MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Suicyte Notes' source. Wed, 24 Dec 2008 18:09:28 +0100 http://suicyte.wordpress.com/2008/12/21/ubiquitin-on-lake-garda-reloaded/ Hardcore readers of this blog might remember my reports on the EMBO conference “Ubiquitin and Ubiquitin-like modifiers in cellular regulation” in September 2007 in Riva del Garda. See e.g. here, here, and most scientifically here. As I wrote before, this was one of the best conferences I have been to so far, with an excellent scientific content, great atmosphere, and a beautiful setting. I have just been informed that there will be 2nd such conference in September 2009, at the same venue in Riva del Garda. The 2009 title will be “Ubiquitin and Ubiquitin-like modifiers in health and disease“. Again, the organizers (mainly the Rubicon folks) have assembled a very promising line-up of invited speakers,  including Aaron Ciechanover, Allan D’Andrea, Allan Weissman, Br... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=2056259 Sun, 21 Dec 2008 13:46:37 +0100 2056259 http://suicyte.wordpress.com/2008/12/16/microarrays_problems/ I normally do not blog about topics related to my daytime job, which involves a lot of microarray data analysis. However, a series of recent blog posts [here, here and here] talk about microarray-related problems that differ so much from my own experiences that I cannot let them go uncommented. I am the last person to claim that microarrays are a perfect tool for tackling all questions conceivable . They are not.  DNA microarrays can be seen as some kind of hammer that is being (rightfully) applied to a few nails, but unfortunately also to lots of objects with no nail-like properties whatsoever. Microarray data are problematic in many different ways. However, we should be careful not to throw out the baby with the bath water. Here are the main points of criticism that have been raised in ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=2040359 Tue, 16 Dec 2008 22:17:27 +0100 2040359 http://suicyte.wordpress.com/2008/08/11/chaperone-mediated-autophagy/ Nature Medicine is not one of the journals I usually follow. Today, several of my literature alerting services - and several press releases as well - pointed to a paper in the AOP section of Nature medicine that appeared to be a must-read. As usual, the press releases are vague about what the study actually does, but they contain all the words needed to get me interested: autophagy, ubiquitin-proteasome system, Alzheimer’s and Parkinson’s disease - and, of course, the ultimate cure for aging. If you are a liver, that is. The paper by Cong Zhang and Ana Maria Cuervo is entitled Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function, which in the press coverage becomes Cellular rubbish may hold key to ageing process or Big st... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1696409 Mon, 11 Aug 2008 22:29:38 +0100 1696409 http://suicyte.wordpress.com/2008/08/04/search-engines/ Everybody seems to be blogging about new search engines these days. Most of them discuss the new CUIL search, which I found mostly disappointing. But so did everybody else. Over the last months, I have tried a couple of other search engines. What I typically do is a highly sophisticated benchmark involving a well-balanced testbed of three common search tasks: Search for the term “ubiquitin OR proteasome”. Check how many entries are found, and read all of them. Search for my own name. Vanity rules. High-scoring matches are typically 15-year old Usenet postings of mine, asking silly questions that nobody cares to answer. Runners-up are caused by other people appropriating my name, including one European scientist accused of scientific misconduct. Yuck. That wasn’t me, I pr... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1679569 Tue, 05 Aug 2008 08:32:31 +0100 1679569 http://suicyte.wordpress.com/2008/06/12/is-it-research-or-just-data-analysis/ Genome Technology blogs about the genome sequencing of Candidatus Korarchaeum cryptofilum, which appears to be an early-branching archaeon. Probably very interesting, although archaea are rarely the focus of my interest, I am mostly working on sequences from a species that should properly be called Candidatus Homo sapiens. What caught my eye, though, was the statment on author contributions (isn’t this the part of a paper that everybody reads first?). Anyway, this is what they say: Author contributions: J.G.E., P.R., M.K., and K.O.S. designed research; J.G.E., M.P., B.P.H., A.L., E.G., K.B., and G.W. performed research; J.G.E., M.P., D.E.G., K.S.M., Y.W., L.R., C.B.-A.,V.K., I.A., E.V.K., P.H., N.K., and K.O.S. analyzed data; and J.G.E., D.E.G., E.V.K., and K.O.S. wrote the paper. Yo... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1512310 Thu, 12 Jun 2008 08:41:48 +0100 1512310 http://suicyte.wordpress.com/2008/06/07/turning-part-of-the-proteasome-on-its-head/ I am a bit short on time, but I have seen that the Glickman paper on the proteasome base structure has finally appeared in print - this event should not go unnoticed. Before I begin to discuss the paper, I must admit that I haven’t really read it - I have heard Michael talk about this model at least three times, and had lengthy discussions with him and others during the Lake Garda meeting.  