tag:blogger.com,1999:blog-86730640478775694432024-03-06T10:24:47.896+01:00Postdoc Exploring<strong><p> Bits and pieces from the life of a scientist. This blog is a reminder why I still (mostly) like science, a collection of scientific information, not necessarily related to my research, a place for noting tips and tricks for the lab and often an exhaust pipe (related to the "mostly" above). </p> <p> Disclaimer: The opinions expressed here are entirely my own and should not be attributed to the institution where I work in any way.</p></strong>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.comBlogger32125tag:blogger.com,1999:blog-8673064047877569443.post-57636435605154135282013-09-18T00:59:00.003+02:002013-09-18T00:59:46.049+02:00A Capella Science<br />
The scientist in me will not let me rest until I post this here. The lyrics on their own are absolutely cool, for the performance judge for yourselves:<br />
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Whoa, Tim- how long did it take to put all of this together? Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-52432441633322445212013-02-11T16:42:00.002+01:002013-02-11T16:42:54.149+01:00LOL CAT scientific video by NatureI laughed really hard at this Nature video. In a good way I mean.<br />
Finally a piece of scientific news presented in a fun and amusing way. Keep going guys- I want to see more. (though how will you incorporate loz into plant science is still beyond me)<br />
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As for the rest of you: enjoy!</div>
Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-9978665161356029282012-11-29T18:07:00.002+01:002012-11-29T18:20:07.256+01:00Hat Tip - Blasted BioinformaticsI recently got in touch with NGS data in my attempt to set up a new proteomics method on a set of not-fully sequenced plants. I am new both to Next-Gen sequencing and to interspecies comparison so things are moving slow especially as I need annotated reads before I can use them.<br />
Fighting with BLAST+ I recently run into the aptly named "<span class="Apple-style-span" style="color: #111111; font-family: Georgia, Utopia, 'Palatino Linotype', Palatino, serif; font-size: 14px; line-height: 19px;"><a href="http://blastedbio.blogspot.de/">Blasted Bioinformatics!?</a>" blog. </span><span class="Apple-style-span" style="color: #111111; font-family: Georgia, Utopia, 'Palatino Linotype', Palatino, serif; font-size: 14px; line-height: 19px;">Clear and easy to read, with enough pointers in the text and comments to solve a bunch of issues. As a wet-bench scientist I can just say: thanks Peter and keep posting.</span>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-2175474515072381482012-01-31T12:33:00.001+01:002012-01-31T12:34:21.764+01:00... there goes my carnival Berry!<div style="text-align: justify;">
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Ok ok cliche, I know, but could not help it.</span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">My first ever carnival participation (<a href="http://postdoc-exploring.blogspot.com/2012/01/food-from-sun-elysia-chlorotica.html">Food from the sun</a>) at <a href="http://berrygoround.wordpress.com/">Berry Go Round</a>, hosted by <a href="http://mossplants.fieldofscience.com/">Moss Plants and More</a>.</span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">And links to a thon more exciting posts too.</span></div>
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<br /></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-76137034839441321192012-01-25T01:00:00.004+01:002012-01-25T01:04:17.415+01:00Grumpy post: Junk mail & Firewalls<br />
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Part 1: Junk mail- it's where all the important stuff goes: </span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Did I mention I'm writing a proposal these days? Well I'm almost done and deadline is on the 31st. So last week I sent it to the boss in the "New institution" to read it over…. and never heard back from him.</span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">After a polite period of a few days I sent a reminder to be told that my mail ended up in his spam folder. Ugh… <a href="http://postdoc-exploring.blogspot.com/2010/07/spam-rules-world.html">but it happens to the best of them and I can relate</a>! And I mean how many times have you ended up with an important mail marked as spam? There was a time when I thought these things have a way of sensing when you really need something so they suck it in. </span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Part 2: Firewall- stops communication among dependent devices:</span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">After the holidays I was unable to use one of our LTQ machines… First someone generously contaminated it with- "a contaminant". I got landed with the clean up job. I mean- it happens. But what was supposed to be routine clean up ended up a marathon calibration attempt. It was working, but if you try to calibrate after a certain point the ion intensity just dropped… It wasn't until a more tech savvy colleague looked it up and connected it to a software problem. But we haven't done any software updates. Or have we?</span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Turns out someone activated a fire wall on this PC, and the machine could not get aces to some of it's maser files. So although I have enormous respect for our IT support (t<a href="http://www.computerjokes.net/134.asp">hey deal with this more often than not</a>), guys please...</span></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-60252727977782082602012-01-21T23:56:00.001+01:002012-01-22T03:32:39.782+01:00Introduction to LC-MS Part 1: Playing with the big toys- exchange of LC auto-sampler plate<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizbSmyx4MIJVWecon1nP2K9aygosmSuEmpLh3fIYFXjDqtxjrnN77Y6WlcfdP6KkJqFPX4b9Gu-UVf1dFfmKF3U1baVeV6dvxKiV2IpfDtmHLZS_1ksW850PggwQvclGSYHfoiG0_0HaIV/s1600/LC_working1_s.JPG" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><span class="Apple-style-span" style="font-size: small;"><img border="0" height="190" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizbSmyx4MIJVWecon1nP2K9aygosmSuEmpLh3fIYFXjDqtxjrnN77Y6WlcfdP6KkJqFPX4b9Gu-UVf1dFfmKF3U1baVeV6dvxKiV2IpfDtmHLZS_1ksW850PggwQvclGSYHfoiG0_0HaIV/s200/LC_working1_s.JPG" width="200" /></span></a><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Some of you may know that one of the techniques I'm currently using is mass spectrometry in order to study the plant proteome. In short we refer to this as LC-MS/MS (liquid chromatography, tandem mass spectrometry). One of the things I like about the practical aspect of this job is the possibility to leave the wet lab and actually do some maintenance on the machines. I found that once I started this hands on approach, I begun to understand the process much more (reminder: biologist at heart talking here).</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5X_f4gfdjZ3MfIQlJmUWTpptQegaG3dkMMS0zVcgOLDOD3LbjFosL_Jqvv_pp8jeHCn-IF6XD9eDNsuTdl5KVG5griD3eIZnK6X-ISf0MuoW66DU5Q6kTPAMf_9aNBFR1NQPcWY0YuOwW/s1600/%25C2%25B5plate_s.JPG" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><span class="Apple-style-span" style="font-size: small;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5X_f4gfdjZ3MfIQlJmUWTpptQegaG3dkMMS0zVcgOLDOD3LbjFosL_Jqvv_pp8jeHCn-IF6XD9eDNsuTdl5KVG5griD3eIZnK6X-ISf0MuoW66DU5Q6kTPAMf_9aNBFR1NQPcWY0YuOwW/s200/%25C2%25B5plate_s.JPG" width="200" /></span></a><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">In proteomics we use liquid chromatography to pre-fractionate a complex sample. The proteins have already been cut up in little pieces by special enzymes before we apply them in the LC. But in order to identify them on the MS, we need to separate them from each other, to allow the MS to identify as many of them as possible (if all peptides arrive at once, the MS will only identify some, but if you send them in one by one- then the number of totally identified proteins increases).</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoFECBgG_UA2bf2uIpShS9FdnppA8yb7VsatwA1Aywz3JQinz8CECb0SIcohASbhz0FnslE5x7qIx_l_Sk7mayE8VqHBTNu4gQ7T3_HEm3ixn5PuBE4tt5cDmzCU6y-TVlsT8jPO_L3Wfp/s1600/Autosamplerplate1_s.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><span class="Apple-style-span" style="font-size: small;"><img border="0" height="199" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoFECBgG_UA2bf2uIpShS9FdnppA8yb7VsatwA1Aywz3JQinz8CECb0SIcohASbhz0FnslE5x7qIx_l_Sk7mayE8VqHBTNu4gQ7T3_HEm3ixn5PuBE4tt5cDmzCU6y-TVlsT8jPO_L3Wfp/s200/Autosamplerplate1_s.jpg" width="200" /></span></a><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Recently we had a situation where most of our LCs were somehow malfunctioning, so I tried to get one working machine out of two broken ones… One of the better LCs had a malfunctioning auto-sampler plate, basically the fan that kept the samples cool was broken. While I was exchanging it, I took some of these photos and decide to give you a glimpse inside the machine.