
-
        <li>ZF11+pLcI4 in DH5@</li>
+
-
        <li>ZF11+PLCI4 IN T7 express</li>
+
-
        <li>NEB MsssI + PLcI4 in ER1821 (small tubes in tip box, tape label on top of box - use 50uL)</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>7-Aug<ol>
+
-
        <li>Look through the miniprep boxes and see which minipreps are relevant to the project and have <10uL left, innoculate fresh cultures of those for miniprepping tomorrow</li>
+
-
        <li>BsoBI - methylation insensitve isochizmer of avaI</li>
+
-
        <li>order more cpg methylase</li>
+
-
        <li>Design gibson dcas9 primers</li>
+
-
        <li>make alliquots of K, A and C</li>
+
-
        <li>Make plate LIMS </li>
+
-
        <li>project abstract</li>
+
-
        <li>co transform TALE 18 + pbad1 in T7 express, TALE18+pLcI4 in T7 Express, TALE18+pBad1 in DH5a, TALE18+pLcI4 in DH5a, ZF11+pBad1 in DH5a, ZF11+pLcI4 in DH5a</li>
+
-
        <li>grow up NEB+pbad1 and NEB+pLcI4 for induction experiment</li>
+
-
        <li>meet with issadore to talk about new device</li>
+
-
        <li>work on iterating the device</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 735: Line 134:
<h2>WEEK 10</h2>
<h2>WEEK 10</h2>
         <div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2>
         <div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px"">
-
        <li>8-Aug<ol>
+
      <p><b>Goals:<br></b>
-
        <li>Do t7 induction and methylation sensitive digest for zinc finger co-trans</li>
+
<p>   We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br>
-
        <li>Induce NEBMsssI with reporters for methylation sensitive digest</li>
+
<p><b>Achievements:<br></b>
-
        <li>Prepare presentation for Orkan and Thuy</li>
+
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br>
-
        <li>Do minipreps of: pBad1, NEBMsssI in the fridge</li>
+
-
        <li>LIMS all the minipreps in random racks in the freezer</li>
+
-
        <li> pick colonies from yesterday's cotransformations</li>
+
-
        <li>transform zif 11 + pbad1 in dh5@</li>
+
-
        <li>transform zif 11 + plci4 in dh5@</li>
+
-
        <li>transform for methylation repression screen: k584000, k774007, j04450, k079050</li>
+
-
        <li>design primers to gibson assemble luxi into pdawn</li>
+
-
        <li>ligate and transform t9002 in psb1ak3</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>9-Aug<ol>
+
-
        <li>send tale18 for re-do sequencing</li>
+
-
        <li>induce TALE co trans for digestion assay. choose pLcI4 or Pbad1 and bstui or avaI respectively</li>
+
-
        <li>transform TALE18, ZF11 in T7 express to grow up tomorrow for SDS Page, glycerol stock, and miniprep</li>
+
-
        <li>redo zinc finger gel, linearizing, </li>
+
-
        <li>CUT QUORUM SENSING PROJECT</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>12-Aug<ol>
+
-
        <li>Miniprep TALE4 , new fusion clone, and send for sequencing asap</li>
+
-
        <li>Image and send out gel</li>
+
-
        <li>get mikes compatible GFP vector gorw it up</li>
+
-
        <li>Send out notes from JMIL</li>
+
-
        <li> Glycerol stock ZF11 T7, TALE 18 T7 express</li>
+
-
        <li>Is it possible the co-trans work in BL21 and not in T7 express or dh5a?-- T7express is a BL21 derivative, no reason cotrans should work in one over the other, we're moving it all to one plasmid anyway </li>
+
-
        <li>make more LB</li>
+
-
        <li>Miniprep ZF11 T7, TALE 18 T7 express</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>13-Aug<ol>
+
-
        <li>verify order of (R)MsssIGA2</li>
+
-
        <li>type up cas9 assembly protocol and go over</li>
+
-
        <li>send chris biseq primers</li>
+
-
        <li>Design way to add target to TALE and ZF and MsssI</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>14-Aug<ol>
+
-
        <li>Send out report on zinc finger linker length, if we can perfectly reproduce it or not.</li>
+
-
        <li>Learn assembly protocol from JT</li>
+
-
        <li>Send chow Timeline and what expts, by when, by whom, resource allocation</li>
+
-
        <li>Incorporate Chow and others suggestions into the powerpoint</li>
+
-
        <li>need to check TALE binding sequence</li>
+
-
        <li>SDS page </li>
+
-
        <li>check which items we need for future protocols</li>
+
-
        <li>talk to chris about 'perfect primers'</li>
+
-
        <li>move glycerol stocks in row F of 2012 box to a 2013 box, re-LIMS</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 794: Line 146:
