UCLAiGEM:Notebook/Organization/2015/04/17

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"}ol.lst-kix_eomk9agl4por-3.start{counter-reset:lst-ctn-kix_eomk9agl4por-3 0}.lst-kix_eomk9agl4por-7>li{counter-increment:lst-ctn-kix_eomk9agl4por-7}ol.lst-kix_pumaoo38l22v-0.start{counter-reset:lst-ctn-kix_pumaoo38l22v-0 0}ol{margin:0;padding:0}.c8{widows:2;orphans:2;text-indent:36pt;height:11pt;direction:ltr;margin-left:36pt}.c2{padding-left:0pt;widows:2;orphans:2;direction:ltr;margin-left:108pt}.c0{padding-left:0pt;widows:2;orphans:2;direction:ltr;margin-left:36pt}.c5{padding-left:0pt;widows:2;orphans:2;direction:ltr;margin-left:72pt}.c4{padding-left:0pt;widows:2;orphans:2;direction:ltr;margin-left:144pt}.c7{padding-left:0pt;widows:2;orphans:2;direction:ltr;margin-left:180pt}.c9{widows:2;orphans:2;height:11pt;direction:ltr}.c10{max-width:468pt;background-color:#ffffff;padding:72pt 72pt 72pt 72pt}.c11{widows:2;orphans:2;direction:ltr}.c1{margin:0;padding:0}.c6{color:#1155cc;text-decoration:underline}.c12{color:inherit;text-decoration:inherit}.c13{height:11pt}.c3{font-weight:bold}.title{widows:2;padding-top:0pt;line-height:1.15;orphans:2;text-align:left;color:#000000;font-size:21pt;font-family:"Trebuchet MS";padding-bottom:0pt;page-break-after:avoid}.subtitle{widows:2;padding-top:0pt;line-height:1.15;orphans:2;text-align:left;color:#666666;font-style:italic;font-size:13pt;font-family:"Trebuchet MS";padding-bottom:10pt;page-break-after:avoid}li{color:#000000;font-size:11pt;font-family:"Arial"}p{color:#000000;font-size:11pt;margin:0;font-family:"Arial"}h1{widows:2;padding-top:10pt;line-height:1.15;orphans:2;text-align:left;color:#000000;font-size:16pt;font-family:"Trebuchet MS";padding-bottom:0pt;page-break-after:avoid}h2{widows:2;padding-top:10pt;line-height:1.15;orphans:2;text-align:left;color:#000000;font-size:13pt;font-family:"Trebuchet MS";font-weight:bold;padding-bottom:0pt;page-break-after:avoid}h3{widows:2;padding-top:8pt;line-height:1.15;orphans:2;text-align:left;color:#666666;font-size:12pt;font-family:"Trebuchet MS";font-weight:bold;padding-bottom:0pt;page-break-after:avoid}h4{widows:2;padding-top:8pt;line-height:1.15;orphans:2;text-align:left;color:#666666;font-size:11pt;text-decoration:underline;font-family:"Trebuchet MS";padding-bottom:0pt;page-break-after:avoid}h5{widows:2;padding-top:8pt;line-height:1.15;orphans:2;text-align:left;color:#666666;font-size:11pt;font-family:"Trebuchet MS";padding-bottom:0pt;page-break-after:avoid}h6{widows:2;padding-top:8pt;line-height:1.15;orphans:2;text-align:left;color:#666666;font-style:italic;font-size:11pt;font-family:"Trebuchet MS";padding-bottom:0pt;page-break-after:avoid}</style></head><body class="c10"><p class="c11"><span class="c3">Administrative</span></p><ol class="c1 lst-kix_pumaoo38l22v-0 start" start="1"><li class="c0"><span>Committees</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1 start" start="1"><li class="c5"><span>Financial</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>SPARK launch date finalized for July 13th</span></li><li class="c2"><span>We need to write up a detailed budget proposal for the $5000 we&rsquo;re trying to raise.</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>Using the budget for reagents and lab supplies. </span></li><li class="c4"><span>We&rsquo;ll schedule a conference call with the Spark people afterwards</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2" start="3"><li class="c2"><span>SGI -- How much free synthesis, gibson reagents? Protein cage team have an idea of how much they&rsquo;ll be using?</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>Will offer some reagents, potentially some Gibson related materials. </span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2" start="4"><li class="c2"><span>Any other groups still designing oligos/gBlocks?</span></li><li class="c2"><span>Extra fundraisers</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>Donuts, etc. </span></li><li class="c4"><span>Fundrager, perhaps. </span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="2"><li class="c5"><span>Lab Management</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>7731 is ok for us to use now -- should we move our equipment over?</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span class="c3">Schedule a day for people to move our stuff over to 7731</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-4 start" start="1"><li class="c7"><span class="c3">Next Monday, April 20th, at 1:00pm.</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3" start="2"><li class="c4"><span>Reminder: for now, no bacterial work allowed in 7731. </span></li><li class="c4"><span>I talked to a grad student from the Grundfest lab, he gave a tentative OK for us to use their bacteria shaker/incubator</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-4 start" start="1"><li class="c7"><span>This grad student is also currently using 7731</span></li><li class="c7"><span>Email Jesse about this incubator.</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="3"><li class="c5"><span>Info media</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>Our social media has to improve in the next few months</span></li><li class="c2"><span>We&rsquo;ll be giving everyone access to our Twitter account</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>Still need a centralized person to oversee it.</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2" start="3"><li class="c2"><span>Megan will be adjuncting into our committee</span></li><li class="c2"><span>Will be ordering T-shirts on Monday!!!!!