tag:blogger.com,1999:blog-31906372672916888752024-03-14T11:24:47.413+02:00The Friedman Lab ChroniclesStarting a new lab in the middle of a research careerFoobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.comBlogger157125tag:blogger.com,1999:blog-3190637267291688875.post-32362858518300218802012-10-23T18:14:00.006+02:002012-10-23T18:14:47.095+02:00A functional selection model explains evolutionary robustness despite plasticity in regulatory networks<div style="text-align: justify;">
Its out on the <a href="http://www.nature.com/msb/journal/v8/n1/full/msb201250.html" target="_blank">Molecular Systems Biology website</a>. Yay!</div>
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This paper summarizes quite a bit of work by Naomi and Ilan. It started with "here is a short 2-week project" and ended as big part of Naomi's PHD and a massive paper.</div>
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Highlights (from our synopsis):</div>
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<span style="font-family: Verdana, arial, Helvetica, sans-serif; font-size: 13px; font-weight: bold; line-height: 1.3em;">By tracing the evolutionary history of transcriptional networks across 23 fungi, two seemingly contradictory trends are observed: rapid target turnover and conserved function. This is reconciled by a model that invokes strong selection to conserve the overall function of a motif, but not its individual targets.</span></div>
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<a href="http://www.nature.com/msb/journal/v8/n1/images/msb201250-i1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="238" src="http://www.nature.com/msb/journal/v8/n1/images/msb201250-i1.jpg" width="320" /></a></div>
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<li style="list-style-image: none; margin-top: 15px; text-align: justify;">The vast majority of <i>cis</i>-regulatory elements in genes’ promoters are rapidly gained and lost across species.</li>
<li style="list-style-image: none; margin-top: 15px; text-align: justify;">Despite this rapid turnover, most transcription factors are associated with a conserved function even at great evolutionary distances.</li>
<li style="list-style-image: none; margin-top: 15px; text-align: justify;">A functional selection turnover model reconciles these two phenomena by invoking a preference to conserve the overall function of the motif but not the individual target genes.</li>
<li style="list-style-image: none; margin-top: 15px; text-align: justify;">Our model fits the variation in measured transcription factor binding profiles across species in both yeasts and mammals.</li>
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Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com2tag:blogger.com,1999:blog-3190637267291688875.post-53653635515512582332012-10-18T18:30:00.000+02:002012-10-19T18:31:01.127+02:00Another farewell party<div style="text-align: justify;">
It seems that we are facing a mass exodus. Today we had a small scale party to say goodbye to Michal who is returning to MIT/Broad to finish her PHD.</div>
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You might remember that Michal is long-term visitor in the lab who works with us the last few years. Next week she is flying back to Boston, and apparently next time she visit Israel will be after she will finish her PHD. In addition to that exciting event, she will also be a mom next time we meet her...</div>
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We had a small party. Due to experiments running on (more on that later), we switch the plan from going out to ordering food in. And since the options were limited, we had a Pizza Party! to remind Michal what she is about to enjoy a lot of in different meetings in the States :-)</div>
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Michal treated us to a very impressive (and tasty!) cake.<br />
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And also a surprise present of a ball. It turned out that the ball was a puzzle that required some effort.<br />
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Although we will continue collaborating with Michal, we will miss her presence at the lab.</div>
Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com4tag:blogger.com,1999:blog-3190637267291688875.post-75500266376166149102012-10-15T20:53:00.000+02:002012-10-15T20:53:10.911+02:00Farewell to Naomi<div style="text-align: justify;">
The last week was marked with farewell events to Naomi. </div>
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It started on Tuesday with a trip and picnic. Since Naomi is (was) a joint student of both Hanah Margalit and myself, we had a trip with the two groups.</div>
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After the trip we had a nice lunch in a forest. Daniela was the star of the event, sitting in the middle and checking the choice of food.</div>
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Then came the more official part of the ceremony where we said our farewell wishes and exchanged cards and presents :-)</div>
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On Thursday afternoon we had the dissertation exam. Unlike the custom in many universities, in the Hebrew University the exam is a private event - the judges and the student without any audience. Naomi surveyed the results from her dissertation and the judges asked questions.</div>
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After the presentation and Q&A, the judges convened, and after a short discussion decided this was a great presentation and wonderful dissertation. We called Naomi to tell her the news.<br />
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Yesterday Hanah and I took Naomi for a lunch to have a chance for a more intimiate farewell. </div>
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Today Naomi came to finish the TODO list on an ongoing project with Avital and Mor (from Hanah's lab). And at 3:30, she left, after tearful hugs with everyone. </div>
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We wish Naomi easy move to Cambridge, MA, and much fun and success in her postdoctoral fellowship!</div>
Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-53114756978948091362012-09-24T23:30:00.000+02:002012-09-27T09:59:01.699+02:00A week of visitors<div style="text-align: justify;">
This week we had several visitors to the lab.</div>
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On Sunday we hosted a delegation from the <a href="http://www.helmholtz.de/en/" target="_blank">Helmholtz Association</a>. This delegation included the president of the association as well as directors from several research centers. They did a whirlwind tour of Israel. Their schedule at the Hebrew University was for half a day, and included a general introduction and then topic-oriented meeting. I was chosen to host the Biology meeting in the lab. The guests included the President of the association, the Director of Research of the <a href="http://www.helmholtz-muenchen.de/en" target="_blank">Helmholtz Zentrum Munich</a> and the Director and Vice-Director of Research of the <a href="http://www.mdc-berlin.de/en/" target="_blank">Max Delbruck Center</a> in Berlin. </div>
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As you can guess this was a very important crowd, and we assembled a team of scientists (established and new) to meet with them. The meeting ended up crowding 16 people in our small meeting/kitchen room, and as consequence was very informal. We also had a short tour of the robotics room.</div>
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This visit was a an excuse for us to do a thorough cleanup day on Thursday last week. I think that since it was open the lab never was so clean. The cleanup included also out of sight areas, such as the cold room, which was reorganized by Amit and Noa, who sorted through all the shelfs, removed old and outdated plates, and rearranged things in an accessible way.</div>
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On Monday, we were part of the country-wide "Scientists Night" events. The <a href="http://community-youth.huji.ac.il/.upload/program2.pdf" target="_blank">event</a> at the Hebrew University included tours in labs, and our lab was one of the advertised tours. Each group was of 10 teenagers that didn't know much about labs and biology. Avital and Noa took charge of hosting the visit and explaining to the energetic youth why we have robotics.</div>
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One last, unexpected and less prestigious, visitor was a chameleon that started visiting my office window regularly. </div>
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The first sighting of this science-curious lizard was when we had a meeting with five people in the room, and suddenly I noticed that everyone was focused on the window behind me. </div>