<h2>WEEK 11</h2>
<h2>WEEK 11</h2>
         <div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2>
         <div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" >
-
        <li>15-Aug<ol>
+
      <p><b>Goals:<br></b>
-
        <li>at 4: grow up addgene dcas9, pET26b+sgRNA lig (1 or 2) for miniprepping</li>
+
<p>   We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br>
-
        <li>phosphorylate and anneal target oligos for dcas</li>
+
<p><b>Achievements:<br></b>
-
        <li>miniprep and glycerol stock pET26b in T7 (1 and 2), INBNC-mCherry in BL21 (k), intein-mCherry in BL21(amp)</li>
+
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br>
-
        <li>digest pET26b with NotI and XhoI, column purify (3X)</li>
+
-
        <li>digest pET26b+sgRNA1 with BamHI and XhoI, column purify</li>
+
-
        <li>ligate target oligos with pET26b/sgRNA backbone (for cas plasmid)</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>16-Aug<ol>
+
-
        <li>miniprep dcas9, pET26b+sgRNA</li>
+
-
        <li>phosphorylate/ligate target oligos with pET26b backbone for ZFN/TALE/M.SssI</li>
+
-
        <li>transform all ligations (TALE/ZFNM.SssI Target, Cas9 Target) in pET-26B</li>
+
-
        <li>Sort Purchase spreadsheet for Brian</li>
+
-
        <li>Use Brian's tips to refine the intro slides from the powerpoint</li>
+
-
        <li>Make detailed plan of when we are spending money, why we are spending it, and how much of it we will be spending</li>
+
-
        <li>make detailed plan of what figures we need (once plasmids are cloned), what assays to perform</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>18-Aug<ol>
+
-
        <li>glycerol stock and miniprep backbones with target sequence</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>19-Aug<ol>
+
-
        <li>PCR sequenced zinc finger fusion, M.SssI, tale fusion (so XbaI and NotI can be used to digest/ligate onto backbone) using primers (F) OnePlasInsert and (R) OnePlasInsert</li>
+
-
        <li>PCR M.SssI template that DC Gibson assembled with (F) M.SssIGA2 and (R) M.SssIGA3 - see note on JT's dcas protocol about this reverse primer</li>
+
-
        <li>PCR Cas9 from Addgene plasmid</li>
+
-
        <li>digest pET26b+target backbone with XbaI and NotI, gel extract</li>
+
-
        <li>digest pET26b/sgRNA+target backbone with NcoI and NdeI, gel extract</li>
+
-
        <li>send out new and improved video plan </li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>20-Aug<ol>
+
-
        <li>digest zf, tale, M.SssI PCR products with XbaI and NotI, column purify</li>
+
-
        <li>order new bisulfite seq  primers</li>
+
-
        <li>work on modularity of one plasmid system</li>
+
-
        <li>FILM DAY</li>
+
-
        <li>miniprep dcas and zfn target backbones, elute with water instead of buffer</li>
+
-
        <li> How else can we clone MsssI into pET26b+Target? (order primers)</li>
+
-
        <li>ligate pET26b+target (after digestion) with zf, tale PCR products (after digestion); remember the no-insert control</li>
+
-
        <li>transform pET26b+target + zf, tale ligations into DH5a</li>
+
-
        <li>Gibson assemble the digested pET26b/sgRNA+target backbone (in-progress B4, conc 12.0) with the PCR'ed cas9 and PCR'ed M.SssI that DC Gibson assembled; call NEB for instructions on how to do this</li>
+
-
        <li>transform the Gibson assembly into DH5a</li>
+
-
        <li>repeat assay of backbones+target with AvaI and BglII, using new minipreps, in vitro methylation time course</li>
+
-
        <li>confirm pet26b+Target lig5 (aka zfn target lig 5) by re-doing the col pcr on both this miniprep and normal pet26b miniprep and running only a small amount on a 2% TBE gel to get distinct bands with 30 bp difference</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>21-Aug<ol>
+
-
        <li>checking tale and ZF PCR, then digest with XbaI and NotI-HF with cutsmart, ligate to pET26b/target backbone (in-progress box B5, 11 ng/uL) then transform based on typed protocol</li>
+
-
        <li>gibson assemble and transform CAS plasmid, using backbone pET26b/sgRNA/target (in-progress B4, conc 12.0) </li>
+
-
        <li>redo miniprep of target+backbones and do methylation test on pet26b+sgran+target. Methylation asay in progress</li>
+
-
        <li>PCR MsssI, run Gel, Digest with NdeI and NotI, gel extract the larger band</li>
+
-
        <li>bk is running gel for MsssI PCR</li>
+
-