</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>S - 4</span></li><li class="c4"><span>M - 8</span></li><li class="c4"><span>&nbsp;L - 5</span></li><li class="c4"><span>Carter</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2" start="5"><li class="c2"><span>Need to update our igematucla.com website. Each project team create a page giving a synopsis of the field/context and project goals.</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>Honeybee silk, functionalization, protein cages needs an update</span></li><li class="c4"><span>send a blurb to Anuved via email by Monday, 5 pm (20 April)</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="4"><li class="c5"><span>Communications (Michael)</span></li><li class="c5"><span>Social Coordinator/Event Planner</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>Slack</span></li><li class="c2"><span>Cricket, next Sunday, 11am. &nbsp;(4/26)</span></li><li class="c2"><span>May 1st, Sri&rsquo;s happy hour if you&rsquo;re over 21 or especially have a fake (jk)</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="6"><li class="c5"><span>Recruitment/Training</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>Document training / recruiting from previous quarter</span></li><li class="c2"><span>Google Drive, program structure folder, summarize what we did Fall and Winter quarter. &nbsp;Use a template for this information. &nbsp;Feedback system. &nbsp;Contact Nithin for Slack. &nbsp;</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="7"><li class="c5"><span>Outreach/Publicity</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span class="c3">Contact Aalhad for a Daily Bruin article right before our Spark campaign. &nbsp;</span></li><li class="c2"><span class="c3">Reach out to UCLA Newsroom (Sri will contact Stuart Wolpert). </span></li><li class="c2"><span>Collaborating with Thunderclap</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-3 start" start="1"><li class="c4"><span>send an email to Penny</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1" start="8"><li class="c5"><span>Time/Scheduling</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>Create some sort of spreadsheet/ calendar to show who is in lab and when. &nbsp;(for Jessica) </span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-0" start="2"><li class="c0"><span>Any other administrative announcements</span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-1 start" start="1"><li class="c5"><span>Idk how you guys have been documenting all your project stuff so far, but until we figure out a better system, please put everything into the &ldquo;project team&rdquo; folder in the Google drive. &nbsp;</span></li><li class="c5"><span>I typed out a tutorial for exporting Google Docs to OpenWetWare. </span></li></ol><ol class="c1 lst-kix_pumaoo38l22v-2 start" start="1"><li class="c2"><span>Please note that images will not be properly exported using this method.</span></li><li class="c2"><span>Also, in these meeting notes, please use Google Doc&rsquo;s native outline formatting tool! It looks like this:</span></li></ol><p class="c11"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 53.33px;"><img alt="" src="images/image00.png" style="width: 624.00px; height: 53.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c11"><span class="c3">Project updates</span></p><ol class="c1 lst-kix_ve86q0d635dn-0 start" start="1"><li class="c0"><span>Cages</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1 start" start="1"><li class="c5"><span>Meeting with Yeates on Wednesday 11AM. Had discussions on preliminary papers and are setting up an agenda for the meeting. </span></li><li class="c5"><span>Talking Points: </span><span class="c6"><a class="c12" href="https://drive.google.com/open?id=1OUFKKXoWr0sEX0IDTZffHLOxJ_Nyml6NMAHXFkwoL78&amp;authuser=0">https://drive.google.com/open?id=1OUFKKXoWr0sEX0IDTZffHLOxJ_Nyml6NMAHXFkwoL78&amp;authuser=0</a></span></li><li class="c5"><span>Introduce ourselves, how are program is structured, what our program timeline and project is like. &nbsp;Ask what is feasibly possible, potential ideas, protease induced release, drug targeting, novel cage designs for biobricks, etc. </span></li><li class="c5"><span>Cage applications at the end would be very good for us to talk about today. &nbsp;</span></li><li class="c5"><span>Andreas Martin </span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-0" start="2"><li class="c0"><span>Functionalization</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1 start" start="1"><li class="c5"><span>This week we isolated cells from the cultures grown last week and performed a standard alkaline lysis to collect the lysate extract (4x 10mL samples). &nbsp;Extracts were frozen in -20 and the Affinity Column was prepared. &nbsp;</span></li><li class="c5"><span>The first round of purifications were conducted today. &nbsp;One issue is that we have a LOT of proteins, which would require doubling of the standard protocol and would use more buffer. &nbsp;Also would run into the issue of diluting the sample far below the conditions needed for a good Western Blot signal or coomassie stain. &nbsp;</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Could try using less elution buffer.</span></li><li class="c2"><span>Could try concentrating the sample down</span></li><li class="c2"><span>Could try packing with less resin BV. </span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1" start="3"><li class="c5"><span>Need to purchase a ring stand, tubing for the affinity column, get Bradford assay kit, come up with a source for standardization of the reaction (BSA).