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Since then it revisited almost every day, and finally I decided that it is calls for some pictures. The window is not 100% clean, but that ended up giving the images a bit of interesting blurs.</div>
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Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com1tag:blogger.com,1999:blog-3190637267291688875.post-29132579858513879512012-08-29T17:25:00.002+03:002012-08-30T09:33:04.141+03:00Evolution of Transcription Factors Binding paper is accepted!<div style="text-align: justify;">
Yay!</div>
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Just got email that a paper by Naomi, Ilan Wapinski, Aviv Regev, Hanah Margalit and me was accepted to <a href="http://www.nature.com/msb/index.html" target="_blank">Molecular Systems Biology</a>. This paper represents almost two years of work by Naomi and Ilan, and undergone several dramatic ups & down during this time. So it is great to hear that it is officially accepted.</div>
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It made just in time for Naomi to print her dissertation listing this paper as "accepted for publication" instead of "in review".</div>
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We celebrated by an impromptu toast in the lab.</div>
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More details once the paper appears....</div>
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This is also a good chance to add a picture of Naomi & Ilan from a trip to CSHL at the time we started talking about this project.</div>
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Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com2tag:blogger.com,1999:blog-3190637267291688875.post-62866972446401766892012-08-24T00:18:00.000+03:002012-08-26T17:34:59.849+03:00Light box<div style="text-align: justify;">
As you may recall from early posts, we use agar plates for <a href="http://nirfriedmanlab.blogspot.co.il/2010/01/singer-followup.html" target="_blank">growing</a> and <a href="http://nirfriedmanlab.blogspot.co.il/2010/04/mating-yeasts.html" target="_blank">manipulating</a> libraries of yeast strains. We also keep "replicating" copies of these plates to maintain a "live" copy of the libraries.</div>
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One of the potential problems is that we mis-copied a plate, or introduced a contamination. One way to check that is to examine the plate pattern. Basically, each library plate has different set of empty spots. This means that we can easily identify plates by these "finger prints". Moreover, a contamination would fill the empty spaces by new colonies. </div>
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Thus, it was clear early on that we need a tool for taking pictures of plates and recording/analyzing the colonies. We could use the standard gel camera we have in the shared room, but that was both unwieldy and exposed our plates (and us) to ethidium bromide (which is used by other labs for dying DNA on gels).</div>
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Instead we aimed for a dedicated station for imaging plates. We found some solutions by commercial companies. These however, were very very expensive. And so we decided for a Do It Yourself solution. We consulted with the local electrician, and helped by Meretz, a retired electrician built our own solution.</div>
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The box is an old wooden box that was originally for a nikon microscope. The local workshop built us a device to hold the plate in a precise location. Since the plate is asymmetric this ensures that the images are of the correct orientation. We bought a Nikon camera that can have external power supply and remote operation. It is an overkill for the image quality we need, but it does work without battery replacement or manual operation.</div>
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As a light source, Meretz suggested using a led strip. He built these leds below the plate holder. This meant that the image colonies showed up as silhouettes.<br />
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I wrote a simple program that identifies colonies, their location and their size (which is useful for estimating the fitness of different strains). Eli Peker, who worked as a summer student, wrote a program for uploading images and storing them in a database. This interface allowed different people in the lab to keep track of libraries and compare to previous versions.</div>
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Recently, Amit (who deserve his own post soon) suggested we also examine the color and texture of the colonies. This appears to be a known phenotype. However, since the light source was below the colonies we could not use our box. We again contacted the local electricians who installed additional led strips for forground lighting.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-Yj0tpDHCmmM/UDUHW86w2QI/AAAAAAAA4HE/8J-OfanLA6Q/s1600/P8168909.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://1.bp.blogspot.com/-Yj0tpDHCmmM/UDUHW86w2QI/AAAAAAAA4HE/8J-OfanLA6Q/s400/P8168909.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">"Disco" foreground lights</td></tr>
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As you can see, the forground lights turned out to be a bit excessive ("disco" as Amit put it). Now we could make out the color and the texture of the colonies.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-YSahczUwQsE/UDoxaruZtKI/AAAAAAAA4IU/MomIJuRlibI/s1600/DSC_2491.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="265" src="http://1.bp.blogspot.com/-YSahczUwQsE/UDoxaruZtKI/AAAAAAAA4IU/MomIJuRlibI/s400/DSC_2491.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Same plate, with foreground lighting</td></tr>
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However, now some of these disco lights are reflected in the image and look like small colonies (top part of the image). To deal with this, we added our own DIY screen (paper) to soften the light. </div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-n5M5nD1XNaw/UDac1VPYPwI/AAAAAAAA4Hw/2vtkwPPg6v8/s1600/P8239017.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://3.bp.blogspot.com/-n5M5nD1XNaw/UDac1VPYPwI/AAAAAAAA4Hw/2vtkwPPg6v8/s400/P8239017.jpg" width="300" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Foreground lights with diffused screen</td></tr>
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Which lead to removal of the annoying reflections on the agar.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-2LP45nR1iF8/UDoxcA8PvMI/AAAAAAAA4Ic/35-hL7N4mAg/s1600/DSC_2498.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="265" src="http://2.bp.blogspot.com/-2LP45nR1iF8/UDoxcA8PvMI/AAAAAAAA4Ic/35-hL7N4mAg/s400/DSC_2498.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Same plate, with diffused foreground lighting</td></tr>
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<br />Notice that in this plate there are few white colonies (two small ones) and some that are more yellow. These differences are easier to see if zoom in on a region of the image.<br />
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<a href="http://3.bp.blogspot.com/-fhS5AKY7ZiE/UDoze2oDd2I/AAAAAAAA4Is/9h6hiPxwQnE/s1600/DSC_2498-3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="226" src="http://3.bp.blogspot.com/-fhS5AKY7ZiE/UDoze2oDd2I/AAAAAAAA4Is/9h6hiPxwQnE/s320/DSC_2498-3.jpg" width="320" /></a></div>
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Moreover, some colonies have a different texture, these differences are enhanced when we examine a gray-level version.<br />
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<a href="http://1.bp.blogspot.com/-oENg_U8VgBo/UDozZ4yt8mI/AAAAAAAA4Ik/AOGqgxqJLO0/s1600/DSC_2498-2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="226" src="http://1.bp.blogspot.com/-oENg_U8VgBo/UDozZ4yt8mI/AAAAAAAA4Ik/AOGqgxqJLO0/s320/DSC_2498-2.jpg" width="320" /></a></div>
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For now we use the lightbox to record the plates with different strains. We didn't yet write an automated color classifier (relatively easy) or a texture classifier (a bit harder).<br />
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Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-15691911377478309312012-08-22T17:22:00.001+03:002012-08-22T17:26:16.676+03:00Robot Updates<div style="text-align: justify;">
As part of ongoing attempts to get the system to work to our liking we run into two problem.</div>