</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1udUyMflV6DGLtu97OenZsear8RjiSzYCdN4p_vhU0QZ9wiqvUEpSoZJj6mou4qWQxW9BUgiLt-_vBwPn-0mHBuVapOX9Avx-3EoskefQvqPsRut7g7ARKZ3OOe3guGRbCFbYTtSR5hdd/s1600/Autosamplerplate-coolingfan1_s.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><span class="Apple-style-span" style="font-size: small;"><img border="0" height="145" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1udUyMflV6DGLtu97OenZsear8RjiSzYCdN4p_vhU0QZ9wiqvUEpSoZJj6mou4qWQxW9BUgiLt-_vBwPn-0mHBuVapOX9Avx-3EoskefQvqPsRut7g7ARKZ3OOe3guGRbCFbYTtSR5hdd/s200/Autosamplerplate-coolingfan1_s.jpg" width="200" /></span></a><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">On the first picture you see the working LC in its better days. The samples are in an auto-sampler plate which is kept cool to minimize evaporation. The sample is picked by the auto-sampler needle and loaded onto a very thin liquid chromatography column (First photo, marked with the arrow). The machine you see on the side is a mass spectrometer, which is used for peptide and thus protein identification. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFwWDSIO-DFndmShYeDgK4tj5VOmXslWKBtNvGmWvXGUPQQTx22gzdRFbVhJxV5G9kbL0mk9V2UbjpfVd4qJcy9xBiLSg-Dom1swas2UVv3gEdWnLiocuCIr8XFkm3wLbDcU01xyMhkXpF/s1600/LC_inside_side_s.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFwWDSIO-DFndmShYeDgK4tj5VOmXslWKBtNvGmWvXGUPQQTx22gzdRFbVhJxV5G9kbL0mk9V2UbjpfVd4qJcy9xBiLSg-Dom1swas2UVv3gEdWnLiocuCIr8XFkm3wLbDcU01xyMhkXpF/s200/LC_inside_side_s.jpg" width="150" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0itLgbkoRRbhGO03e-EFgqp9wTRf50kKxQtyyCd88wvGlLUU3e0oBU6-NgjnZgUsCekcMHuzn7bXpQnzmwnbDVEm_Muc6XVcooj3wRe230H3KH7r6XYHYZaTbuUakhyD2a0sFnWjPLUJv/s1600/LC_inside_side_s.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><span class="Apple-style-span" style="font-size: small;"></span></a><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;">As this is a nano-LC, the complex samples are put in a µ-well plate shown on the second photo.</span><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;"> The µ-well plate is inserted in the auto-sampler plate of the LC (third photo) and on the back of it is a simple fan and some copper plates that are functioning in keeping the whole thing cool (fourth photo). </span><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: small;"> On the last photo you can see how the whole thing looks from the side. The tray which carries the entire auto-sampler setup can be seen at the bottom right (remember, the plate is removed at this stage). The auto-sampler needle is indicated with the arrow. It is attached on an automatic arm which can move it above each well from the plate and lower it to pick up the sample. The sample is then pushed onto the column mentioned above. On the other side of the LC are a number of pumps. One of them functions in the sample pickup itself, while others mix the elution solutions in specific percentages in order to elute peptides from the column onto the MS based on their chemical properties. In fact if you return to the first photo you will see the mixing gradient of the two elution solutions on the screen of the working LC (shown on the bottom left graph).</span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Well this little creature can do that. The mollusk feeds on algi, which just like the higher plants can turn the energy from the sun into food. In plants, this occurs in parts of their cells called chloroplasts. Well, when Elysia feeds, it keeps the chloroplasts intact in the gut and amazingly they continue to produce food like in the plants. You can find more information (and a nicer version some of the videos below) <a href="http://sbe.umaine.edu/symbio/3Slug/3about.html">here</a>.</span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Below are four videos, the first two show Elysia in action. But just in case you need more words the third and fourth videos are an interview of two students from the university of Maine and a powerpoint presentation that talk informing you a bit more about these animals.</span><br />
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">UPDATE: wow there is a <a href="http://www.seaslugforum.net/factsheet.cfm?base=solarpow">sea-slug forum focusing on this topic</a>. I'm impressed! (and If I do not post for a few days... well I found myself some new reading material)</span><br />
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">The first feeding of a young snail.</span><br />
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">The next day, it is full with chloroplasts.</span><br />
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">The students that do the job: u<span class="Apple-style-span" style="color: #333333; line-height: 18px;">ndergraduates Helen Mattsson and Susan Devine</span></span></div>
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<span class="Apple-style-span" style="color: #333333; line-height: 18px;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Dr. Rebecca Johnson</span></span></div>
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<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Update 31.1.2012: this post is part of <a href="http://berrygoround.wordpress.com/">Berry Go Round</a> #48, hosted at <a href="http://mossplants.fieldofscience.com/">Moss Plants and More</a>. </span>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-1425729073282079042012-01-13T00:06:00.000+01:002012-01-13T21:53:25.768+01:00Proposal writing reflections (a silent post)<div class="separator" style="clear: both; text-align: center;">
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http://www.nih.gov/catalyst/back/97.11/cartoon.html</div>
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<br /></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-44261555297996311972012-01-12T00:29:00.002+01:002012-01-12T00:30:35.237+01:00Viva Vox- a welcome distraction<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Nothing directly to do with science this time around. </span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">I've been absolutely obsessed with these guys for the past two days (I just wish the audience was quieter).</span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Enjoy. </span><br />
<div class="separator" style="clear: both; text-align: center;">
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/Od52gJs-8M0?feature=player_embedded' frameborder='0'></iframe></span></div>
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br /></span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">And thanks <a href="http://www.youtube.com/user/vivavoxchoir/featured">Viva Vox</a> for getting me through a difficult few days of writing.</span>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-75542843773351806882012-01-08T23:46:00.000+01:002012-01-08T23:46:49.447+01:00European Union take on plant GMOs<div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">I do not really want to comment here, this is just a summary of information that I was looking for and may need to return to it in the future. Maybe someone else will find it useful as well. </span></div><br />
<ul><li style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; border-collapse: collapse;">AM04-1020</span> <a href="https://irmm.jrc.ec.europa.eu/news/Pages/GMOcertifiedreferencematerialsforAM04-120potato.aspx">potato</a></span></li>
<li style="text-align: justify;"><a href="https://irmm.jrc.ec.europa.eu/news/Pages/0912_new_gmo_crms.aspx"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; border-collapse: collapse;"><b>98140 maize, </b></span><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; border-collapse: collapse;">GHB119 cotton</span></span></a></li>
<li style="text-align: justify;"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; border-collapse: collapse;"><a href="https://irmm.jrc.ec.europa.eu/news/Pages/IRMMhasextendeditsrangeofGMOCertifiedReferenceMaterials(CRMs).aspx"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">GMO certified reference materials</span></a></span></li>
</ul><br />
<div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">The news published by the European commission joint research centre can be found <a href="https://irmm.jrc.ec.europa.eu/News/Pages/Newsarchive.aspx?field=Food,%20biotechnology%20and%20health">here</a>.</span></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-13254129154553548532012-01-07T04:37:00.000+01:002012-01-07T04:37:27.760+01:00Application thresholds- do they exist?<div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Hi everyone,</span></div><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Just a brief one as a return from my "non blogging hibernation":</span></div><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">If been wondering lately if there is such a thing as sending too many job applications before the quality of the applications you are sending out starts to drop.</span></div><br />
<ul><li style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Current situation: 1 application pending, 1 withdrawal (I was shortlisted, luckily I initiated a visit where I realized I do not fit in the group constellation), 2 application deadlines coming up at the end of January, and one grant proposal to be submitted before the end of january as well. I still have a few months on my current position.</span></li>