        <li>redo Target in Pet26b ligation and transformation </li>
+
-
        <li>write updated budget for brian</li>
+
-
        <li>Work on Human Practices Essay</li>
+
-
      </ol></li>
+
       </div>
       </div>
Line 860: Line 159:
<h2>WEEK 12</h2>
<h2>WEEK 12</h2>
         <div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2>
         <div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px">
-
        <li>22-Aug<ol>
+
      <p><b>Goals:<br></b>
-
        <li>check for sequencing on pet26b+sgrna+target so we can go ahead and gibson assemble and transform with cas-msssI</li>
+
<p>   Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br>
-
        <li>gibson assemble and transform CAS plasmid, using backbone pET26b/sgRNA/target (in-progress B4, conc 12.0) </li>
+
<p><b>Achievements:<br></b>
-
        <li>Do minipreps, digest methylation time course with xbai and avai, do methylation assay with controls</li>
+
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br>
-
        <li>Digest MsssI pcr producrt with ndei and noti, gel extract the larger band</li>
+
-
        <li>Digest pet26b+target with ndei and noti for msssi ligation, gel extract larger band</li>
+
-
        <li>make fresh buffer PE </li>
+
-
        <li>re-do making pet26b+target; look up if overhangs are stable and decide about using backbone digest or re-doing digest and then ligate and transform</li>
+
-
        <li>Fundraise for next year's team</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>23-Aug<ol>
+
-
        <li>check for sequencing on pet26b+sgrna+target so we can go ahead and gibson assemble and transform with cas-msssI</li>
+
-
        <li>gibson assemble (in-progress C7) and transform CAS plasmid into NEB10</li>
+
-
        <li>Send out methylation time course results</li>
+
-
        <li>Digest MsssI pcr producrt with ndei and notiHF, gel extract the larger band</li>
+
-
        <li>bisfulite primers = look at virtual gels, Go over with spencer or mike in AM, send for approval</li>
+
-
        <li>re-arrange the inprogress box</li>
+
-
        <li>Digest pet26b+target with ndei and noti for msssi ligation, gel extract larger band</li>
+
-
        <li>colony PCR on pet26b+target with new (F)Target2Primer and pet26brevseq, include pet26b as control</li>
+
-
        <li>prepare finalized plasmid maps - PST backbone. cas with his tag from (R)MsssIGA2</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>24-Aug<ol>
+
-
        <li>colony PCR the Gibson assembled cas plasmid, grow up colonies - no colonies :\</li>
+
-
        <li>miniprep pet26bsgrnaTarget#3 and tell josh the concentration</li>
+
-
        <li>ligate MsssI and PST3, transform</li>
+
-
        <li>miniprep TALE and ZF</li>
+
-
        <li>Digest TALE, ZF and backbone pet26b+sgRNA1+Target ligation 3 (aka PST3) with NcoIHF and XbaI. Gel extract, ligate, transform</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>25-Aug<ol>
+
-
        <li>gibson assemble (in-progress C7) and transform CAS plasmid into NEB10</li>
+
-
        <li>Miniprep Pet26b+sgrna+target 3 (PST3)  - borrow column or save culture in fridge for Miniprep tomorrow</li>
+
-
        <li>digest PST3 with NcoIHF and XbaI, gel extract</li>
+
-
        <li>Ligate your PST3 with Tale, and with ZF, and NIC, and transform into NEB10</li>
+
-
        <li>Digest PST3 with NdeI and NcoIHF, column purify</li>
+
-
        <li>Ligate this PST3 with MsssI in progress box, and NIC, and transform </li>
+
-
        <li>Order bisulfite primers for ON target</li>
+
-
        <li>redo outro voice over</li>
+
-
        <li>prepare "notebook" pages for website</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 910: Line 171:
<h2>WEEK 13</h2>
<h2>WEEK 13</h2>
         <div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2>
         <div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px">
-
         <li>1-Sep<ol>
+
         <p><b>Goals:<br></b>
-
        <li>COBRA for ON target pilot attempt - methylated and unmethylated</li>
+
<p>   Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br>
-
        <li>Order BiSeq primers for OFF target </li>
+
<p><b>Achievements:<br></b>
-
        <li>replate T7 transformations of ZF and TALE clones</li>
+
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br>
-
        <li>Transform your overnight ligation mix of MsssI and NIC, plate all on full plates</li>
+
-
        <li>Prepare ZF and TALE sequencing of all clones for early submission Tuesday AM</li>
+
-