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First, many of the steps in our yeast growth protocols use individual pipetting actions for each well. For this reason we have an arm with individual pipettes. Initially we configured the arm with four fixed tips and four disposable pipettes. The fixed tips are easier to use and do not consume plasticware. On the other hand to get perfect sterility we need to use plastic tips.</div>
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So far we learned that the fixed tips (with a wash between uses) is sufficiently clean for our purposes. And so we use these a lot. The problem is that the time it takes to "process" a plate (e.g., remove individually tailored amounts per well for growth dependent dilutions) was too long. The main time consuming steps is the tip washing. </div>
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After consultation with Neotec people, we decided to switch two of the disposable pipette heads with fixed tips. This will give us more tips and thus less washes (as the washes are done in parallel and take the same amount of time for 4 or for 6 tips).</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-IdPzCwA3L_Y/UDTqQEtGBjI/AAAAAAAA4Go/JXL2jRZnM4M/s1600/P8168919.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://2.bp.blogspot.com/-IdPzCwA3L_Y/UDTqQEtGBjI/AAAAAAAA4Go/JXL2jRZnM4M/s400/P8168919.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Six fixed tips in action</td></tr>
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The second problem is much more serious - the robotic manipulation arm kept getting out of alignment. This lead to serious of failure in our longer experiments. The blame fell onto the plate shaker, which we use a lot in our protocol. The design of the shaker has to allow a robotic arm to place/remove a plate, but at the same time hold the plate firmly during the shaking. The solution in the shaker we had was a spring that held the plate in place. Every time the arm came down to the shaker it would press on a lever and release the plate from the spring. Apparently these repeated presses moved the arm out of place (not by much but sufficiently to cause problems)</div>
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The solution was to replace the shaker head to one with a different locking mechanism based on a higher stand that kept the plate sitting down. This required adaptation of a solution Tecan built for arms that hold the plate from above (and not from the side like ours).</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-yMXQeMVXBbA/UDTqSjl3egI/AAAAAAAA4Gw/hQbVWuCDQFI/s1600/P8168922.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://1.bp.blogspot.com/-yMXQeMVXBbA/UDTqSjl3egI/AAAAAAAA4Gw/hQbVWuCDQFI/s400/P8168922.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">New shaker head</td></tr>
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So far it seems that the system is indeed more stable. It worked for two days without issues and we are counting.</div>
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Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com4tag:blogger.com,1999:blog-3190637267291688875.post-25711337745106507092012-08-01T20:26:00.000+03:002012-08-01T20:26:01.830+03:00Gone SailingOne of the events that took place during the "blackout" period (when I did not blog) is worth reporting.<br />
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Ayelet, the command center of our lab, has collected all her saved vacation days (and borrowed some from the future) to take a 6 month vacation. To be honest, she warned me about that plan when we first met to discuss her position as a lab manager. Ayelet's plan was to take a boat and sail with the family in the Mediterranean from Israel to Italy and back, visiting Cypres, Turkey, Greece, and Croatia on the way. Back then it seemed far away and beyond care.<br />
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When Ayelet told me they bought a boat, I realized that the plan might actually be carried out. I even got a chance to sail with Ayelet and Udi one nice day out from Jaffa port (where they had a mooring point).<br />
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<a href="http://1.bp.blogspot.com/-GhRzTj4tuaE/TYfApU9823I/AAAAAAAAtmM/DXiMz0Ajlkg/s1600/DSC_5089.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="267" src="http://1.bp.blogspot.com/-GhRzTj4tuaE/TYfApU9823I/AAAAAAAAtmM/DXiMz0Ajlkg/s400/DSC_5089.jpg" width="400" /></a></div>
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But since September the threat become more realistic. As the target date in April was closing in, Ayelet worked hard to make sure there are no loose ends left in the lab. She finished all the experiments she was performing, made sure our supply and daily operations are defined by a robust set of instructions. She left different lab members in charge of different aspects of the lab, and left strict instructions how to behave.<br />
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Surprisingly, we managed to avoid a major crisis so far. Things are working relatively smoothly, and we carry on the momentum Ayelet left us. This does not mean she will not have a lot of work when she comes back :-)<br />
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So what about the trip? Well, a week after passover, they set off. I was recruited on the last minute to drive some of the family and last of the supplies to the port. And so I got to send them off from the boat's berth. (They actually sailed some few kilometers north to Hertzelia where they could go through official border check to legally leave the country.) I also took the official goodbye picture.<br />
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<a href="http://3.bp.blogspot.com/-E6BmSkeZ4v8/T4lueI_jxlI/AAAAAAAAAAQ/7CYHvVaMQFE/s220/%25D7%2591%25D7%2599%25D7%25A4%25D7%2595.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="260" src="http://3.bp.blogspot.com/-E6BmSkeZ4v8/T4lueI_jxlI/AAAAAAAAAAQ/7CYHvVaMQFE/s320/%25D7%2591%25D7%2599%25D7%25A4%25D7%2595.jpg" width="320" /></a></div>
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Ayelet has been keeping a <a href="http://rahatsailing.blogspot.com/" target="_blank">blog of the trip</a>. It is worthwhile to take a look, as there are some amazing stories.<br />
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The observent readers might point out that Ayelet shows up in the pictures from <a href="http://nirfriedmanlab.blogspot.com/2012/07/bubbles-away-morans-sendoff-party.html" target="_blank">Moran's sendoff party</a>. This is not a mistake. The party was planed for the week Ayelet came back to Israel for a "mid-vacation" break to see her older kids and meet with her extended family.Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-74612584725861403532012-07-31T20:00:00.000+03:002012-08-01T20:01:52.608+03:00Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response<div style="text-align: justify;">
The monster is out! </div>
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A work that started more than 2 years ago, finally resulted in a publication. The <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001369" target="_blank">paper</a> came out in <a href="http://www.plosbiology.org/" target="_blank">PLoS Biology</a>. This work is tight collaboration between Ollie's lab and ours, with Assaf and Hsuiyi as first co-authors. Avital and Ayelet also played an important part and are coauthors on the paper.</div>
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<a href="http://4.bp.blogspot.com/-1lQYsPUC8mA/UBlgggEXR2I/AAAAAAAA3os/rXVmf2NjDRE/s1600/Weiner_2012_Fig_S1.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="357" src="http://4.bp.blogspot.com/-1lQYsPUC8mA/UBlgggEXR2I/AAAAAAAA3os/rXVmf2NjDRE/s400/Weiner_2012_Fig_S1.tif" width="400" /></a></div>
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This publication is also the first time we publish experimental work done in our own lab. We can say that we are officially an experimental lab! Figure 2 (below) is all about microscopy measurements that we collected on our system.</div>
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<a href="http://3.bp.blogspot.com/--9oaMEItE_Y/UBlgZXKBZSI/AAAAAAAA3ok/9fjg1VUC_cQ/s1600/Weiner_2012_Fig2.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://3.bp.blogspot.com/--9oaMEItE_Y/UBlgZXKBZSI/AAAAAAAA3ok/9fjg1VUC_cQ/s400/Weiner_2012_Fig2.tif" width="308" /></a></div>
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<br /></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com2tag:blogger.com,1999:blog-3190637267291688875.post-34221381579617305572012-07-17T23:44:00.000+03:002012-07-20T00:46:12.402+03:00Bubbles away - Moran's sendoff party<div class="separator" style="clear: both; text-align: center;">