</ul><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Given that I can only do this after my days' work, I started noticing that these three are a bit more difficult to write in parallel. I wonder if there is some statistics out there? </span><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">How many applications people send on average - and not random applications but for positions for which they are well suited, before one of them works? How many positions are there for a highly qualified scientist, specializing in a particular field, assuming your geographical limitation is the current continent? (Wow, almost tempted to try and calculate this!)</span></div><br />
<div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br />
</span></div><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">And how do you decide what your thresholds are? Some of my wants and deal-breakers are listed below</span></div><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br />
</span></div><div style="text-align: justify;"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">I'd like to:</span></div><div style="text-align: justify;"></div><ul><li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Stay in academic research (my publications are OK and more will be coming in 2012, so I can take the risk at least for another year or two)</span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Fit within the group and particularly have mutual respect with the boss. I'm not a slacker so that is not an issue but I prefer groups that collaborate rather than compete within.</span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Have a <u>scientific</u> project rather than be turned into a technician just because I've touched a big machine before... </span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Have a chance to form collaborations</span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Have a chance to learn new things (this fits with having a scientific = biological project where you follow a story, rather than routinely and randomly measure something for millions of people)</span></li>
</ul><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Particular deal breakers (as long as I have a choice):</span><br />
<div style="text-align: justify;"></div><ul><li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">If I feel the boss will not give me credit for my work, or worse if I feel i can not count on his/her support when needed.</span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">From above: if I do not fit in the group. Even if the project is great, I would probably take the second best position if it is clear to me that I can not communicate/ work/ get along with the people.</span></li>
<li><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><a href="http://postdoc-exploring.blogspot.com/2010/07/postdocs-unite.html">An issue I've blogged about before</a>, if the position comes without any insurance (social, health, retirement). I'm on one of these fellowships now and I feel it's time for that to change.</span></li>
</ul><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">As I mentioned though, I know about the deal-breakers because I've been through them. And if I lived through them once, I can do so again. So if a push comes to a shove, I'll take whatever I can. A postdoc has got to eat, but I hope that if I know what I want (thus this post) and get organized, the chances of something good happening will increase. </span>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-10860612236772727462011-04-20T16:55:00.002+02:002011-04-24T21:00:24.824+02:00Handbook of Biological StatisticsRecently I've been traing to make sense of some proteomics data and needed a comprehensive overview of some statistical methods.<br />
By comprehensive I mean- that a biologist like myself could understand them.<br />
I run into the <a href="http://udel.edu/%7Emcdonald/statintro.html">handbook of biological statistics</a> by John H. McDonald and liked it so much I thought I'd share it with you.<br />
<br />
If you are a book worm and prefer hard copies you can find it in a .pdf version ready for free download and printing, you could order a printed copy for the cost of printing and shipment or just use it on-line.<br />
<br />
I found it readable, liked the biological examples and the pointers for extra reading, for when things get more serious. <br />
<br />
Thanks John McDonald.Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-47167749816941821782011-01-05T18:59:00.002+01:002011-01-05T19:18:24.073+01:00The freeze-thaw indicatorsOk, given my experience with <a href="http://postdoc-exploring.blogspot.com/2011/01/not-so-express-delivery.html">shipping frozen samples</a>- I played just a bit today, using things that were lying on my work bench, and here is what came out.<br />
Take a 1.5mL tube, add some basic solution (I used 200µL, 2M NaOH in the tests, but will decrease the molarity for the actual shipment if I go with this combination). Snap freeze it in liquid Nitrogen (or the freezer, if you can be bothered to wait).<br />
Then, I added 100µL water and froze it again and finally I added 100µL of Coomasie Brilliant Blue (G-250). I should note that for the tests I took an already activated Coomasie, prepared as in <a href="http://www.ncbi.nlm.nih.gov/pubmed/2466658?dopt=Abstract">Neuhoff</a> <i>et</i> al. I guess for the future a bit of Coomasie stain in water will do as well.<br />
I snap froze everything and could see a white bottom and a distinct blue ring on top.<br />
<br />
To test leave it on room temperature, or mix very gently... I noticed 2 things<br />
1- The Coomasie thawed first, followed by the 2M NaOH. The water thawed last.<br />
2- As soon as the two main liquids had thawed, they started gently mixing (very slowly, unless you agitate a bit) the result was a reddish mixture, which even when re-frozen was different from the initially frozen test-tube.<br />
<br />
So what am I thinking: given my <a href="http://postdoc-exploring.blogspot.com/2011/01/not-so-express-delivery.html">lack of luck</a> with sending samples, I will include one of these in my shipment next time, to tell me if my samples underwent a temperature change.<br />
Also, probably using some of the <a href="http://www.precisionnutrition.com/wordpress/wp-content/uploads/2008/12/ph-indicator-chart.jpg">standard pH indicators</a>, or simply 2 colored liquids will work as well to avoid shipping high or low pH liquids. If you are willing to tinker you can look up freezing temperatures of various liquids and thus know how high the temperature rose... But I currently have no time to play with this... Still if you do work up a nice combination, be kind and let me know.<br />
Finally, thanks again to the friend who tipped me about this sweet little trick-this was not my idea!Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-14416550021527252192011-01-05T01:17:00.004+01:002011-01-05T17:20:19.371+01:00The NoT so express deliveryThis is a story of 2 postdocs that tried to finish something just before the holdays.<br />
<br />
Basically, my part would have ended by shipping spome samples on dry for a colaborative project. Unfortunatelly DHL does not ship dry ice, and our institute tends to use TNT anyway .<br />
<br />
Wanting to test them I sent about 5% of the samples on the first week (15.12) and they arrivved within 2 days. My collaborator told me that there was plenty of dry ice left. <br />
So on 21.12 I sent the bulk shipment. OK the weather conditions were bad but the package was 7.8kg for 200g of samples. The rest was the styroform box and dry ice.<br />
The first thing we noticed was that the tracking number was not in the system. My collaborator told me, that on one search attempt he could see the number being tracked to Hong Kong- while the shipment was addressed to a west European country. Then the number was gone. I called TNT and was told that the tracking number is not in the system. But, this was only day 1. <br />
<br />
On day 2 the shipment was listed as still being stored in a neighbouring city in Germany. But there was some extra dry ice in there so I had hopes that not all was lost.<br />
<br />
Unfortunatelly, I left for my home country on day 3 and was unable to check my mail so I just learned that my shippment arrived on 28 or 29th. It seems that TNT did re-fill the dry ice, at some point, but only after everything thawed! Thanks for nothing.<br />
I will not even begin to speculate what was happening in the entire time the the package was missing.<br />
<br />
In total, it costs me more than 1 month work ro grow and prepare the shipment. It costs us a massive delay for the project... I wonder if TNT will even re-emburse the shippment money!<br />
<br />
I learned 2 things from this experience:<br />
1- Never, ever ship before holidays and<br />