</span></li><li class="c5"><span>Protein yields quantification. &nbsp;Coomassie staining and using ladder, loading control, cell lysate, and purified proteins at different elution concentrations. &nbsp;</span></li><li class="c5"><span>Microplate analysis of cell lysates would be a great starting point for a first experiment. &nbsp;What we will first do is verify Tamura purity using SDS/Westerns, then do a fluorescence microplate analysis to verify. &nbsp;</span></li><li class="c5"><span>Julian created additional constructs of Tamura in pSB1C3, and amplified the ABD gBlock. &nbsp;Once we get enough yield from the PCR, we will do the Silver fusion to ligate the ABD and displace the GFP in the pSB1C3 Tamura construct. &nbsp;After sequence verification and colony PCR, we will re-transform and express the ABD, and perform downstream experiments from there. &nbsp; </span></li></ol><p class="c8"><span></span></p><ol class="c1 lst-kix_ve86q0d635dn-0" start="3"><li class="c0"><span>Materials</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1 start" start="1"><li class="c5"><span>Completed dialysis</span></li><li class="c5"><span>Will purchase dialysis tubing and PEG 10k for concentrating</span></li><li class="c5"><span>Will contact Seidlits or Wu regarding use of their lyophilizer</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Density, concentration of silk in gel, porosity, diffusion constant, stiffness, fluorescence assays for Tamura, thermostability (degradation rates)</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-3 start" start="1"><li class="c4"><span>read into Wu&rsquo;s papers</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1" start="4"><li class="c5"><span>Our group is thinking about possibly designing constructs for functionalizing other materials aside from threads</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Do we have the budget/manpower for this, or should the materials group just split up and join the other groups after we&rsquo;re familiar with the protocols?</span></li><li class="c2"><span>read into Silk Elastin-like proteins</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-0" start="4"><li class="c0"><span>Honeybee silk</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1 start" start="1"><li class="c5"><span class="c6"><a class="c12" href="https://www.google.com/url?q=https%3A%2F%2Fbenchling.com%2Fs%2Fp7bClpzQ%2Fedit&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNGoGgKjKQlXM0TVYfYXX-o4PgQU5g">https://benchling.com/s/p7bClpzQ/edit</a></span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>G block just ordered.</span></li><li class="c2"><span>Primers designed to amplify out various things as well put it into (the primers have been designed, but we&rsquo;ll order them as we need them)</span></li><li class="c2"><span>If time, go over the conflict with pET14b found in the paper </span><span class="c6"><a class="c12" href="https://www.google.com/url?q=https%3A%2F%2Fwww.embl.de%2Fpepcore%2Fpepcore_services%2Fstrains_vectors%2Fvectors%2Fpdf%2FpET-14b_map.pdf&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNEi7Qs1rcgD0ajDzU6fd_cs_xH6Rw">https://www.embl.de/pepcore/pepcore_services/strains_vectors/vectors/pdf/pET-14b_map.pdf</a></span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1" start="2"><li class="c5"><span>Next on the docket (While waiting for Gblock)</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Plan out purification scheme with just silk protein in order to hammer out the protocol. (Does not use tag purification, so will be a modifed protocol from the one the other functionalization groups are doing)</span></li><li class="c2"><span>Figure out all materials necessary and make a detailed wishlist as well as work flow (The paper uses BugBuster lysis kit for ex.)</span></li><li class="c2"><span class="c6"><a class="c12" href="http://www.google.com/url?q=http%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0142961209013805&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNGsGx7eRnf3YUeH5gBeWKgKCpR8mQ">Here</a></span><span>&nbsp;</span><span>is the paper that details the protocol: </span></li><li class="c2"><span>Think about SpyTag, and making a construct asso. with SpyTag (SpyTag-GFP/Albumin)</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1" start="3"><li class="c5"><span>Sometime late next week, amplify out silk, and clone the construct into the biobrick backbone, as well as hopefully an expression vector. &nbsp;</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Contact Dr. Arbing to request vector. (pET 14b hopefully) </span></li><li class="c2"><span>Think about adapting Tamura experimental designs to do the work much easier and with good quality data. &nbsp;</span></li></ol><p class="c9"><span></span></p><ol class="c1 lst-kix_ve86q0d635dn-0" start="5"><li class="c0"><span>ICA/Ishmael</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1 start" start="1"><li class="c5"><span>Made all MaSp 2 constructs</span></li><li class="c5"><span>Still making more due to low yield after gel purification; will use a new kit </span></li><li class="c5"><span>Plan for next week</span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-2 start" start="1"><li class="c2"><span>Clone all MaSp2&rsquo;s into psb1c3 and do transformation </span></li></ol><ol class="c1 lst-kix_ve86q0d635dn-1" start="4"><li class="c5"><span>T4 ligase, T7 ligase, Taq DNA ligase, test different buffer combinations, different temperatures, different temperature &ldquo;ramp-down&rdquo; protocols.</span></li><li class="c5 c13"><span></span></li></ol><p class="c9"><span></span></p></body></html>