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As you might recall, Moran is trying to finish her PHD soon. In fact, she already got plane tickets to Boston. This week she had two causes for celebration. First, she handed in her dissertation. Yay!</div>
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Second, we had a sendoff party. Its a bit early, but since it was the only time when all the relevant people are in Israel, she had it today.</div>
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Moran, being Moran, organized a party with all the lab alumni that overlapped with her and are still in Israel. She and Liron (her husband) organized activities to match the festivities.</div>
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<a href="http://1.bp.blogspot.com/--pvACSr0OhE/UAaqz8corlI/AAAAAAAA3S4/25k_qgrD3Fw/s1600/DSC_0864.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://1.bp.blogspot.com/--pvACSr0OhE/UAaqz8corlI/AAAAAAAA3S4/25k_qgrD3Fw/s400/DSC_0864.jpg" width="400" /></a></div>
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And so we found ourselves on the lawn of the university, on the late afternoon of a relatively hot day blowing huge bubbles. Everyone had tons of fun, and we attracted a lot of attention from the passing students.</div>
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<a href="http://1.bp.blogspot.com/-8zCtNS_1r-o/UAaq7kJVzeI/AAAAAAAA3Ko/QwVOOFECmhE/s1600/DSC_0867.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://1.bp.blogspot.com/-8zCtNS_1r-o/UAaq7kJVzeI/AAAAAAAA3Ko/QwVOOFECmhE/s400/DSC_0867.jpg" width="400" /></a></div>
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It was impressive to see the large number of people that were related to the lab at some point in the last few years. </div>
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<a href="http://4.bp.blogspot.com/-9pdrIHaVMiM/UAawF9dmDTI/AAAAAAAA3OU/s8r-_E55Vl4/s1600/DSC_1093.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="267" src="http://4.bp.blogspot.com/-9pdrIHaVMiM/UAawF9dmDTI/AAAAAAAA3OU/s8r-_E55Vl4/s400/DSC_1093.jpg" width="400" /></a></div>
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<tr><td class="tr-caption" style="text-align: center;">Ofer</td></tr>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-Talstyqiosc/UAaw0OuKNiI/AAAAAAAA3O8/aMQq36Aoeeg/s1600/DSC_1147.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="267" src="http://4.bp.blogspot.com/-Talstyqiosc/UAaw0OuKNiI/AAAAAAAA3O8/aMQq36Aoeeg/s400/DSC_1147.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Avital</td></tr>
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<tr><td class="tr-caption" style="text-align: center;">Merav & Avital</td></tr>
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<tr><td class="tr-caption" style="text-align: center;">Michal C. & Alon</td></tr>
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<tr><td class="tr-caption" style="text-align: center;">Jenia</td></tr>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-lr2oNThnnmQ/UAax8w0BzbI/AAAAAAAA3UU/nMhECKfT_iQ/s1600/DSC_1219.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://3.bp.blogspot.com/-lr2oNThnnmQ/UAax8w0BzbI/AAAAAAAA3UU/nMhECKfT_iQ/s400/DSC_1219.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Assaf</td></tr>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-tRp9rC5G1bY/UAasgGqXYyI/AAAAAAAA3TQ/9JwmF8X4rug/s1600/DSC_0920.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="285" src="http://3.bp.blogspot.com/-tRp9rC5G1bY/UAasgGqXYyI/AAAAAAAA3TQ/9JwmF8X4rug/s400/DSC_0920.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Michal R.</td></tr>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-B4GDRdgE5TY/UAh-jOBXtCI/AAAAAAAA3X0/qHTjHdl-HsU/s1600/DSC_1069.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="258" src="http://1.bp.blogspot.com/-B4GDRdgE5TY/UAh-jOBXtCI/AAAAAAAA3X0/qHTjHdl-HsU/s400/DSC_1069.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Inbar (hiding beyond her camera)</td></tr>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-O0sitkRayBg/UAazdab0cLI/AAAAAAAA3VI/xSLIqk1wtaQ/s1600/DSC_1280.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://1.bp.blogspot.com/-O0sitkRayBg/UAazdab0cLI/AAAAAAAA3VI/xSLIqk1wtaQ/s400/DSC_1280.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Ruty</td></tr>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-9ZYOWIma5NA/UAa1OiUcxJI/AAAAAAAA3XQ/hi-G3REHgDg/s1600/DSC_1340.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://3.bp.blogspot.com/-9ZYOWIma5NA/UAa1OiUcxJI/AAAAAAAA3XQ/hi-G3REHgDg/s400/DSC_1340.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Ido</td></tr>
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I<span style="background-color: white;">t was even more impressive to see the large number of children at various ages.</span></div>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-sGg7gaCFlXY/UAarWVAiC9I/AAAAAAAA3Xk/KXHZO9nK800/s1600/P7175417.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://1.bp.blogspot.com/-sGg7gaCFlXY/UAarWVAiC9I/AAAAAAAA3Xk/KXHZO9nK800/s400/P7175417.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Oren & Liron (Moran's family)</td></tr>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-j14jlmideps/UAarjxxK93I/AAAAAAAA3LE/Ih15xO62Vm8/s1600/P7175443.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://4.bp.blogspot.com/-j14jlmideps/UAarjxxK93I/AAAAAAAA3LE/Ih15xO62Vm8/s400/P7175443.jpg" width="298" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Daniela & Ariel (Naomi's)</td></tr>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-Vdp64GL2-Qs/UAauMROJWRI/AAAAAAAA3M4/bBQEBtBjRQw/s1600/DSC_1006.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://1.bp.blogspot.com/-Vdp64GL2-Qs/UAauMROJWRI/AAAAAAAA3M4/bBQEBtBjRQw/s400/DSC_1006.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Oren, back in the action</td></tr>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-YSzYMW_pKAk/UAaxK5ZmkPI/AAAAAAAA3PM/4qDj6qf29jU/s1600/DSC_1166.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="285" src="http://4.bp.blogspot.com/-YSzYMW_pKAk/UAaxK5ZmkPI/AAAAAAAA3PM/4qDj6qf29jU/s400/DSC_1166.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Naomi, Ariel & Daniela</td></tr>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-GzCTLsN6Nqg/UAava4PVnBI/AAAAAAAA3N4/BQV0DK4b2aM/s1600/DSC_1051.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="285" src="http://4.bp.blogspot.com/-GzCTLsN6Nqg/UAava4PVnBI/AAAAAAAA3N4/BQV0DK4b2aM/s400/DSC_1051.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Marek & daughter</td></tr>
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<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-xYCjZhIbfn8/UAav0XNxp8I/AAAAAAAA3UA/trx_80K1dyc/s1600/DSC_1084.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://2.bp.blogspot.com/-xYCjZhIbfn8/UAav0XNxp8I/AAAAAAAA3UA/trx_80K1dyc/s400/DSC_1084.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tal showing off the latest acquisition</td></tr>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-uL4nZfy3PmU/UAaxvTxgzKI/AAAAAAAA3Po/MTIKc804XpE/s1600/DSC_1212.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="267" src="http://3.bp.blogspot.com/-uL4nZfy3PmU/UAaxvTxgzKI/AAAAAAAA3Po/MTIKc804XpE/s400/DSC_1212.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><br /></td></tr>
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<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-28Fq_E_aVfw/UAaqjVoUOzI/AAAAAAAA3KQ/p7k6iewJpv4/s1600/DSC_0836.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://2.bp.blogspot.com/-28Fq_E_aVfw/UAaqjVoUOzI/AAAAAAAA3KQ/p7k6iewJpv4/s400/DSC_0836.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cecile</td></tr>
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<tr><td class="tr-caption" style="text-align: center;">Michal (Matan's) checking the food</td></tr>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-w5759qXwQ04/UAaygf5fLaI/AAAAAAAA3U8/BrHLizwrHng/s1600/DSC_1250.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://1.bp.blogspot.com/-w5759qXwQ04/UAaygf5fLaI/AAAAAAAA3U8/BrHLizwrHng/s400/DSC_1250.jpg" width="285" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Matan, preparing Michal for the circus</td></tr>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-1f9ORJdGA8k/UAh-P5RfPLI/AAAAAAAA3Xs/T59RC5yQL2M/s1600/DSC_0988.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="267" src="http://1.bp.blogspot.com/-1f9ORJdGA8k/UAh-P5RfPLI/AAAAAAAA3Xs/T59RC5yQL2M/s400/DSC_0988.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tal, Amit, and Shachr (Inbar's)</td></tr>
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<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-BJH6vHBEY3A/UAawnhdsOxI/AAAAAAAA3Ow/8Ds34xeD670/s1600/DSC_1135.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="285" src="http://2.bp.blogspot.com/-BJH6vHBEY3A/UAawnhdsOxI/AAAAAAAA3Ow/8Ds34xeD670/s400/DSC_1135.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Maya (Matan's)</td></tr>