2- Include freezing indicators. In this case it was obvious the samples thawed, but sometimes it is not so easy to see. A friend just suggected I consecuetively freeze 2 different coloured liquids on top of eachother in a small vial and include it in the shipment. The logic is that if the temperature rizes the liquids will thaw and the colours will mix indicating the raise of temperature. I'll give it a try in the next attempt. <br />
<br />
Ah damn, I have to do it all over again.Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-79841121545601445752010-11-23T22:48:00.007+01:002010-11-23T23:27:02.453+01:00The follow up post<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Before I launch into the recent <a href="http://postdoc-exploring.blogspot.com/2010/11/postdoc-exploring-aka-when-life-takes.html">ongoings</a> (basically- I'm saving this post for the weekend when I have more time), here is an update on few older things.<br />
<br />
First- this is the good news, I <a href="http://postdoc-exploring.blogspot.com/2010/08/run-run-run.html">finally registered for 2 runs</a>- yey. The first one is the <a href="http://www.scc-events.com/events/berliner_halbmarathon/2011/index.en.php">Berlin half marathon</a> in April next year. I have already run this event and it has always been great fun, so I figured it is a sure bet. It's a while away but I have become a bit lazy so - it's all-right. Hopefully the prospect of running 21km in the presence of other people, will keep me moving over the winter.<br />
The second run I am not going to announce yet, for 2 main reasons a) it's quite far into the future and b) it's scary to even think about it. I will let you know in due time, promise.<br />
I also looked up and joined a local gym, so now I just have to go there. :-)<br />
<br />
The bad news is that <a href="http://postdoc-exploring.blogspot.com/2010/09/tic-tac-tic-tac.html">my proposal</a> did not get through :,-/ so now I will have to try and re-submit in a few month's time. On the good side- I am not jobless, so I can not complain too much.<br />
<br />
FInally, during the few weeks in the <a href="http://postdoc-exploring.blogspot.com/2010/11/postdoc-exploring-aka-when-life-takes.html">conference</a> preparation period I generated so much data that I will have stuff to analyze till February. But at least I seem to be in <a href="http://postdoc-exploring.blogspot.com/2010/07/sunday-in-berlin.html">calmer waters</a> again, so at least I can <a href="http://postdoc-exploring.blogspot.com/2010/07/just-1-hour.html">enjoy the weekends</a> and have stopped dreaming about my experiments.<br />
On that note- good night everyone.</span>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-2039637095942382702010-11-17T22:24:00.002+01:002010-11-17T23:28:35.568+01:00Postdoc Exploring a.k.a When life takes overWell, this postdoc was exploring and that's all I can say for my prolonged absence... Ok that kind of beats the purpose to this blog so here is a short re-cap.<br />
<br />
Chapter 1- The lazy abstract<br />
As early as April this year, I submitted an abstract for my first ever proteomics conference. Of course, coming from a molecular biology field- I had no idea that in the "omics" world things sometimes move much slower than expected... After the organisers prolonged the deadline about a million of times- I finally heard from them in the middle of September that the abstract is accepted. This was a medium sized conference, and I am new to this field so I was pleased about this. Especially, since I submitted a beginners project which of course I had not touched at all. about 1 week later, a second e-mail arrived announcing that the abstract has been selected for a talk...<br />
And this is where things got a bit crazy. Whereas for a poster I thought I could get away with a few graphs and measurements, for a talk I actually need some decent data... So I blocked the groups machine and most of the computer power and I measured....<br />
<br />
Chapter 2- The conference<br />
This was something different. Until now I have stayed within my field, but after changing topics- i wanted a purely mass spectrometry (MS) conference, so I can get into the field. As the conference was centred around a methodological point- the participants originated the entire bio-medical palette of sciences... This was both good and bad.<br />
Good because I got to hear a lot of various approaches, gather ideas which can be implemented in my own research and bad because quite often I had an imaginary question-mark above my head. All in all- it was great though.<br />
<br />
Chapter 3- The actual exploring<br />
As a way of rewarding myself for all the hard work- I actually stayed on a few extra days in this new country. I enjoyed my time, and photos will follow in some of the next posts.<br />
<br />
Finally- I'm officially back and have a lot to blog about, my coming schedule is also fairly busy- but I do not expect that part to change.Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-53291563424280931922010-09-29T00:11:00.004+02:002010-11-23T22:54:04.836+01:00The Trained Chimp Job<div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Few days ago, for the first time in my postdoc lab- I had to do a routine preparation job.</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Now this job is neither difficult to perform nor a mentally challenging task, it is simply necessary. For a long time there was a student worker in the lab, paid to do this simple job and I somehow always got away. </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">So in the middle of my "big and important experiment" Yours truly realised that we need more of the little thingies... I mean, how time consuming can it be?!</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"><br />
</span></span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"> </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">At the end of the day two things were noteworthy:</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">a) I have a new found respect for technical assistants and student workers. </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Thank you guys for saving my time and making my life easier!</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">and</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">b) Being bored out of my mind- with a colleague, we decided we should try to order a few trained chimps to do this job.</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"><br />
</span></span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"> </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Of course, we had to take it a step forward so today we filled in an actual order form that went something like this:</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">From distributor: Berlin Zoo</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Order Details</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Amount: 2</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Description: Trained Chimps</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Order number: 666</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Price:</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"><br />
</span></span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"> </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Oredered by: Funny Colleague and Bori</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Sighend by:___________________</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">At this point we took the order form to the group-leader (giggling like teenage kids, on top of everything) and asked for a signature.</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">Now I'm not sure if I just put a lid on my scientific career - but the expression on my bosses face was priceless.</span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"><br />
</span></span><span class="Apple-style-span" style="font-size: small;"> </span><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;"> </span></span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-family: inherit;"><span class="Apple-style-span" style="font-size: small;">As obviously we will not be getting any chimps- we are S1 lab only... I am considering to bring a bunch of bananas to our next group meeting. Looks like we are stuck with the Chimp Job. </span></span></div><div><br />