        <li> Gibson assemble Cas plasmid</li>
+
-
        <li>Order primers for cloning msssi biobricks</li>
+
-
        <li>Submit reporter biobricks</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>2-Sep<ol>
+
-
        <li>Col PCR MsssI and Gibson Assembly</li>
+
-
        <li>COBRA for ON target pilot attempt - methylated and unmethylated</li>
+
-
        <li>need to get TaqÃ¥I enzyme for COBRA @ target site. waiting response from NEB</li>
+
-
        <li>write up cobra workflow</li>
+
-
        <li>get brian to sign travel grant</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>3-Sep<ol>
+
-
        <li>col pcr gibson assembly</li>
+
-
        <li>send Cas clone1 for seq</li>
+
-
      </ol></li>
+
-
</br>
+
-
<li>4-Sep<ol>
+
-
        <li>Clone msssi biobrick with your primers</li>
+
-
        <li>clone msssi in pst3 backbone</li>
+
-
        <li>methylation time course - GELS FOR PENN APPS</li>
+
-
        <li>attempt digestion of tale , zf clones</li>
+
-
        <li>zf target site missing?</li>
+
-
        <li>do COBRA with taqI enzyme and XhoI enzyme </li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 950: Line 183:
<h2>WEEK 14</h2>
<h2>WEEK 14</h2>
         <div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2>
         <div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px"">
-
         <li>5-Sep<ol>
+
         <p><b>Goals:<br></b>
-
        <li>poster presentation 5-630 bodek lounge tues 9/10; meeting with brian next tues 8am?; waiting to hear from orkan and david gdula.</li>
+
<p>   Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br>
-
        <li>consider alt tale binding sites implications for meth digest</li>
+
<p><b>Achievements:<br></b>
-
        <li>test OFF target cobra primers</li>
+
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br>
-
        <li>call NEB about bisulfite converting plasmid</li>
+
-
        <li>send fusions for seq</li>
+
-
        <li>col pcr on biobricks </li>
+
-
        <li>cas col pcr with proper pos ctrl</li>
+
-
        <li>essay for bioethics journal</li>
+
-
        <li>prep interview questions</li>
+
-
        <li>Mack Institute blurb</li>
+
-
        <li>travel grant proposal</li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>6-Sep<ol>
+
-
        <li>look at danny's triplicate gels and figure out what s what and redo the graphs</li>
+
-
        <li>run the gel</li>
+
-
        <li>call neb and pick up the thing from chris</li>
+
-
        <li>CAS</li>
+
-
        <li>use phosphatase on msssi ligation</li>
+
-
        <li>cobra- digest off target site and get bisulfite kit from chris to see if we can get more complete bisulfite data</li>
+
-
        <li>order columns/xbaI</li>
+
-
        <li>wiki</li>
+
-
        <li>work on magellin</li>
+
-
        <li>Compare ON primers 3&6 with ON 1&5 for Cobra</li>
+
-
        <li>PCR OFF target with 3&7 in 50uL for purification and digestion</li>
+
-
        <li>Digest OFF from 3&7 with TaqI and BamHIHF</li>
+
-
        <li>presentation for chow</li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 987: Line 195:
<h2>WEEK 15</h2>
<h2>WEEK 15</h2>
         <div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2>
         <div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"">
-
        <li>18-Sep<ol>
+
      <p><b>Goals:<br></b>
-
        <li>write up websites for biobricks, grow up cultures</li>
+
<p>   We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br>
-
        <li>miniprep biobricks (psb1c3 msssI's and reporters) and go to postoffice</li>
+
<p><b>Achievements:<br></b>
-
        <li>Digest out RFP (wonders f10); gel extract it **alongside gel fragment of the backbone In Progress F1** and ligate to PST BB backbone</li>
+
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br>
-
        <li>Digest MsssI and MsssILinker (in progress box) and ligate to PST BB backbone</li>
+
-
        <li>Col PCR new ZF target with (F)Target2Primer *note exact primer name</li>
+
-
        <li>Digest and ligate new ZF target backbone with ZF fusion </li>
+
-
        <li>Digest and Ligate PST3 with MsssI</li>
+
-
        <li>Run gradient on biseq primers</li>
+
-
        <li>Work with MO- who is digesting MsssI and MsssI linker (in progress box) and ligate to PSB1C3 because that colony pcr was sketchy</li>
+
-
        <li>animation</li>
+
-
        <li>Essay</li>
+
-
        </ol></li>
+
       </div>
       </div>
     </div>
     </div>
Line 1,008: Line 207:
<h2>WEEK 16</h2>
<h2>WEEK 16</h2>