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Each of us brought something to eat and drink, and so we had a nice selection. </div>
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Moran, who is known for her cooking/baking passion, outdid everyone with a fancy desert.</div>
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Thankfully, the official speech ceremony was short [I think I was ok ;-)]</div>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-6nRZPiuIlYQ/UAa0g2goINI/AAAAAAAA3Vk/q-Xf3b3xyy4/s1600/DSC_1293.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://1.bp.blogspot.com/-6nRZPiuIlYQ/UAa0g2goINI/AAAAAAAA3Vk/q-Xf3b3xyy4/s400/DSC_1293.jpg" width="267" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Moran, ready for battle!<br />Ayelet in the background</td></tr>
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Before breaking up the party, we managed to get a group picture together.</div>
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<br /></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-88697206998643516712012-06-14T20:08:00.000+03:002012-06-20T18:33:51.290+03:00CSLS Yearly Retreat<div style="text-align: justify;">
One of our local sources of excellence is the undergraduate program in "Computer Science and Computational Biology" which is often nicknamed CSLS. This elite program accepts relatively few students (~20/year) with very high entry grades. The students study both Computer Science and Life Sciences as well as specialized courses. To meet these requirements the program has a very high courseload. </div>
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Overcoming the challenges of such a program is often dependent on team spirit. Classes that formed a supporting social group usually had better success and the students felt they learned more and were happier. To help form such interactions we employ various activities, including specialized classes and study sessions for this group. One of the most important activities is the <a href="http://nirfriedmanlab.blogspot.co.il/2011/05/csls-retreat.html">yearly retreat</a>. </div>
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In the retreat, which takes place toward the end of the academic term, we take students in all stages of the program together with the teachers and TAs of the program.</div>
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The location of the retreat is Hof Dor, a beautiful beach that borders a large nature reserve along on of the most unique shorelines in Israel. </div>
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Although we spent two days next to the beach, most of the day was in the lecture hall. </div>
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The packed program had talks by senior year students who presented their final project. These projects involve working with researchers at the Hebrew University on a range of topics. </div>
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The talks in the retreat serve as a milestone in the project, as they provide a chance to present the research question, methods and results to a supportive audience. For the younger students these talk open a window to current research questions and how computational analysis plays a role in a range of biological studies.<br />
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Many credits go to Naomi for mentoring the projects throughout the year and working with the students on the presentations.</div>
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In addition we had a a keynote talk by Nathalie Balaban on non-genetic variability in bacteria and it's evolutionary importance. </div>
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However, sitting in a hot room listing to talks can be tiring.<br />
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To fight the sleepiness, Naomi arranged for an impromptu streach session, and later a musical interlude.</div>
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In spite of the heat, many of the talks inspired interesting discussions.</div>
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To top things off we ended the meeting with a guided trip in the nature reserve. <br />
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<span style="background-color: white;">Alon and me took advantage of the flat sea to do two quick dives (one in the evening and the other early in the morning) at the local beach.</span><br />
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<br />Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-5268889231638295142012-06-12T20:00:00.000+03:002012-06-12T20:00:14.514+03:00Dan David Prize<div style="text-align: justify;">
The last two days were a celebration of the <a href="http://www.dandavidprize.org/">Dan David Prize</a>. This is a prize donated by the late Dan David and hosted by Tel Aviv university. The main prize is very large, and every year is given in three areas representing the past, the present and the future. This year the future looking subject was "genome research" an area close to us. The winners were David Botstein, Eric Lander, and Craig Venter. All three were main players in the sequencing of the human genome, but did much more before and after this milestone. </div>
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<tr><td class="tr-caption" style="text-align: center;">From the left: Craig Venter, Eric Lander, David Botstein, TAU rector, Lady Gilbert, Smadar Fisher.</td></tr>
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One of the nice aspects of the Dan David prize, is that each winner "donates" 10% of the prize to fellowships that are awarded to graduate students in the same field. Both Moran and Michal were selected as recipients of the graduare student prize work in the genomre research catagory. In total 5 Tel Aviv students and 5 international students were awarded. Thus out of the 5 non-TAU winners, two were related to our group.</div>
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<tr><td class="tr-caption" style="text-align: center;">Michal getting a hug from Eric</td></tr>
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To add to the story, Moran and Michal were of the same year in undergradute studies here in our Computational Biology program, and are good friends. Moran continued to do her MSc with me, while Michal did her MSc at the Weizmann. Moran continued to her PhD studies with me, but during the course of a collaboration with Aviv Regev at the Broad, she became co-advised by Aviv. More or less at the same time Michal started her PhD studies in MIT, and after a year of rotations elected to study with Aviv. I became involved with Michal's research through a collaboration. Since then Michal spent several long visits in our group and is now an integrated part of our lab. </div>
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And so, both Moran and Michal were awarded the Dan David graduate prize by Eric Lander the head of the Broad Institute, where they both do research. </div>
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<br /></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-49137130833502218562012-06-07T19:16:00.000+03:002012-06-09T16:46:32.915+03:00IBS 2012<div style="text-align: justify;">
Today I was hosting the IBS 2012 meeting. Officially the "14th Israeli Bioinformatic Symposium" which is the annual meeting of the "Israeli Society for Bioinformatics and Computational Biology" of which I was the president until few hours ago.</div>
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The meeting brings together researchers in Bioinformatics, Computational Biology and Systems Biology from all the universities in Israel. Traditionally we have an invited speaker from abroad, and this year it was Manolis Kellis from MIT.</div>
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The last few weeks were hectic with setting up the website for registration and poster abstract submissions, selecting caterer, and such. Late last week we decided to order buses to transport people to/from the meeting from all the other major academic universities. This meant that we had to set up sign-up forms and make sure all the people made it to the bus. </div>
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Yesterday, I was away, but my local help (Dikla and Cecile) made the preliminary arrangements. When I showed up at 7am, the outer area was already with poster stands. Since we had more than submitted posters, we needed quite a few stands.</div>
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Not long afterwards, the florist showed with a nice flower arrangement. I was working with the A/V people to set up the stage properly. The large Wise auditorium was ready for action.</div>