</div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-65958879083543646142010-09-23T23:09:00.005+02:002010-09-29T00:25:33.351+02:00TIc-tac, tic-tac<div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">... Just as time is slowly ticking away, so is my contract- undeniably running out! Recetnly, </span><a href="http://microbiologistxx.blogspot.com/2010/09/my-big-news-in-form-of-riddlesort-of.html"><span class="Apple-style-span" style="font-size: medium;">MicrobiologistXX</span></a><span class="Apple-style-span" style="font-size: medium;"> had successfully gone through the system (congrats again- it's great to know it is possible!), but for my proposal there is no reply yet. I'm guessing that the tedious Germany bureaucracy can not be helping here, but from the online tracking system- it seems that my proposal is stuck with the reviewers... still!</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Now the </span><a href="http://www.dfg.de/en/research_funding/proposal_process/quo_vadis_proposals/index.html"><span class="Apple-style-span" style="font-size: medium;">DFG </span></a><span class="Apple-style-span" style="font-size: medium;">seems to have four stages of their process, that they are going to announce on the online </span><a href="http://www.dfg.de/en/research_funding/proposal_process/elan/index.html"><span class="Apple-style-span" style="font-size: medium;">web-portal</span></a><span class="Apple-style-span" style="font-size: medium;">. After you send it in and they receive it- you will receive an acknowledgement and an account on their portal elan.de. Your proposal will be marked as in the "Processing" stage- in the case of the individual grants proposal, which is where I am applying, and especially if it is your first-time proposal, they will contact you if something has gone amiss with the documents. This is very nice of them. Once all the papers are there, they send it off to review....</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">And in my case it is where it still is- for three months and counting! I could not find the information about the period that the reviewers are expected to reply in (but for a scientific paper- you get something like 2 weeks to a month right?!).</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Now, should the reviewers reply positively, the proposal should enter the (for me) hypothetical stage "preparing for decision"- where the way I understand, the DFG again checks if everything is order, possibly from the financial aspect. Finally the "decision" step is carried out in a Joint committee or a Grants committee meeting. I could not find a link, but I fear that these meetings happen quarterly (do hope I am wrong and they take place more often)... because the way it looks right now, my proposal will miss the Autumn meeting, judging from the time of last-lears (could find no info about this year's date- but a press release from last year places in </span><a href="http://www.knowledge-exchange.info/Default.aspx?ID=62&M=News&NewsID=67"><span class="Apple-style-span" style="font-size: medium;">early October</span></a><span class="Apple-style-span" style="font-size: medium;">).</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Initially my project was planned to begin at October, but I placed this date accounting for some delay, and it would be totally OK if the project starts January next year. </span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">The problem is- that with no decision, I can not hold off posting applications any longer. I found a few places that fit quite nicely to what I am doing, and to my freinds accross the big pond I say- some of them are in the US! </span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">So far so good. My problem- I know that if I apply for one of these- I will do my best to get it. What I "fear" is the best case scenario, or more precisely looking irresponsible if I would have to leave a group leader hanging, or reject the first ever grant that I wrote from scratch! I guess that's naive thinking.</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Of course, choosing between two good things is much better than being left with no options at all- so off to application writing I go, but it would be soooo much easier if the reviewers just decided. So come on you lot- move on!</span></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-76537964231773453512010-09-07T22:07:00.001+02:002010-09-29T00:25:56.827+02:00From the archive...<div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">... the cold room archive, that is!</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">I was cleaning up my shelf today and found a couple of buffers which I made in 2002 and 2003. Wow! </span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">That's like light years away. I must have made them when I first came here as a trainee in my "First-lab". They somehow survived, not only the period when I was back home to graduate from university, but also the entire period in my "First lab" where I did my PhD. They stayed clean enough for me to transport them to my "Postdoc-lab" and now were rediscovered...</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">(OK, one of them was "alive" but the second- mostly sodium chloride inside, nothing growing- I guess that is why I have not gotten rid of it untill now)</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Almost felt sorry to throw it away.</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Similarly, a former student-worker, now a PhD student in our lab, who returned after his masters degree ( again, in another country) simply went to his "old" shelf- collected the usable buffers from a year and a half ago and carried on... </span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">But I was joking with him today: there should be a lab relicts museum of some sort.</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">Ah wait there are- the </span><a href="http://www.sciencemuseum.org.uk/"><span class="Apple-style-span" style="font-size: medium;">science museums like the one in London</span></a><span class="Apple-style-span" style="font-size: medium;"> , although I do not think we'll be seeing any "living" buffers there. By the way, I remember seing that place when I was 18 and thinking it was cool, and yes- that was last century.</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px; min-height: 14.0px;"><span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: 12.0px Helvetica; margin: 0.0px 0.0px 0.0px 0.0px;"><span class="Apple-style-span" style="font-size: medium;">But enough reminiscing on my side- what is your coolest find till now?</span></div><div><br />
</div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-65359485062846650012010-09-01T02:32:00.006+02:002010-09-29T00:27:02.483+02:00I spy with my little eye something beginning with "B"<div class="separator" style="clear: both; text-align: center;"><span class="Apple-style-span" style="font-family: Helvetica;">Do you remember this game that we all played, in one form or another, when we were little kids?</span></div><div class="separator" style="clear: both; text-align: center;"><span class="Apple-style-span" style="font-family: Helvetica;">Well it just fir for me today, so here we go: I spy with my little eye- something beginning with "B<b>"</b></span></div><div class="separator" style="clear: both; text-align: center;"><span class="Apple-style-span" style="font-family: Helvetica;"><b>Bikes</b></span><span class="Apple-style-span" style="font-family: Helvetica;">: Bikes to rent for 1€ per day; bikes to ride on the quay by the Garonne; bikes as an extreme sport. </span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigMmUncn2xRg1pLJDZGUf94oxnkCPdKB8EyyrYCsui253fCgngWGRUaGb-hkeU-jljkNA4mkvjnKH85B_3Oo5LguTWxjSO5y6Aqc7HJojla9jCiqePlFRRcDXxEhU9kKA_2dVxq2PNF7c-/s1600/P1010410+copy_bike.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigMmUncn2xRg1pLJDZGUf94oxnkCPdKB8EyyrYCsui253fCgngWGRUaGb-hkeU-jljkNA4mkvjnKH85B_3Oo5LguTWxjSO5y6Aqc7HJojla9jCiqePlFRRcDXxEhU9kKA_2dVxq2PNF7c-/s200/P1010410+copy_bike.JPG" width="200" /></a></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;"><br />
</span> </b></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-height: 14px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;">Boats</span></b><span class="Apple-style-span" style="font-size: medium;"> : on the river- of course. And on that note- I wonder why is the water so murky!</span></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;">Boards</span></b><span class="Apple-style-span" style="font-size: medium;">: to lie on and enjoy the sun, I actually came up with this post right there and then. (Skate-)boards to show off- this guy actually stopped me and asked me to take a photo of him.</span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEitGhuglVeHZqBYI2LY3BYhJt7XZn5SI8j0N0uaw2zn95CqO2JuEaXS7XQozC53W6bIRRRZ_X4Gjr8-L-llFNHOYCn6IUudRrLYZpyrjZQ6xKLOJ6wB33-jbsdAgutHDyAmAsPsWwghwgkC/s1600/P1010328_skateboard.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="145" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEitGhuglVeHZqBYI2LY3BYhJt7XZn5SI8j0N0uaw2zn95CqO2JuEaXS7XQozC53W6bIRRRZ_X4Gjr8-L-llFNHOYCn6IUudRrLYZpyrjZQ6xKLOJ6wB33-jbsdAgutHDyAmAsPsWwghwgkC/s200/P1010328_skateboard.JPG" width="200" /></a></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;">Birds</span></b><span class="Apple-style-span" style="font-size: medium;">- like in every city</span><br />
<span class="Apple-style-span" style="font-size: medium;"><br />
</span></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;">Buildings</span></b><span class="Apple-style-span" style="font-size: medium;">- old and new, beautifully lit at night.</span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqTkNjzWKzZl-7dxpEstGbSso5dVuUtYxFakgqEoFDVMu-h-0kYLbi3Okiwkq6luA2rX89hNbrZDMvaJ-lumL48eyQKod60lws3nWomy2Cw-y6gjXYDeM82SX91bX84EIOhVf9kYiTDnKp/s1600/P1010475+copy_night2b.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqTkNjzWKzZl-7dxpEstGbSso5dVuUtYxFakgqEoFDVMu-h-0kYLbi3Okiwkq6luA2rX89hNbrZDMvaJ-lumL48eyQKod60lws3nWomy2Cw-y6gjXYDeM82SX91bX84EIOhVf9kYiTDnKp/s200/P1010475+copy_night2b.png" width="200" /></a></div><div class="separator" style="clear: both; text-align: center;"><br />