         <div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2>
         <div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px">
-
         <li>19-Sep<ol>
+
         <p><b>Goals:<br></b>
-
        <li></li>
+
<p>   We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br>
-
        <li></li>
+
<p><b>Achievements:<br></b>
-
        <li></li>
+
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br>
-
        <li></li>
+
-
        <li></li>
+
-
        <li> </li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        </ol></li>
+
-
</br>
+
-
<li>25-Sep<ol>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
      </ol></li>
+
       </div>
       </div>
     </div>
     </div>
<div>
<div>
 +
<h2>WEEK 17</h2>
<h2>WEEK 17</h2>
         <div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2>
         <div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2>
-
         <img class="image" src="https://dl.dropboxusercontent.com/sh/h4cxid18rzzjgan/Yn0SK0Y0-7/snap.JPG?token_hash=AAGlfzG2xZpKrOTI8pyH02EbYxY1vK3QLUWKsWuYdaPbYg">
+
         <img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px">
-
        <li>26-Sep<ol>
+
      <p><b>Goals:<br></b>
-
        <li></li>
+
<p>   In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br>
-
        <li></li>
+
<p><b>Achievements:<br></b>
-
        <li></li>
+
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br>
-
        <li></li>
+
-
        <li></li>
+
-
        <li> </li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
        <li></li>
+
-
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<h2>WEEK 18</h2>
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<h2>WEEK 18 (North America Regionals)</h2>
         <div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2>
         <div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2>
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        <li>3-Oct<ol>
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      <p><b>Goals:<br></b>
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<p>   We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br>
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<p><b>Achievements:<br></b>
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        <li></li>
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<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br>
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<h2>WEEK 19 </h2>
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         <div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2>
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      <p><b>Goals: <br></b>
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<p>  We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br>
 +
<p><b>Achievements:  <br></b>
 +
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br>
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<h2>WEEK 20</h2>
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        <div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2>
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        <img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px">
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 +
      <p><b>Goals:<br></b>
 +
<p>  This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br>
 +
<p><b>Achievements:<br></b>
 +
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br>
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<h2>WEEK 21</h2>
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        <div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2>
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        <img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px">
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      <p><b>Goals:<br></b>
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<p>  Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week.  </p><br>
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<p><b>Achievements:<br></b>
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<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree.  </p><br>
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<center><a href = "https://2013.igem.org/Team:Penn"> Home  </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a>
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Penn iGem &copy; 2013
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Latest revision as of 02:08, 29 October 2013