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Toward 8:30 we had our registration desk with name tags set up and waiting for people to arrive. We had large signs and posters up and ready. The first wave of attendees were on the bus from Rehovot. </div>
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After welcome remarks by our Vice President, we had the pleasure of hearing Manolis. He did a great job of showing why the new flood of data can make a difference in personalized medicine and how this is going to come about.</div>
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<a href="http://2.bp.blogspot.com/-LxgnoaefoI0/T9NLQ2vThLI/AAAAAAAA2eo/l0hVLYRBEZs/s1600/P6073271.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="http://2.bp.blogspot.com/-LxgnoaefoI0/T9NLQ2vThLI/AAAAAAAA2eo/l0hVLYRBEZs/s400/P6073271.jpg" width="400" /></a></div>
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Overall we had more than 350 registrations. Not everyone who registered showed up, but we also had quite a few walk-in. I think it is safe to say we had more than 300 attendees, maybe closer to 350. (We ordered food for 350 and it was all finished).</div>
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The closing ceremony involved the "Best Poster Awards" that were selected by a committee of faculty members (I was not involved). It was a nice surprise to find out that our very own Assaf was one of the poster winners.<br />
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By 5:30pm, the meeting was over. I helped wrap things up, and thenI headed to my office to find a <a href="http://nirfriedmanlab.blogspot.co.il/2012/06/leaky-sprinklers.html">water leak :-(</a></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0Wise Auditorium, Givat Ram, Jerusalem, Israel31.778544122482447 35.1964509487152131.777700622482449 35.195216948715213 31.779387622482446 35.197684948715207tag:blogger.com,1999:blog-3190637267291688875.post-30909755657786065582012-06-05T16:44:00.000+03:002012-06-09T16:45:00.173+03:00Leaky sprinklers<div style="text-align: justify;">
Some of our readers might think that once we finished the renovations our infrastructure issues were solved. In my view we don't pass a week without some sort of problems or issues to deal with.</div>
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This week it was the sprinkler system. Some explanation is needed.</div>
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Few years ago one of the chemistry building went up in flames (as chemistry buildings often do). As a result, the building had to be totally renovated. Luckily the damages were mostly (or only) financial. After this unfortunate event the firm that provide insurance for the university raised the premium as long as the university does not put in fire prevention devices. This resulted in a long process in which new sprinkler systems were added to existing buildings.</div>
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Our turn was up earlier this year. We went through a series of meeting where were told of the importance of this move, and how the best choices have been made to minimize the chances of a fire (on the one hand) and accidental dosing (on the other). We were told that the firm that installs these sprinklers meets the highest standards for quality and cleanliness and would be "virtually unnoticed" when they worked. I was one of a group of researchers who expressed worries about our delicate equipment getting damaged by the installation works or getting water damaged post-installation. As such we were further soothed by responsible administrators that there will be tight supervision of the works and the "acceptance tests".</div>
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The following months were rather annoying. The worker closed part of our parking lot and used it for cutting pipes. They had to drill halls through the concrete structure along the hallways and between hallways and labs to traverse the whole building. When they worked inside the lab we had to remove all items from benches and shelves and cover these to protect everything from the dust (as they needed to make large holes in concrete). Luckily for us, the work in the robot room was less painful, as they found pre-made holes they can use and did not need to drill new ones.</div>
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Few weeks ago the system became operational. Although it was supposedly checked for leaks, the first day we had a leakage in our corridor. When they came to fix it, they did not drain the water properly and caused a major flood along part of the corridor (luckily further out from our lab).</div>
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Today, I came in and noticed that the floor in Cecile's office (the outer room to my office) is wet. Initially I took it to be remains of the cleanup earlier in the day. But then I noticed that the wall was also wet. A quick examination showed that the slow, but steady, leak was from the ceiling. Opening the ceiling tiles, I immediately saw the source --- a junction in the sprinkler system. </div>
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<a href="http://3.bp.blogspot.com/-caMufUAzFOA/T9NTKBBXmFI/AAAAAAAA2e8/2oos16W-BRA/s1600/P6053213.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="301" src="http://3.bp.blogspot.com/-caMufUAzFOA/T9NTKBBXmFI/AAAAAAAA2e8/2oos16W-BRA/s400/P6053213.jpg" width="400" /></a></div>
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Calling the maintenance department, I got a response relatively fast. It turned out they increased the water pressure this week, and therefor they were discovering junctions that were not properly sealed. To fix the problem, the fellow banged on the junction with a hammer and claimed that this puts the o-ring into place. I was not convinced, but after waiting an hour it seemed that the leaking stopped.</div>
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And so, we all wasted an hour and half during one of the busiest day of the recent months. I should be thankful that this did not occur above any sensitive equipment.</div>
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PS. Two days later, I returned to the office (I was out due to conferences and such) to find the whole area wet. Seems that the leak returned. This was late afternoon and I had to call an emergency maintenance person. He closed the water to the whole corridor and depressurized the system. </div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-18334178196160886052012-05-29T14:48:00.001+03:002012-05-29T16:48:37.455+03:00Moran's PHD talk<div style="text-align: justify;">
Today Moran gave her PHD progress talk. This an occasion to celebrate the impressive achievements she made during her time here. (We have few more months until the official farewell, but why skip a chance to celebrate?)</div>
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<a href="https://lh5.googleusercontent.com/-AbV1rflTm2w/T8S2Go-2IfI/AAAAAAAA2c8/TrDRWzXQw3Y/s640/blogger-image-687256195.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://lh5.googleusercontent.com/-AbV1rflTm2w/T8S2Go-2IfI/AAAAAAAA2c8/TrDRWzXQw3Y/s640/blogger-image-687256195.jpg" /></a></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-76303807807760612342012-05-29T14:27:00.001+03:002012-05-29T14:27:29.479+03:00Long silenceThis blog has been silent for almost a year. During that time the number of events to report grew and thus the backlog made it harder to restart. <br />
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I will not summarize everything that happened. Rather as I report I will try to give proper context. <br />
Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-20535083919107289522012-05-08T18:36:00.000+03:002012-05-31T12:48:41.693+03:00Three minutes about science<p style="text-align: justify;"> Our training as Scientist is aimed at giving clear, precise and scholarly presentations. Public presentations are often different, as they need to hide many details and fine points, and instead focus on why this is interesting and exciting. </p><p style="text-align: justify;">Recently there was a call for a <a href="http://www.mada.org.il/famelab" target="_self" title="">national competition</a> for students to give 3 minute public talks about science. This is the Israeli branch of the <a href="http://famelab.org/" target="_blank" title="">FameLab</a> competition. </p><p style="text-align: justify;"> Our very own Naomi participated in one of the two preliminary competitions. She disappeared from the lab for half a day. When we next met her we learned that she one of finalists that were vote to participate in the national competition.</p><p style="text-align: justify;"> We immediately asked for a repeat performance. I recorded it with my iPhone. Our version was 3:11, a bit over the target time. It's in Hebrew, so my apologies to non-Hebrew speakers. </p><p style="text-align: justify;">Naomi's talk was about the <a href="http://nirfriedmanlab.blogspot.com/2010/12/you-are-what-your-father-ate.html" target="_blank" title="">epigenetic inheritance</a> research we published with Ollie Rando's a bit more than a year ago. <br></p><iframe title="YouTube video player" class="youtube-player" type="text/html" width="560" height="340" src="http://www.youtube.com/embed/HV_HaSeXCRs" frameborder="0" allowfullscreen=""></iframe><p style="text-align: justify;"> </p><p style="text-align: justify;">Unfortunately, the final competition took place when Naomi was traveling, and so we did not get to see her advance to the international competition.</p><p style="text-align: justify;"> </p> <br/><br/>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-57105917807808393482011-07-12T21:16:00.002+03:002011-07-12T21:19:33.984+03:00Behind the cover<div style="text-align: justify;">Getting<a href="http://nirfriedmanlab.blogspot.com/2011/07/we-made-cover.html"> a cover image for a journal</a> was a first for me. As such I thought it would be interesting to revisit the behind the scenes. I am going for a short recap.</div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">Initially when the paper was accepted the editor encouraged us to sugget a cover image. We (actually the Broad people, Manfred, Brian, and Aviv) recruited Sigrid Knemeyer who collected ideas and came up with some concept images. We (the three mentioned above, Moran, and me) then had several rounds of emails with Sigrid where each of us made comments, said what we liked or not about the options. Sigrid came up with a more detailed concept, which we sent to the editor. The editor wasn't too excited about it, and so we went back to the drawing board.</div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">This time Sigrid, came up with four initial concepts.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-nY6_35ltOEU/ThyOrvscDhI/AAAAAAAAuts/DAAGUx5vkTk/s1600/grabherr_revised_concepts.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://4.bp.blogspot.com/-nY6_35ltOEU/ThyOrvscDhI/AAAAAAAAuts/DAAGUx5vkTk/s400/grabherr_revised_concepts.png" width="391" /></a></div><div style="text-align: justify;">We really liked some elements of each, but thought that the vortex of letters does not capture the idea of short reads. The stacks and stacks of papers was also nice, but didn't make it clear that the reads are short.</div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">The next concept was to replace stacks of papers with short strips, like fortunes (as in fortune cookies), and combine it with the vortex.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-Qt1kErO9hNM/ThyNmaTX_4I/AAAAAAAAusY/1s1fnl8lyzA/s1600/NBT_vortex_1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://4.bp.blogspot.com/-Qt1kErO9hNM/ThyNmaTX_4I/AAAAAAAAusY/1s1fnl8lyzA/s400/NBT_vortex_1.jpg" width="301" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">We really liked this, but the final touch was adding the assembled sequence coming out of the vortex. This and change of color tone resulted in the concept that we sent to the journal.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://2.bp.blogspot.com/-c6zJSffzopo/ThyNkWG_aSI/AAAAAAAAusU/lOPffjS9rLA/s1600/NBT_vortex_4.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://2.bp.blogspot.com/-c6zJSffzopo/ThyNkWG_aSI/AAAAAAAAusU/lOPffjS9rLA/s400/NBT_vortex_4.jpg" width="301" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">They really liked it, and sent it to their graphic editors who came up with the final version. </div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://www.nature.com/nbt/journal/v29/n7/covers/largecover.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://www.nature.com/nbt/journal/v29/n7/covers/largecover.gif" width="302" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">As you can see, they dispensed with the fortune-cookie strips, but kept the letters in "words" that capture the idea of short fragments and made other visual changes.<br />
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In conclusion, this was an interesting process. Sigrid was great in making this happen, and deserve a lot of credit. Thanks!<br />
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</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com2tag:blogger.com,1999:blog-3190637267291688875.post-26950315344761330722011-07-12T00:17:00.000+03:002011-07-12T00:17:51.134+03:00We made the cover!<div style="text-align: justify;">Our paper on <a href="http://nirfriedmanlab.blogspot.com/2011/05/full-length-transcriptome-assembly-from.html">transcript assembly appeared online few weeks ago</a>. Now the actual issue came out, and we made the cover, with a striking image.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://www.nature.com/nbt/journal/v29/n7/covers/largecover.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://www.nature.com/nbt/journal/v29/n7/covers/largecover.gif" width="302" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">The idea came out of iterations between all of us (Manfred Grabher, Brian Haas, Moran, Aviv and me) and Sigrid Knemeyer who is an artist/illustrator working at the Broad Institute. Sigrid was great in developing the concept with our input of rough concepts, and this whirlwind was the final outcome.</div><div style="text-align: justify;"><br />
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</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-21807442284580328342011-07-01T15:14:00.001+03:002011-07-03T11:21:34.641+03:00Party: One Farewell + Two Welcome<div style="text-align: justify;">Recently it seems that we have many farewell party. Another one today, to celebrate Noa's graduation and to say farewell on her departure to the Weizmann Institute. At the same time we also welcomed two new additions to the extended lab family: Oren and Daniela who born recently.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://1.bp.blogspot.com/-XjpEV_ERM8Q/Tg9VLovSIEI/AAAAAAAAuow/WDQ1JpL8pzM/s1600/DSC_8467.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://1.bp.blogspot.com/-XjpEV_ERM8Q/Tg9VLovSIEI/AAAAAAAAuow/WDQ1JpL8pzM/s400/DSC_8467.jpg" width="275" /></a></div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://2.bp.blogspot.com/-IRGHRd7CwhQ/Tg9R5j7xNCI/AAAAAAAAunU/aSG3U0ouzpM/s1600/DSC_8332.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="273" src="http://2.bp.blogspot.com/-IRGHRd7CwhQ/Tg9R5j7xNCI/AAAAAAAAunU/aSG3U0ouzpM/s400/DSC_8332.jpg" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-8pv7wLQbmBY/Tg9SFm5UIPI/AAAAAAAAunY/t7HBE8k-AX0/s1600/DSC_8339.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://4.bp.blogspot.com/-8pv7wLQbmBY/Tg9SFm5UIPI/AAAAAAAAunY/t7HBE8k-AX0/s400/DSC_8339.jpg" width="285" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">We had a nice picnic in a park near Jerusalem, and enjoyed the presence of current and recent lab members and the many young children of the next generation. As noted by few participants, the lab has been extremely productive on that front...</div><div style="text-align: justify;"><br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://1.bp.blogspot.com/-geVsyt4q-9E/Tg9Tl-4SPpI/AAAAAAAAuoI/LlvZjCpZYXM/s1600/DSC_8404.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="267" src="http://1.bp.blogspot.com/-geVsyt4q-9E/Tg9Tl-4SPpI/AAAAAAAAuoI/LlvZjCpZYXM/s400/DSC_8404.jpg" width="400" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://3.bp.blogspot.com/-rIWynVBeTy8/Tg9TvTYKPNI/AAAAAAAAuoM/Agb4jPA1z2s/s1600/DSC_8412.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="308" src="http://3.bp.blogspot.com/-rIWynVBeTy8/Tg9TvTYKPNI/AAAAAAAAuoM/Agb4jPA1z2s/s400/DSC_8412.jpg" width="400" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://1.bp.blogspot.com/-A_zqsUpf8lA/Tg9T9KaTc0I/AAAAAAAAuoU/KKsaFlZtgVA/s1600/DSC_8418.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="267" src="http://1.bp.blogspot.com/-A_zqsUpf8lA/Tg9T9KaTc0I/AAAAAAAAuoU/KKsaFlZtgVA/s400/DSC_8418.jpg" width="400" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-E2BUoxoXp7s/Tg9SoD0AVtI/AAAAAAAAuno/JU5bImDdRD0/s1600/DSC_8362.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="273" src="http://4.bp.blogspot.com/-E2BUoxoXp7s/Tg9SoD0AVtI/AAAAAAAAuno/JU5bImDdRD0/s400/DSC_8362.jpg" width="400" /></a></div><div style="text-align: justify;"><br />
</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-32876873967310819882011-06-29T18:07:00.000+03:002011-06-29T18:07:33.096+03:00Substantial Histone Reduction Modulates Genome-wide Nucleosomal Occupancy and Global Transcriptional Output<div style="text-align: justify;">The recent wave of publications seem to continue, and a<a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001086">nother paper just appeared in PLoS Biology</a>. Like the <a href="http://nirfriedmanlab.blogspot.com/2011/06/patterns-and-mechanisms-of-ancestral.html">previous one</a>, this one was in the reviewing rounds for very long, and so we are very happy that it finally appeared.<br />