</div><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1v6V9wrfasKgy2cJFE0s_PGCTDL-AcpR6fdS8Urr-gtgB3sCY4cNowP-hlN5UeZz4FMUBoGYIlWL39dzLRenrl_NmnWd18BroDEqhMcoKuTAMLNUX3gd-Bl8FCj18UapssXTVu_yFBo7-/s1600/P1010474+copy_night1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="99" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1v6V9wrfasKgy2cJFE0s_PGCTDL-AcpR6fdS8Urr-gtgB3sCY4cNowP-hlN5UeZz4FMUBoGYIlWL39dzLRenrl_NmnWd18BroDEqhMcoKuTAMLNUX3gd-Bl8FCj18UapssXTVu_yFBo7-/s200/P1010474+copy_night1.jpg" width="200" /></a></div><div class="separator" style="clear: both; text-align: center;"><br />
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</div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><b><span class="Apple-style-span" style="font-size: medium;">Bibliotheque</span></b><span class="Apple-style-span" style="font-size: medium;">- a mobile library, this made me smile quite a bit.</span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjBbHKXAHm7EwLLKfFG3WQipycpIN61UEGZR7yZ97CeTciZWGU_QacwNvXBZzNwbxOtX2cmdhOdHtD21i5Yeh_a9OT2geAslRWNZy3ddPgz0l6r2cOibivmScjNrzd5ugrqCJCadQgMvys/s1600/P1010423+copy_bibliotheque.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="106" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjBbHKXAHm7EwLLKfFG3WQipycpIN61UEGZR7yZ97CeTciZWGU_QacwNvXBZzNwbxOtX2cmdhOdHtD21i5Yeh_a9OT2geAslRWNZy3ddPgz0l6r2cOibivmScjNrzd5ugrqCJCadQgMvys/s200/P1010423+copy_bibliotheque.JPG" width="200" /></a></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><span class="Apple-style-span" style="font-family: Times;"><span class="Apple-style-span" style="font-size: medium;"><b></b></span></span><br />
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<div style="text-align: center;"><span class="Apple-style-span" style="font-weight: normal;"><b><b><b><div class="separator" style="clear: both; display: inline !important; text-align: center;"><span class="Apple-style-span" style="font-family: Helvetica; font-weight: normal;"><b>Bilboards</b>- just about everywhere. sometimes obscuring the view</span></div></b></b></b></span></div></b><br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisxzWZ3zQaNCf9RkQYByJM0rd9X4GMFCQOoJRtDYG4aPUpc-p8QaUY-eVGLAClY1NUHhhQk63QPEoKU7Y62qSuHv3n8WBluxM0cPak4BnNac_USH7ZZMwgYiZv2ZAcctjEWkIYIkrZ4OG9/s1600/P1010407+copy.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisxzWZ3zQaNCf9RkQYByJM0rd9X4GMFCQOoJRtDYG4aPUpc-p8QaUY-eVGLAClY1NUHhhQk63QPEoKU7Y62qSuHv3n8WBluxM0cPak4BnNac_USH7ZZMwgYiZv2ZAcctjEWkIYIkrZ4OG9/s200/P1010407+copy.JPG" width="150" /></a></div><div style="font: normal normal normal 12px/normal Helvetica; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; text-align: center;"><span class="Apple-style-span" style="font-size: medium;"><br />
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<span class="Apple-style-span" style="font-size: medium;">But all in all </span><b><span class="Apple-style-span" style="font-size: medium;">beautiful BORDEAUX</span></b></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEja_AeKiohKGxFIdCB8Ed310lIbBDcVJNh5vJOG2TE4Qsuy_vY5yXULW1r-mmnPf3jkqj9Bix_zkFMcMqsuXoYOJoxLfEogMNYGQ7R_Fm-c7vsWuvHZIJcaDc2SOXPDmTbjQ6yfODhFoFn2/s1600/P1010293_bordeaux.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="124" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEja_AeKiohKGxFIdCB8Ed310lIbBDcVJNh5vJOG2TE4Qsuy_vY5yXULW1r-mmnPf3jkqj9Bix_zkFMcMqsuXoYOJoxLfEogMNYGQ7R_Fm-c7vsWuvHZIJcaDc2SOXPDmTbjQ6yfODhFoFn2/s200/P1010293_bordeaux.JPG" width="200" /></a></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-71818088305674753352010-08-28T01:06:00.003+02:002010-08-28T01:14:41.718+02:00Run, run, run...Or at least I should be. But a as always I need a goal to motivate me... and the goal is usually a half-marathon.<br />
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I never run when I was younger, with one exception at the age of 18- when I had to fill in a place for 1500m race in my school. My preferred activities were walking/hiking, skiing, swimming, table-tennis... until 2008.<br />
A few years after I arrived in Germany, and missing the mountains on the horizon (Berlin is flat!) I took up running in an attempt to fight the PhD fat. In 2009 I run <a href="http://www.scc-events.com/events/berliner_halbmarathon/2010/">my first half marathon</a>, with two more to follow. <br />
I'm not fast- but I enjoy going the distance... because the journey there, on the actual day, is a form of completion.<br />
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However, my favourite autumn runs - <a href="http://www.dresden-marathon.de/">Dresden</a>, which I also run last year, and the <a href="http://www.laufzeit-online.de/mueggelsee_hm/">Muggelsee Halfmarathon</a> - which seems really friendly are unfortunately overlapping with a conference I'm attending and lab retreat. Also this year, I left it quite late to decide if/when I'm going to run. Thus, my fitness level is below optimal for anything in September...<br />
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Ok, enough mussing about- now I need a run!<br />
These are some of my options:<br />
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<a href="http://www.teltowkanal-halbmarathon.de/">7.11.2010 HM Teltow (Berlin)</a><br />
<a href="http://www.scc-events.com/events/crosslauf/2010/">7.11.2010 9km-XC (Berlin)</a><br />
<a href="http://www.fitl.htwk-leipzig.de/laufen/awl/awl.html">20.11.2010 HM Leipzig</a><br />
If I'm really undecided I can always go for the same track as my very first run:<br />
<a href="http://www.plaenterwaldlauf.de/pwl.php">12.12.2010 20km/10km/5km Plänterwald, Berlin</a> although this is a bit later than I hoped.<br />
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Hmmm not too many half-marathon choices that I like.<br />
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Revelation: how about instead of a HM, I go for the 9km XC in November and the 10km in December. Both are nice simple runs- without many bells and whistles. They are close, and relatively cheap. The Xc is new while the Plänterwaldlauf is familiar. And I can focus on improving my 10km time, as throughout all my HM-s so far I run the first 10 as planned but always drop my pace at the second half....<br />
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I think I just made a plan. :-)<br />
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Finally, I just want to finish with the link to <a href="http://www.runnersworld.com/">runner's world magazine</a>, as that's where I've been getting most of my running tips.<br />
Ok, there and from a few running scientists in my institute. Good night everyone!Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com2tag:blogger.com,1999:blog-8673064047877569443.post-58319274930946502852010-08-17T23:23:00.001+02:002010-08-17T23:24:00.472+02:00The story of "Fat" and "Stubborn"Introducing:<br />
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*Fat - a 5 kb kinase that refuses to be ligate into anything I've tried.<br />
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*Stubborn- a 3kb kinase encoding an intramembrane domain. Stubborn's intracellular fraction was easilly cloned, but the full length gene just refuses to properly transfer into bacteria.<br />
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*Yours truly- The Postdoc - explorer a.k.a. Bori; the author of this blog and the scientist eager to move on to the interesting experiments.<br />
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Intro (for the non-biologists):<br />
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If you look up "cloning" let us say in <a href="http://en.wikipedia.org/wiki/Cloning">Wikipedia</a> it will say (among other) that cloning is the process of producing multiple copies of DNA.<br />
Fat and Stubborn have been selected because their DNA encodes for some interesting proteins, whose function we would like to study. In order to produce these proteins, I hope to fuse their DNA in a larger vector, which will then be inserted into bacteria. As the bacteria multiply they will multiply the copies of Fat and Stubborn DNA as well, and we can easily purify large amounts of this this DNA and use it per example for down- (or up- ) regulating the amount of Fat or Stubborn in their original species. Alternatively (depending on the vector used and the bacterial strain), the bacteria's transcription and translation machinery will subsequently produce the proteins of Fat and Stubborn, while producing the remaining proteins needed for the bacterial organism. Then the protein of Fat and Stubborn can be purified and used in a list of experiments to figure out what they do.<br />
Well, that is the (brief) theory!<br />