Penn iGEM

WEEK 1

June 4 2013 - June 11 2013

Goals:

This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.


Achievements:

We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.


WEEK 2

June 11 2013 - June 18 2013

Goals:

This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.


Achievements:

We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time.


WEEK 3

June 18 2013 - June 25 2013

Goals:

It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.

Achievements:

This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.


WEEK 4

June 25 2013 - July 2 2013

Goals:

This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.

Achievements:

We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave.


WEEK 5

July 2 2013 - July 9 2013

Goals:

We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project.


Achievements:

We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.


WEEK 6

July 10 2013 - July 17 2013

Goals:

As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation.


Achievements:

We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.


WEEK 7

July 18 2013 - July 24 2013

Goals:

This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.


Achievements:

We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before.


WEEK 8

July 25 2013 - July 31 2013

Goals:

We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.


Achievements:

We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc.


WEEK 9

Aug 1 2013 - Aug 7 2013

Goals:

We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction.


Achievements:

We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year.


WEEK 10

Aug 8 2013 - Aug 14 2013

Goals:

We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols.


Achievements:

We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.


WEEK 11

Aug 15 2013 - Aug 21 2013

Goals:

We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.


Achievements:

We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.


WEEK 12

Aug 22 2013 - Aug 28 2013

Goals:

Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.


Achievements:

We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.


WEEK 13

Aug 29 2013 - Sep 4 2013

Goals:

Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.


Achievements:

We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE.


WEEK 14

Sep 5 2013 - Sep 11 2013

Goals:

Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.


Achievements:

During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week.


WEEK 15

Sep 12 2013 - Sep 18 2013

Goals:

We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.


Achievements:

We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well.


WEEK 16

Sep 19 2013 - Sep 25 2013

Goals:

We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.


Achievements:

We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results.


WEEK 17

Sep 26 2013 - Oct 2 2013

Goals:

In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.


Achievements:

We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree.


WEEK 18 (North America Regionals)

Oct 3 2013 - Oct 9 2013

Goals:

We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month.


Achievements:

We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling.


WEEK 19

Oct 10 2013 - Oct 16 2013

Goals:

We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase.


Achievements:

We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results.


WEEK 20

Oct 17 2013 - Oct 23 2013

Goals:

This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks.


Achievements:

This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year.


WEEK 21

Oct 24 2013 - Oct 30 2013

Goals:

Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week.


Achievements:

This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree.


Retrieved from "http://2013.igem.org/Team:Penn/Notebook"