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</div><div style="text-align: justify;"></div><div style="text-align: justify;">This project is a collaboration with the group of Alessandra Agresti and Marco Bianchi from San Raffaele University in Milan. They are part of a European consortium that we are also members of, and they approached us to get help on dealing with nucleosome organization. Assaf got involved, into what was dubbed "The Italian Job" in lab meeting. After almost two years, the result is an impressive article.</div><div style="text-align: justify;"></div><div style="text-align: justify;"><br />
To summarize the basic idea, the experiments by Barbara Celona, the main author, and other member's of the Milan group show that deletion in a key gene reduces the number of nucleosomes in the genome. As a result the DNA strands are packed by smaller number of nucleosomes. By mapping the locations of these nucleosomes we can see if nucleosome reduction leads to uniform change in density, or preferential reduction at particular locations, and what is the effect on transcription.<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://www.plosbiology.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001098.g001&representation=PNG_M" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="250" src="http://www.plosbiology.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001098.g001&representation=PNG_M" width="400" /></a></div><div style="text-align: right;"><span class="Apple-style-span" style="font-size: x-small;">Source: PLoS Biology Synopsis by Robin Mejia</span></div><br />
Our results show that nucleosome loss is mostly in locations that are less packed in normal cells, and moreover, that this loss correlates with increased transcription.<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://www.plosbiology.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001086.g007&representation=PNG_M" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="http://www.plosbiology.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001086.g007&representation=PNG_M" width="331" /></a></div><br />
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Cool!<br />
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</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-83411863246637671332011-06-23T22:28:00.008+03:002011-06-25T23:22:55.829+03:00Presidential Conference<div style="text-align: justify;">This week we participated in the <a href="http://www.presidentconf.org.il/en/minisite2011_en.asp">Israeli President's annual conference</a>. This is a the place where important people from Israel and abroad come to talk about the future of the country, the region, and the world.</div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">The Hebrew University was a co-sponsor of the event, and had its own space to presents research highlight. The target audience was not scientifically minded, so the message was to be kept at high level. Each participating lab had a small space where a large poster was presented on a table. We had TV monitors showing a movie about our lab.</div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">Assaf and Avital participated as guides, and got to see the important people and even to talk with few. We did manage to get to hear some of the sessions, although I suspect the main action at these events in beyond the scenes.</div><br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-bCTPFVK-DNM/TgY5R7rvisI/AAAAAAAAukw/L2a5FzlheMg/s1600/DSC_0052.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="257" src="http://4.bp.blogspot.com/-bCTPFVK-DNM/TgY5R7rvisI/AAAAAAAAukw/L2a5FzlheMg/s400/DSC_0052.jpg" width="400" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://1.bp.blogspot.com/-yfFTRVO0MCI/TgY5VY1o0yI/AAAAAAAAuk4/lPW9fVtDfdU/s1600/DSC_0019.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="265" src="http://1.bp.blogspot.com/-yfFTRVO0MCI/TgY5VY1o0yI/AAAAAAAAuk4/lPW9fVtDfdU/s400/DSC_0019.jpg" width="400" /></a></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-81227618692085492692011-06-21T14:25:00.001+03:002011-07-03T11:29:24.354+03:00The Comeback + Visitors<div style="text-align: justify;">About three months ago Moran went off on a maternity leave. Today was the official first step on returning to academic work. To make the transition easier she was accompanied by her family. We got a chance to meet the family and the joy young ones bring.</div><div style="text-align: justify;"><br />
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</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-41270385538251827122011-06-11T22:42:00.002+03:002011-06-25T22:49:32.958+03:00Another weekend divingTwo weekend days to enjoy diving in Eilat. Many good sights and nice company of local people and fellow divers.<br />
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</div><div class="separator" style="clear: both; text-align: center;"><a href="http://1.bp.blogspot.com/-kT0Aa4rXGXs/TgY7N_egtRI/AAAAAAAAulM/XrTNtNzc3R0/s1600/IMG_2173-Edit-2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="http://1.bp.blogspot.com/-kT0Aa4rXGXs/TgY7N_egtRI/AAAAAAAAulM/XrTNtNzc3R0/s400/IMG_2173-Edit-2.jpg" width="308" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://2.bp.blogspot.com/-zkhqlFQ3IRA/TgY7Ii2SZrI/AAAAAAAAulA/Z_KNMm5vsj4/s1600/IMG_2160-Edit.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="308" src="http://2.bp.blogspot.com/-zkhqlFQ3IRA/TgY7Ii2SZrI/AAAAAAAAulA/Z_KNMm5vsj4/s400/IMG_2160-Edit.jpg" width="400" /></a></div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0tag:blogger.com,1999:blog-3190637267291688875.post-73901492027493840342011-06-07T22:02:00.002+03:002011-06-08T12:15:40.782+03:00Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast<div style="text-align: justify;">Hot from the (virtual) press! A <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001075">paper</a> that we have been working on for almost a year appeared today in PLoS Biology. This is three way collaboration between Fred van Leeuwen's group at the Netherlands Cancer Institute, Ollie Rando's group at UMass Medical School and our group. The work on our end was mostly Assaf's who is a co-first author. </div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">The interesting aspect of this paper is that using a trick developed in Fred's group, they can switch a "tag" on a histone H3 protein. This means that up to a certain point all H3 proteins are tagged by one tag, and after the switch they are all tagged with a different tag. Using this switch we can find out where these "old" histones are several generations after the switch. This gives us insight on how the cells perserve old histones during several cycles of replication.</div><div style="text-align: justify;"><br />
</div><div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/-26uTkFvaMKY/Te888ubM3iI/AAAAAAAAuOw/iefvTjelcyk/s1600/journal.pbio.1001075.g001.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="173" src="http://4.bp.blogspot.com/-26uTkFvaMKY/Te888ubM3iI/AAAAAAAAuOw/iefvTjelcyk/s400/journal.pbio.1001075.g001.png" width="400" /></a></div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">To quote ourselves:</div><blockquote style="text-align: justify;"><span class="Apple-style-span" style="color: #303030; line-height: 21px;"><span class="Apple-style-span" style="font-family: Times, 'Times New Roman', serif;">To our surprise, ancestral histones accumulate near the 5′ end of long, relatively inactive genes. Using a mathematical model, we show that our results can be explained by the combined effects of histone replacement, histone movement along genes from 3′ towards 5′ ends, and histone spreading during replication. Our results show that old histones do move but stay relatively close to their original location (within around 400 base-pairs), which places important constraints on how chromatin could potentially carry epigenetic information. Our findings also suggest that accumulation of the ancestral histones that are inherited can influence histone modification patterns.</span></span></blockquote><div style="text-align: justify;">To get to these conclusions Assaf implemented a mathematical model that takes into account the processes that affect nucleosome positions, and then showed that this model can provide a good fit to the data if we consider turnover, passback of nucleosomes (from 3' to 5'), and localized dispersion during replication. </div><div style="text-align: justify;"><br />
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</div>Foobarhttp://www.blogger.com/profile/09265685587777625953noreply@blogger.com0