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On and off I've been cloning these two genes for about a year. About 20 other constructs were successfully finished in the mean time and only these two keep me from moving onto the real experiments.... You do not need to be in science to know how annoying this is.<br />
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This post summerises what I have tried and what I hope to try.<br />
For the biologists: If anyone has any advice- I'l be happy to listen!<br />
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Fat is probably the bigger problem (and not just in size). It caused problems from the very beginning so:<br />
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<div>1- PCR has been optimised to generate the initial DNA strands from cDNA. Usually this is a <i>Pfu</i> PCR and if TA cloning is to be carried out, an incubation with <i>Taq</i> is carried out in the end. Throughout time, we also acquired a BAC clone carrying the genomic DNA of Fat, and further attempts have proceeded in parallel for the cDNA and genomic DNA of Fat.<br />
<br />
2- As the end vector allows only <i>Sma I</i> (or potentially <i>Xma I</i> cloning) on both ends, the appropriate primers add this sequence to the ends of the gene. Attempts to insert the product into pGEM-T (3kb); pCR zero 2 (3.5kb) and the final vector(5.9kb)- here I incubate the PCR product with <i>Sma I</i> before ligating into the <i>Sma I</i> cut vector.<br />
<br />
3- Transformation yields colonies, but upon DNA purification I can not confirm the presence of the insert into the vector. Blue white cloning results in the usual blue and white colonies to aid selection, so I guess ligation would work. Restriction analysis gives inconclusive results, as weak bands can sometimes be seen at the right sizes, but there are other unexplained bands there too, that can not be explained by incomplete digesion. Checking just the sizes of the uncut vectors shows the recombinant vector often running at a faster rate than the empty vector! ( see below for my theories) FInally sequencing yields only background noise.<br />
<br />
I fear that because the resulting vector is so large (mind you, in cases of Sma I ligation, i potentially have 2 vectors fused together) the DNA forms a three dimensional structure which will "hide" the restriction sites. But for sequencing I use a primer which should anneal to a promoter region of the vector.... so If nothing else I would expect to receive vector sequence as a result! (yes the primer works in other cases)<br />
I have heard of cloning strategies which involve inserting the gene in the vector part by part, but I have not used this method yet. I guess this is the plan for the next step.<br />
<br />
Stubborn is just being plane annoying. Either that or for the first time in my life I've met a gene that will produce a toxic product in bacteria (I could believe this because the full length protein incorporates an intra-membrane domain, I'm reluctant to believe it because I thought that the promoters in vectors like pGEM-T are supposed to be tight). Long story short:<br />
<br />
1- Stubborn can easily be amplified from cDNA, using PCR reaction. Once the problems persisted (and there was no BAC clone available) I even used genomic DNA thinking that the presence of the 1 tiny intron might mess up the possible protein expression. However the intron is after the intra-membrane domain though, so any stop codons appear too late!<br />
<br />
2- I think, the ligation into the pGEM-T works. (Note to self: try directly into the end vector... simply because I have not tried it yet)<br />
<br />
3- The problem arrises when I look a the colonies and try to produce DNA out of them. The colonies grow Slowly (capital "S") and the DNA yield is very very low, or almost none.... I can't explain it and it makes me feel stupid! (I've tried re-transforming with potentially good DNA preparations of low yield- to purify more DNA in the next round to totally fail. Similarly treatment as a low-copy vector and scaling up the cultures did not help. Using a different bacterial strain did not help either... ( and for the logical scientists reading this: the DNA purification method works, as other constructs have been successfully purified in parallel to these attempts)<br />
<br />
What am I missing?<br />
<br />
Needless to say the names Fat and Stubborn arise simply from the reluctance of these two pieces of DNA to co-operate, and have nothing to do with their actual structures.<br />
Also, I wish I was good at drawing because I can just see a comic where yours truly is driven to insanity by the tiny but strong resistance of these 2 genes to my cloning attempts. I do not know how else to finish this post but by one big: Grrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr....!</div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com4tag:blogger.com,1999:blog-8673064047877569443.post-1509794455346058322010-08-02T00:15:00.001+02:002010-08-28T03:02:29.427+02:00How close is too close?Ok here is what I've been thinking about: How closely do you work with your colleagues in the lab?<br />
<div style="text-align: justify;"><br />
</div><div style="text-align: justify;">In my case, we are all focusing on separate projects, although often we use same techniques. </div><div style="text-align: justify;">The more experienced in a certain field, be it molecular biology or data analysis will often share advice and/or teach the less experienced, but usually we stop at the stage of training and do not interfere with the actual experiments of the scientist in charge (apart from the group leader- who of course is involved in just about everything, and a technician if one has been allocated to help). </div><div style="text-align: justify;">For the first time since I joined my new group I offered to do something more for a bunch of people, basically I'm just preparing a southern-blot probe and thought if I'm doing it I might as well make a lot of it and save everyone else the trouble. </div><div style="text-align: justify;">Given that we form a nice constellation right now, I know that the folks will help me if/when I need it- so I'm fine with it. </div><div style="text-align: justify;">This went even further in my previous lab, where we used to have one stock for certain buffers for the entire lab. Although, I found this did not always function nicely and is not a practice I recommend. To be fair it worked in the case of the 10x buffers for DNA electrophoresis, but for anything more important than that- I'll always make my own stocks from now on. </div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">I'd like to know how is this organised other labs? Do you guys have specific tasks you need to take care off on regular basis, aside from your normal research? I'm not counting teaching, grading or ordering consumables here, more in the direction of experiment preparation. Let me know- I'm curious! </div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">The second point is about "closeness" in the sharing of private life information. </div><div style="text-align: justify;"><br />
</div><div style="text-align: justify;">Within my group, especially with certain people whom I deem close- I'll talk about some private stuff, we'll go out every now and then and usually we have a great time talking about just about anything. </div><div style="text-align: justify;">Within the wider community we are friendly to each other but we keep our jokes on general or professional level. What I mean to say is: we separate our personal and professional life in the most cases. </div><div style="text-align: justify;">The recent situation involves a colleague from the "lab far, far away". They are a different group and we do not interact much, but on every occasion we talk this person made very private and inappropriate comments on my account. </div><div style="text-align: justify;">At first I did not do much as I thought, well it's a different country- different people, but the Germans at work are usually polite people!!! </div><div style="text-align: justify;">When last week I received one of these stupid remarks in an e-mail and I just had to react: my logic was that this colleague is not my best friend and given that we've never talked about personal things together- I do not see why they should be brought up in work-realted conversations. So, in a private confrontation I asked this person to stay out of my business. I do believe I was clear but also I think I was a bit rude.... Ummm, I'm glad I said it. I'm sorry I was not as calm as I wanted to be during the talk, but most of all I'm angry at myself for allowing to get pissed off and showing it... I guess, even professional confrontations for unprofessional matter have a learning curve! </div><div style="text-align: justify;"><br />
</div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-31790180332763371222010-07-28T23:05:00.001+02:002010-07-28T23:11:18.500+02:00My Favourite ListToday I had a crazy and long day at work. I did some classical silly mistakes and thus I wanted to post the "you'know you've been in the lab too long when" list.<br />
It's so old it's already a classic, it's so true it almost hurts, and today it simply fits.<br />
I picked it up from <a href="http://community.livejournal.com/microbiology/140013.html">here</a>. I thank whomever put this together, cause I know you've been there. May your bacteria thrive!<br />
<br />
<br />
Now, without further ado:<br />
<br />
You know you've worked too long in a lab when:<br />
<br />
<div>1. You wonder what absolute alcohol tastes like with orange juice<br />
2. You can tell what cheap and expensive white coats look like<br />
3. You can't watch CSI without cursing at least one scientific inaccuracy<br />
4. You use acronyms for everything and never stop to elaborate<br />
5. Liquid nitrogen is only about a 1/3 as dangerous as you thought<br />
6. You always seem to use the microscope after the person with the impossible close together eyes<br />
7. Accident reports are a badge of honour<br />
8. You've wondered why you can't drink distilled water in the lab - It should be clean?<br />
9. You give the lab equipment motivational pep talks "Work for me today or i'll reprogram you with a fire axe" is my favourite<br />
10. You've worked out that a trained chimp could probably do 90% of your job<br />
11. When a non-scientist asks you what you do for a living you roll your eyes and talk science at them until they've loss the will to live (mainly for fun)<br />
12. You have to check the web to find out what the weather is outside<br />
13. You realize that almost anything can be classed as background reading<br />
14. People wearing shorts under a lab coat disturb you slightly as they look as though they might be naked underneath<br />
15. Although all cooking is a glorified chemistry experiment you just still can't seem to get it right<br />
16. Safety equipment is optional unless it makes you look cool<br />
17. Warning labels invoke curiosity rather than caution<br />
18. The Christmas nightout reveals scientists can't dance, although a formula for the movement of hands and feet combined with beats per min is found scrawled on a napkin by a waiter the next day<br />
19. You know which part of the lab you can chill out undisturbed on friday afternoon<br />
20. You decide the courses and conference you want to go on by the quality of the food served<br />
21. You are strangely proud of the collection of junk you've stolen from vendors at trade shows<br />
22. You've used dry ice to cool beer down<br />
23. No matter what the timings in the experiment protocol there is always time for lunch in the middle<br />
24. As has been pointed out to me on several occasions - You can no longer spell normal words but have no trouble with spelling things like immunohistochemistry or deoxyribonucleic acid.<br />
25. Burning eyes, nose and throat indicate that you haven't actually turned on the fumehood/downdraft bench<br />
26. Your slightly too fond of the smell of (pick one or many) Xylene/Agar/Ethanol/Undergraduates/Alcoholic handwash<br />
27. You've left the lab wearing a piece of PPE (personal protective equipment) because you forgot you had it on<br />
28. You bitch about not being able to pipette by mouth any more (Not me but i've worked with people who do!)<br />
29. Security come round at 2 am wondering why the lights are still on only to find you with your arms up to your elbows in a glove-box<br />
30. you have made some kind of puppet out of a nitrile glove and kept it as a pet (I know this isn't just me!) (Putting dry ice in makes for a rapidly expanding if short lived pet)<br />
31. When at a Fall Out Boy gig you wonder why everyone is going round with Faecal Occult Blood (FOB) written on their head<br />
32. You have an irresistible urge to rip your shirt off superman stylie cos it has press stud fasteners just like your lab coat.....Most often occurring as you walk through a door just like exiting the lab.... (The worlds of strippers and lab workers collide, not pretty)<br />
33. You still get amusement out of "freezing" things in liquid nitrogen!<br />
34. Blinking real fast has saved your eyesight on more than one occasion.<br />
35. You've removed your gloves to find a small hole which has left you with either - wrinkly old person hands, a brightly coloured finger (histologists especially) or a burning sensation and dermatitis and some point.<br />
36. You've bent down to pick something up off the floor only to scatter the contents of your top pocket under the largest machine in the lab – Common problem i believe<br />
37.When you rejoice when grabbing a handfull of eppendorfs/bijous/anything and it turns outs to be the exact number you needed<br />
38.You can`t wait for lab clean-up coz you get to do random pointless "experiments" to figure out whats in all the dodgy unlabeled bottles<br />
39. You hate having to change your lab coat to a new one because 'it just won't fit right' and because the wrist bits are way too tight<br />
40. You know you have worked in a lab too long when you actually threaten your cells whilst waving a bottle of virkon (disinfectant)<br />
41.Your nose invariably itches when you're doing mucky stuff with your hands so you develop the habit of scratching it on your upper arm. Unfortunately you sometimes carry this habit over to real life, where it looks like you're sniffing your armpits (Trying to find a clean bit of lab coat can be fun as well)<br />
*************<br />
I'm sure I can add a few more but my thoughts are not very coherent right now... Maybe tomorrow!</div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0tag:blogger.com,1999:blog-8673064047877569443.post-48280889062319465312010-07-25T22:57:00.006+02:002010-07-25T23:55:21.089+02:00A Sunday in Berlin<div class="" style="clear: both; text-align: justify;"><div class="" style="clear: both; text-align: justify;"><span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px;">Today I stay off the scientific topics. I went for a little bike ride through Berlin and was amazed how green and summer-like Tiergarten was. Even more so when you consider that there are more than three million people living here. Of course, the day being beautiful certainly helped, but just to prove my point here are some of the photos I took today. </span></div><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkao7jAX_AQ2W3Ews4dGv_WTTSAQohBkDpqNAOTzO1e0ee2l8L5QpSi6uc6cjWNbV3t76rjd_ysjfAljMNI_c27q1wu6aYNrgqWxlB2wA_OIRQMSVGUCSD1Pnb2pe98X1XMs0kS5sF8-QQ/s1600/Tiergarten_1_2.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkao7jAX_AQ2W3Ews4dGv_WTTSAQohBkDpqNAOTzO1e0ee2l8L5QpSi6uc6cjWNbV3t76rjd_ysjfAljMNI_c27q1wu6aYNrgqWxlB2wA_OIRQMSVGUCSD1Pnb2pe98X1XMs0kS5sF8-QQ/s200/Tiergarten_1_2.jpg" width="150" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tiergarten- Close to Zoologisher garten</td></tr>
</tbody></table><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyOjRjwJBnh2z9xzT8GdUXmBYs0QXkLz1jfkUtAqc5JTfyIJ2Z6iNWK1LrE0JlWFkuLggCmyvmPO3CzbLX4RXUQQeOk1aAnwX-r_CGM9FeYIUeKdY3XQb5Tv9bV-N-NC_OnZ6unIW1PcOj/s1600/Tiergaten2_s2.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyOjRjwJBnh2z9xzT8GdUXmBYs0QXkLz1jfkUtAqc5JTfyIJ2Z6iNWK1LrE0JlWFkuLggCmyvmPO3CzbLX4RXUQQeOk1aAnwX-r_CGM9FeYIUeKdY3XQb5Tv9bV-N-NC_OnZ6unIW1PcOj/s200/Tiergaten2_s2.jpg" width="150" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tiergarten</td></tr>
</tbody></table></div><div class="" style="clear: both; text-align: justify;"><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFcwDtpVM7rxVy-e-npgyekAFC8jsro-MEudd-SN4bzjJwYN8H1zfAz6Jws4SG6kTduli_aQeEEF3APmP0sOTuSz2kAOLP1b_RMhgZqXA-lWy5RZPU0MYStj7wfQ00xfd4RSY6urCeGTU2/s1600/Tiergarten_swan_1s2.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFcwDtpVM7rxVy-e-npgyekAFC8jsro-MEudd-SN4bzjJwYN8H1zfAz6Jws4SG6kTduli_aQeEEF3APmP0sOTuSz2kAOLP1b_RMhgZqXA-lWy5RZPU0MYStj7wfQ00xfd4RSY6urCeGTU2/s200/Tiergarten_swan_1s2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">green is the watter</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhD44xw-5HlyijGtCA0__0Gpk-COXFJVS73CZ64HeTDOpPd2PJT3T1psuF3h0EC0JhQKOn4Ab0-gBNMGLnDhimUeoiwsr3TzFOHV3o3uxZ4khWjAwAIZNsANv83gypWtxhddKhBk5E-A2fv/s1600/waterfall_tiergarten1_s2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhD44xw-5HlyijGtCA0__0Gpk-COXFJVS73CZ64HeTDOpPd2PJT3T1psuF3h0EC0JhQKOn4Ab0-gBNMGLnDhimUeoiwsr3TzFOHV3o3uxZ4khWjAwAIZNsANv83gypWtxhddKhBk5E-A2fv/s200/waterfall_tiergarten1_s2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">waterfall- chen</td></tr>
</tbody></table><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="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgo-KgXU_XmKAYjG2W5A1-4UCBkZOEZk9RDbEimeOfSI4gVLbLT76PzlwjGlD0sgp2novEsMJWRWGaXQAGAnxvwW025Lp3Vhi-k4vs9IsD3_j7XeMoZpHWmWqH24A6HCFOcjhBAXjq_2_Mx/s1600/Stormstr_bridgeview1_s2.jpg" imageanchor="1" style="display: inline !important; margin-left: auto; margin-right: auto;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgo-KgXU_XmKAYjG2W5A1-4UCBkZOEZk9RDbEimeOfSI4gVLbLT76PzlwjGlD0sgp2novEsMJWRWGaXQAGAnxvwW025Lp3Vhi-k4vs9IsD3_j7XeMoZpHWmWqH24A6HCFOcjhBAXjq_2_Mx/s200/Stormstr_bridgeview1_s2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">View over the Spree</td></tr>
</tbody></table></div>Anonymoushttp://www.blogger.com/profile/00488323443790116115noreply@blogger.com0