The new model, now published in Nature Structural and Molecular Biology, departs from the old dogma how subunits of the 19S proteasome regulator complex are arranged. Not surprisingly, reactions from the proteasome field are mixed. It is no coincidence that it took more than a year to get this story published. Before describing the new model, let me briefly recount the conventional wisdom on prot... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1501498 Sat, 07 Jun 2008 22:13:19 +0100 1501498 http://suicyte.wordpress.com/2008/06/01/two-degrees-of-co-authorship/ I remember a piece of dialogue, which I have seen in at least two different movies (can’t remember which ones, though). It went roughly like this: First guy (mostly harmless wannabe-gangster): “Hi, my name is John, but my friends call me Sharky”!  Second guy (much cooler than first one): “My name is Jack, and I don’t have friends”. This line reminds me to some degree of scientists doing social networking. I am not so much thinking of Facebook and the like, but rather of their scientific siblings like Nature Network an SciLink, as they seem to gain popularity in the scientific blogosphere (see here, here, here, here, and here). All of these services ask you for your affiliation, workplace and several other obvious and semi-obvious data. The scientificall... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1485007 Sun, 01 Jun 2008 18:59:58 +0100 1485007 http://suicyte.wordpress.com/2008/05/24/rpn13/ Last Wednesday, two new papers (1,2) were published that describe the function of Rpn13 as a new proteasomal ubiquitin receptor. Since I happen to be a coauthor on one of the papers, I thought it might be a good idea for a blog entry. Actually, it was Ian’s suggestion, but it is not his fault if the text is boring. In any case, it is going to be too long - a complex as interesting as the proteasome deserves more than a few lines. If there is anything the non-expert knows about ubiquitin, it is the fact that ubiquitin becomes attached to other proteins and earmarks them for destruction by the proteasome. In order to do this job, the proteasome has to recognize if a protein carries a ubiquitin degradation signal. The complete 26S proteasome consists of at least 32 different stoichiomet... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1467053 Sat, 24 May 2008 22:08:38 +0100 1467053 http://suicyte.wordpress.com/2008/05/21/gene-naming-vanuatu-style/ A while ago, for reasons that I cannot remember, I ended up reading a post on the blog ‘mistersugar‘ by Anton Zuiker. Neither is the blog science-oriented, nor is this particular entry, dating from 2003 and entitled ‘Naming rights‘. It is interesting nevertheless, as it talks about various traditions of naming children in different cultures. One paragraph in particular caught my attention: In Vanuatu, where I served with the Peace Corps, names proliferate. When a boy is born, his uncles on his father’s side each ‘put’ a name on the new child, with the father’s ‘tawian’ (eldest brother-in-law) choosing the child’s main name. A girl gets her names from the sisters of her mother and one of her mother’s sisters-in-law. As the child grows up in the villag... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1461169 Wed, 21 May 2008 22:47:22 +0100 1461169 http://suicyte.wordpress.com/2008/05/18/one-year-of-suicyte-notes/ I just noticed that this week, Suicyte Notes could celebrate its first anniversary. But is there anything to celebrate? I have started this blog in May last year as an experiment. The idea was to find out if scientific blogging is i) fun, ii) useful, iii) possible while trying to pursue an active scientific career. Let me try to give you a few answers - obviously from my own personal perspective. Is scientific blogging fun? Overall, I would answer this question with a qualified ‘yes’. It would certainly be pure fun if I had an unlimited amount of time at my hands, if I had a better grasp of English, and if I wouldn’t suffer from a permanent writer’s block. Initially, I had intended to write much more posts on strictly scientific topics (read below why I have mostly ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1451953 Sun, 18 May 2008 22:39:53 +0100 1451953 http://suicyte.wordpress.com/2008/04/13/how-to-deal-with-bad-peer-review/ I have just read Dave Lunt’s text on Anonymous peer review, and I can only second every word he writes. I consider reviewer anonymity as essential for giving me the freedom of saying things that have to be said. Like David, I would never dare telling a person I know very well that their latest manuscript is essentially rubbish. Without any doubt, my case history as a reviewer would have severly limited my chances of later collaboration.  Even very good scientists can sometimes submit very bad manuscripts. The other side of the coin, giving ‘rogue reviewers’ the chance to hide behind anonymity has to be addressed, although I would rather see this happen without compromising anonymity. I even have an idea how this could be done. I am sure that some clever people have propo... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1369743 Sun, 13 Apr 2008 22:29:51 +0100 1369743 http://suicyte.wordpress.com/2008/04/10/science-does-a-webcast-on-ubiquitinproteasome-drug-discovery/ Yesterday, I have received two ads - disguised as blog-comments - from Walter Jones, apparently the AAAS expert for viral marketing. While one copy would have probably done the job as well, the topic was interesting and pertinent to my blog. Thus, I am willing to assist the AAAS and make their announcement known to a wider audience: my blog readers. Both of them. In their Webinar series, Science Magazine will offer on May 1, 2008 a webinar entitled “The Ubiquitin-Proteasome Pathway: Targets for Disease Treatment and New Tools for Discovery“. This topic is very similar to that of a conference I have attended recently. There doesn’t seem to be an overlap of speakers, though. As the announcement says, there will be three speakers: Alfred Goldberg from Harvard Medical School ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1362489 Thu, 10 Apr 2008 08:54:19 +0100 1362489 http://suicyte.wordpress.com/2008/04/06/random-stuff-april-08/ Here are just two interesting stories I read on other peoples blogs: First, Jake Young at Pure Pedantry blogs about a recent Cell paper by Sakaue-Sawano et al. who present a clever application of protein ubiquitination for visualizing the cell cycle stage of cells in vivo. Lars Juhl Jensen at Buried Treasure has also picked up this story, and those two blogs provide a lot of detail on the method, including a link to a nice video showing HeLa cells passing through 3 cell cycles. In brief, the authors of this paper exploit the fact that several protein ubiquitination systems are only active during particular phases of the cell cycle. On one hand, there is the APC/Cyclosome system, which degrades target proteins only in late mitosis (APC means Anaphase Promoting Complex) and in G1 phase. Conv... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1354188 Sun, 06 Apr 2008 22:32:01 +0100 1354188 http://suicyte.wordpress.com/2008/04/01/april-the-protein/ Reading an interesting post on the tree of life reminded me that today is April 1st. I will seize this opportunity to make you familiar an interesting protein, which has been discovered in - you might have guessed it - April, exactly 10 years ago. In reality, the name APRIL has nothing to do with the month but rather means “A PRoliferation Inducing Ligand”. You can look it up somewhere in JEM. APRIL is a member of the TNF family, which also contains proteins such as TRAIL and Fas-ligand. Unlike many other TNF family proteins, APRIL does not induced apoptosis, quite to the contrary: By a mechanism that is still very incompletey understood, APRIL upregulates the anti-apoptotic members of the Bcl2 family, most likely by way of NF-kB. Initially, we thought that APRIL had a connecti... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1340872 Tue, 01 Apr 2008 14:25:47 +0100 1340872 http://suicyte.wordpress.com/2008/03/28/strange-paper-ii/ This is today’s 2nd post on recent papers describing the beneficial effect of things gone wrong. The first one was from the area of bioinformatics, this one is about gene silencing by RNA interference (RNAi). A lot is known about the mechanism and application of RNAi, see e.g. the Wikipedia entry. Basically, you can use RNAi to downregulate a gene of interest by designing a short oligonucleotide (siRNA) complementary to the target mRNA and getting it into the cell to do its magic. Inside the cell, the oligonucleotide pairs with the target mRNA and the resulting duplex RNA is recognized by a specific cleavage machinery, which is present in the cell anyway. Most likely, this RNAi cleavage machinery has not been put into the cell by an intelligent designer to facilitate our lab work, bu... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1331518 Thu, 27 Mar 2008 23:39:21 +0100 1331518 http://suicyte.wordpress.com/2008/03/27/strange-paper-i/ This week, I found two strange but interesting papers, one from the area of bioinformatics, the other from gene silencing. The unifying topic is that in both published works something went wrong, but the results were nevertheless as good - or even better - than intended. The first paper, published in the latest issue of Nature Biotechnology, is from Mark Styczynski et al. The title is “BLOSUM62 miscalculations improve search performance“. I must say that I was very surprised to see a paper like this. BLOSUM substitution matrices are widely used throughout bioinformatics. In particular the BLOSUM62 version is popular as it is used per default in NCBI’s protein BLAST applications. I am a heavy user of BLOSUM matrices myself; on my computer it is the BLOSUM45 matrix doing mo... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1331519 Thu, 27 Mar 2008 22:37:47 +0100 1331519 http://suicyte.wordpress.com/2008/02/28/review-confidentiality-and-related-issues/ It looks like the guys at SART take longer than expected to finish their groundbreaking research. This leaves me some time to blog about another topic that has caused some stir in the blogosphere recently. I just was reminded of the story when reading an editorial by Donald Kennedy published in last weeks Science. What seems to have happened is that Pfizer is being sued on side effects of Celebrex and Bextra, and some material published in NEJM is to be used as evidence in this case. It now seems that Pfizer tries to force NEJM by means of subpoenas to let the Pfizer lawyers browse confidential NEJM review material. I am neither familiar with this particular case, nor with the relevant US laws. Here is a short paragraph from the editorial: Pfizer asserts that in some cases plaintiffs are m... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1265263 Thu, 28 Feb 2008 21:08:12 +0100 1265263 http://suicyte.wordpress.com/2008/02/26/reader-oh-reader-where-art-thou/ Seems I have neglected this blog for too long and you, my dear audience, have turned to greener pastures. Well, this calls for some drastic action. You have been warned (Source: Suicyte Notes) Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1258477 Tue, 26 Feb 2008 18:52:25 +0100 1258477 http://suicyte.wordpress.com/2008/02/22/drug-targets-in-the-ubiquitin-proteasome-system-conference/ Just a brief announcement: On March 11-12 2008, there will be a conference on drug targets in the UPS taking place in Berlin, Germany. Judging by the topic and the organizer (Informa) it is safe to assume that the conference will mainly cater for scientists in pharma and biotech companies. As you know from my previous post, industry people are swimming in money, and thus the conference fee is a bit on the expensive side. As there isn’t much UPS industry in Europe, the invited speakers are mainly from the US. Amongst others, there will be presentations from Genentech (Peter Jackson), Millennium (Joseph Bolen), Roche (Lyubomir Vassilev), Novartis (Martin Renatus), Merck (Nathan Bays), Bayer Schering (Bernard Haendler), Progenra (Ben Nicholson), LifeSensors (Tauseef Butt), Hybrigenics (... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1251168 Fri, 22 Feb 2008 22:51:52 +0100 1251168 http://suicyte.wordpress.com/2008/02/21/cui-bono/ I really shouldn’t write a blog posting right now, but rather work on my slides for an upcoming conference. Alas, working on slides is not my favorite occupation, and now I find myself pondering questions like “Is inviting me for talking at a conference a service for me or for the audience?”. A strange question to ask, maybe (unless you have heard one of my previous talks and thus can safely discard the idea that it might be to the benefit of the audience). Here is what made me think about this problem in the first place: On previous occasions (e.g. in my blog, but also in the discussion of other people’s blogs) I have complained about software and web servers that are free to use for academics, but which charge an (often horrendous) amount of money if you happen to... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1246685 Wed, 20 Feb 2008 23:16:34 +0100 1246685 http://suicyte.wordpress.com/2008/01/31/a-busy-january/ I just noticed that January is about to end - a whole month without a single blog posting. This obviously calls for something, if I only knew what. The month has been packed with lots of different stuff, a meeting, a couple of talks, and last but not least, a short vacation at this place here: The idea was to show our little daughter what snow looks like. What can I say, it worked out quite well. The downside of this vacation (like every other vacation of mine) was that I don’t have the kind of work that goes away during my absence. As usual, I was greeted by a big pile of paperwork, plus a (virtual) pile of e-mails going like this: Dear Kay, In early [insert your favorite month here], you promised to send us your [manuscript | review | analysis | report | figures | money]. Unfortu... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1192914 Thu, 31 Jan 2008 22:19:08 +0100 1192914 http://suicyte.wordpress.com/2007/12/05/my-two-euro-cts-on-the-science-vs-faith-debate/ Recently, i have noticed the Science = Faith???? post on The Daily Transcript, where Alex complains (rightfully, I guess) about an article published in the New York Times. I am not going to discuss this article, as I haven’t read it and don’t feel like doing so. Reading Alex’s post, however, reminded me of another blog entry I read a few months ago (can’t remember where, sorry). In this other post, the authors also discussed the idea of science vs. belief and wrote something along the lines of “religious people believe, while I as a scientist do not”. As far as I remember, the arguments were the same: science is not based on faith but on testable hypotheses - scientist do not have to believe, they know. I have just seen that other bloggers too have cover... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1072469 Wed, 05 Dec 2007 16:00:46 +0100 1072469 http://suicyte.wordpress.com/2007/11/20/smallest-primate-ever-discovered/ Nobody who follows the scientific literature can possibly have missed the reports on Craig Venter’s metagenomics effort, trawling the oceans on his “Sorcerer II” yacht on the search for new DNA sequences. Unlike some of my fellow bloggers who know their metagenome, I have never been quite convinced that metagenomics is good for anything (except maybe for yachting on grant money). This notion has changed today, when at around 2 pm CET, people in my group made an earth-shattering discovery while analysing some portion of the global ocean sampling data. It appears that the book on primate biology has to be re-written, or in other words, by overturning a century-old dogma, primate science is experiencing a veritable paradigm shift. To put our epochal discovery into context: U... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1041813 Wed, 21 Nov 2007 12:52:30 +0100 1041813 http://suicyte.wordpress.com/2007/11/20/smallest-primate-ever-discovered/ Nobody who follows the scientific literature can possibly have missed the reports on Craig Venter’s metagenomics effort, trawling the oceans on his “Sorcerer II” yacht on the search for new DNA sequences. Unlike some of my fellow bloggers who know their metagenome, I have never been quite convinced that metagenomics is good for anything (except maybe for yachting on grant money). This notion has changed today, when at around 2 pm CET, people in my group made an earth-shattering discovery while analysing some portion of the global ocean sampling data. It appears that the book on primate biology has to be re-written, or in other words, by overturning a century-old dogma, primate science is experiencing a veritable paradigm shift. To put our epochal discovery into context: U... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1037053 Tue, 20 Nov 2007 00:20:16 +0100 1037053 http://suicyte.wordpress.com/2007/11/14/how-people-get-here-mystery-in-vienna/ Unlike some other blogs that I read regularly and which have quite a long tradition (happy 4th anniversary, Pedro!), my own blog is fairly new and I still feel like a newbie in the blogospere. From time to time, I discover a new feature (new to me, that is) in the wordpress site hosting my humble blog, and I continue to be amazed by the general weirdness of blogging. I am already fairly familiar with the site access statistics, although I don’t understand some of the data I see. One obvious conclusion from analyzing this data is that most people read my blog at work, as there are hardly any page hits during the weekend. This is contrary to my expectations, but maybe not too surprising. I have no idea why there is a strong peak in page hits once per week, typically on thursdays. Maybe... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1025463 Wed, 14 Nov 2007 11:06:37 +0100 1025463 http://suicyte.wordpress.com/2007/11/08/a-bad-day-in-structure-space/ Frequent readers of my blog will know that I am more into sequences than into structure. I don’t want to go into details why this is so, maybe another time. Here is the one-sentence version: My goal is the prediction of protein function, and - contrary to what is being reiterated in the literature - I am convinced that this is better done directly from sequence, paying close attention to evolution. Going via structure is a detour, if not a dead end. Ok, two sentences. Occasionally, though, I have to do some structure analysis. No mistake, I am using structures all the time. Nothing beats a structural superposition if you have to align two extremely divergent sequences. If there is a structure. I also use structures (if available) to make plausibility checks of my sequence-based predi... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=1013445 Thu, 08 Nov 2007 14:40:24 +0100 1013445 http://suicyte.wordpress.com/2007/10/04/gender-issues-fungal/ This is a kind of follow-up to my previous post “Try to explain this to a non-biologist“, where I was making fun of yeast mating type nomenclature. Through a recent posting on Fungal Genomes (and a number of random clicks that I am unable to reproduce), I eventually found a page written by Tom Volk, explaining fungal sex using Schizophyllum commune as an example. I must say that I learned a lot by reading this page (I am often exposed to sequence data from various fungi, typically without having a good idea about their basic biological features and differences). One of the more amazing facts is that Schizophyllum comes in more than 28,000 different mating types. There was one paragraph, though, that reminded my immediately of my former “a vs. α” problem: Many of th... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=926336 Thu, 04 Oct 2007 08:43:29 +0100 926336 http://suicyte.wordpress.com/2007/10/02/ubiquitin-science-on-lake-garda/ Conclusion All in all, a very interesting meeting. Most of the people I have talked to appeared quite satisfied, with only very few critical voices. I overheard some people complain on either too much or too little biology - this is probably hard to avoid. Other people complained that it doesn’t make sense anymore to have meetings on the ubiquitin system (like there are no meetings dedicated to kinase signaling anymore). According to them, ubiquitin topics should be dealt with on a session-basis and find their place in meetings on Endocytosis or DNA repair or Cancer. I am not convinced. For once, we already have UPS sessions as part of several biology-oriented meetings. Moreover, ubiquitination is far more complicated than phosphorylation. There are many components and paradigms shar... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=922056 Tue, 02 Oct 2007 22:47:33 +0100 922056 http://suicyte.wordpress.com/2007/09/28/back-from-riva-del-garda/ I am back from the EMBO conference in Italy. This have been four very intensive days. The pace of the meeting itself was rather relaxed, with plenty of time for coffee breaks and meals. There were something like 200 participants overall, most of them presenting a talk or a poster. As everyone was staying at the conference hotel, there was enough opportunity to talk to a lot of people, including some who wouldn’t normally talk with someone like me (e.g. senior editors of Nature and Cell) As I had expected, the setting was very pleasant, and so was the weather, except maybe for the last day. It was soon decided to move most of the poster session outdoors (and next to the bar). Maybe as a direct consequence, this was one of the very few meetings I have attended where even some of the bi... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=908745 Fri, 28 Sep 2007 00:34:12 +0100 908745 http://suicyte.wordpress.com/2007/09/20/embo-conference-on-ubiquitin/ The next week, I will be out of office, while attending the EMBO conference on “Ubiquitin and Ubiquitin-like modifiers in cellular regulation“. I am very much looking forward to this conference, as the program has an exciting line-up of ubiquitin and proteasome researchers. As the meeting takes place at (supposedly) beautiful Riva del Garda, I am optimistic that I can use the spare time (should there be any) for taking some pictures. This meeting has already cast its shadow backwards in time, as I had to spend all of my free time preparing some slides for my talk, rather than for writing blog postings. Judging by the very modest general interest in my ubiquitin-related blog posts, I assume that there is no point in covering the meeting in this blog. Should I hear something part... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=888711 Thu, 20 Sep 2007 18:47:23 +0100 888711 http://suicyte.wordpress.com/2007/09/13/oedilf/ Via cotch.net, I found the “Omnificent English Dictionary In Limerick Form“, (OEDILF), which is a moderately funny collection of, well, dictionary entries in limerick form. OEDILF claims to have over 44000 user-contributed entries. As you would expect, most of them are not particularly funny (I am not sure if this is intended, but what else is the point of putting definitions in limerick format?). Interestingly, OEDILF has a a quite extensive science section, which includes two entries on apoptosis. As you can see, they are not too bad: (note that the explanations given below the limericks are from OEDILF, there are not mine. I don’t think readers of Suicyte Notes need an explanation what apoptosis is, right?) apoptosis, apoptotic by Steve Ngai Our cells have no bleaker p... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=868297 Thu, 13 Sep 2007 09:54:21 +0100 868297 http://suicyte.wordpress.com/2007/09/08/i-hate-it-if-they-do-that/ One of the things that can drive me up the wall is reading a paper that describes the discovery and characterization of a new protein, without giving a clue to the proteins identity. My bad mood is caused by a paper in the current issue of Cell, entitled “SCRAPPER-Dependent Ubiquitination of Active Zone Protein RIM1 Regulates Synaptic Vesicle Release“. I am interested in this protein because i) I am interested in almost anything connected to ubiquitination, ii) ubiquitination as a regulator of synaptic vesicle release is a new and rather unorthodox concept, and iii) the ubiquitination target RIM1 is no stranger to me. The new Cell paper gives lots of information, a good part of which I still have to digest, but it lacks one important piece of information: what the heck is SCRAP... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=853843 Sun, 09 Sep 2007 21:00:36 +0100 853843 http://suicyte.wordpress.com/2007/09/08/i-hate-it-if-they-do-that/ One of the things that can drive me up the wall is reading a paper that describes the discovery and characterization of a new protein, without giving a clue to the proteins identity. My bad mood is caused by a paper in the current issue of Cell, entitled “SCRAPPER-Dependent Ubiquitination of Active Zone Protein RIM1 Regulates Synaptic Vesicle Release“. I am interested in this protein because i) I am interested in almost anything connected to ubiquitination, ii) ubiquitination as a regulator of synaptic vesicle release is a new and rather unorthodox concept, and iii) the ubiquitination target RIM1 is no stranger to me. The new Cell paper gives lots of information, a good part of which I still have to digest, but it lacks one important piece of information: what the heck is SCRAP... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=850609 Fri, 07 Sep 2007 23:00:11 +0100 850609 http://suicyte.wordpress.com/2007/09/06/up-to-95-of-junk-is-just-junk/ I have noticed that during the last few weeks, after a transient period of high activity, my blog readership is on its way down to the 5-6 hits per day that I know from the first two months. Thus, it is probably time to do something about it, which means: blog about a highly controversial topic. My pick for today is an old favorite of mine: junk DNA. Without any quotes. And, while we are at it, I’ll do alternative splicing, too. In a way this post is related to Jonathan Eisen’s recent rant against “adaptionomics“, which he defines as a vice common among genomics researchers: the finding of something weird in the genome leads to the (unwarranted) conclusion that this particular feature must confer a selective advantage. I don’t have a fancy name for the vice I ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=845847 Thu, 06 Sep 2007 13:48:06 +0100 845847 http://suicyte.wordpress.com/2007/09/06/up-to-95-of-junk-is-just-junk/ I have noticed that during the last few weeks, after a transient period of high activity, my blog readership is on its way down to the 5-6 hits per day that I know from the first two months. Thus, it is probably time to do something about it, which means: blog about a highly controversial topic. My pick for today is an old favorite of mine: junk DNA. Without any quotes. And, while we are at it, I’ll do alternative splicing, too. In a way this post is related to Jonathan Eisen’s recent rant against “adaptionomics“, which he defines as a vice common among genomics researchers: the finding of something weird in the genome leads to the (unwarranted) conclusion that this particular feature must confer a selective advantage. I don’t have a fancy name for the vice I ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=844082 Thu, 06 Sep 2007 00:07:09 +0100 844082 http://suicyte.wordpress.com/2007/08/31/apc-dangerous-for-your-kid/ When I read today’s output of my Pubcrawler alert, I found a headline I had to read twice before I got the message. The title said Human Kid is Degraded by the APC/CCdh1 but Not by the APC/CCdc20 I don’t dare imagine what the tabloids would make from this story. For the degradologists among us, it is quite clear that the Kid in question is the chromokinesin KIF22. Interestingly, this is not the only Kid among our genes - this name is also used for the gap junction connexin GJB2 and the kidney-specific aquaporin AQP6. And while talking about ambiguity in nomenclature, the dangerous APC mentioned here is neither the antigen presenting cell (dangerous for pathogens), nor the adenomatosis polyposis coli gene (dangerous if mutated). It is the anaphase promoting complex, a multi-su... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=835555 Fri, 31 Aug 2007 14:51:13 +0100 835555 http://suicyte.wordpress.com/2007/08/30/pisd/ I am not a glowing open access advocate. Sure, I like the idea and hope that this will be the publishing model of the future. I also have supported OA publishing on many occasions. But unlike most prominent bloggers, I can envisage a peaceful coexistence between OA and commercial publishers. I am also unconvinced that Elsevier really is the devil, or that NPG are a bunch of sexists. And yes, I even dare to publicly talk about non-OA papers on my blog. Shame on me! Anyway, today I noticed (via GTO) the web presence of the PISD coalition, which is truly hilarious. Of course, it is a mockup of the incredibly stupid (and widely blogged about) web page of the PRISM coalition. There are quite a number of highlights on the PISD page, most of which is written in a Q&A style. Here is a quote th... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=831065 Thu, 30 Aug 2007 11:08:22 +0100 831065 http://suicyte.wordpress.com/2007/08/19/why-genome-projects-make-more-sense-than-structural-genomics/ What is the main difference between a genome sequencing project and the structural genomics initiative? Well, one deals with sequences and the other with structures, but this is not what I have in mind. For me, the fundamental difference is that a genome sequencing project has a point where you can call it ‘finished’, while this is not really true for structural genomics (and a number of other large-scale efforts). A very important aspect here is that a projects in the ‘finished’ state is very different from being 99% finished. Only a genuinely complete genome sequence allows conclusions on what is not present in the genome. For many applications, these conclusions can be equally important to what is present. This issue is obviously important if you are interested i... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=808826 Sun, 19 Aug 2007 22:15:54 +0100 808826 http://suicyte.wordpress.com/2007/08/17/try-to-explain-this-to-a-non-biologist/ Here is a little quiz to test if you understand biological nomenclature. The estrogen receptor recognizes estrogen. The GABA receptor recognizes GABA. What does the T-cell receptor recognize ? Yeast comes in two mating types (= sexes). One is called “a”. How would you call the other one ? to be continued… (Source: Suicyte Notes) Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=806042 Fri, 17 Aug 2007 16:36:31 +0100 806042 http://suicyte.wordpress.com/2007/08/12/never-trust-a-hypothesis/ The last decade has seen a gradual replacement of hypothesis-driven research by hypothesis-free high throughput studies - at least when looking at the selection of publications that made the biggest splash. The reasons for this development are obvious: the development of new techniques, the availability of entire genome sequences, and progress in lab automation have enabled high-throughput research. Without any doubt, these large-scale studies yield more results per Euro, as it has always been much easier to find out anything in general rather than something in particular. Imagine an old fashioned biologist, throwing out his hypothesis-driven fishing line into the pond of science, hoping that a particular fish will be attracted by the highly specific bait. Then imagine a group of contempor... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=794253 Sun, 12 Aug 2007 22:29:48 +0100 794253 http://suicyte.wordpress.com/2007/08/09/interesting-papers-aug07-edition/ August has only just begun, but I have already found one paper that deserves featuring in my ‘interesting papers‘ series. I will also talk about a second paper I found today, although I am not yet totally sure if it is really that much interesting. As I mentioned in a previous post, I feel attached to the UBA domain, a small but quite abundant ubiquitin recognition domain. This month’s edition of Molecular Cell features a paper from Kalle Gehring’s group, entitled “Structural Basis for Ubiquitin-Mediated Dimerization and Activation of the Ubiquitin Protein Ligase Cbl-b“. This paper describes a new trick of UBA domains, which expands their repertoire of operating modes. The classical view of UBA and other ubiquitin receptor domains is that they bind to ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=788358 Thu, 09 Aug 2007 00:20:29 +0100 788358 http://suicyte.wordpress.com/2007/08/06/ubiquitin-nation/ Today another silly post (due to lack of time required for serious discussion). Over the weekend, I read three different texts, all dealing with the attachment of ubiquitin to proteins. As usual, the authors could not agree on a single name for this process. Some people call it “ubiquitination”, others call it “ubiquitylation” and yet others (including myself) use either one or the other, depending on daytime, temper, moon phase, or whatever. Some people actually combine the best of both worlds and say “ubiquitinylation”. So, one of the most pressing questions in the field of ubiquitinology remains: which one is correct? First, let us consult the wisdom of the masses. A quick search by Google shows that at least in the discipline, ubiquitination wins han... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=780725 Sun, 05 Aug 2007 23:05:47 +0100 780725 http://suicyte.wordpress.com/2007/07/29/impressions-from-ismb-2007/ It has been a few days since I have returned from Vienna where I attended ISMB07 - this year a joint meeting with the european ECCB series. With about 200 talks and 1000 posters, far too much material to cover it in a blog post. Here a just a few random impressions: Venue Vienna is a beautiful city (if you like the old European capital architecture with plenty of churches and other large representative buildings with lots of gold applications). The weather was far too hot for my taste, but the conference center and probably most hotels have good air conditioning. The conference center itself was quite pleasant, with plenty of space, decent coffee, and unobtrusive badge controls. I must say that I cannot stand these marine-type bouncers with stern expression, enforcing a strict “wear ... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=765031 Sun, 29 Jul 2007 20:14:03 +0100 765031 http://suicyte.wordpress.com/2007/07/23/text-mining-by-microsoft/ Yesterday, I mentioned the problems that text miners have when they want to parse gene names out of scientific texts. Maybe they should just do it the Microsoft way. Few people know that Microsoft has incorporated a high-end text parser in their MS-Excel program, which automatically recognizes and corrects gene names. The recognition rate is so high that the user doesn’t even has to be bothered with a confirmation question. Here is how it works: Text before MS-Excel: Uniprot-ID Gene Description SEPT7_HUMAN SEPT7 Septin-7, Cdc10 homolog Text after MS-Excel: Uniprot-ID Gene Description SEPT7_HUMAN 2007-09-07 Septin-7, Cdc10 homolog (Source: Suicyte Notes) Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=751789 Mon, 23 Jul 2007 22:34:44 +0100 751789 http://suicyte.wordpress.com/2007/07/22/text-mining-in-vienna/ I am currently attending the ISMB conference in Vienna, my first ISMB after a 3 year hiatus. As usual, a packed program that does not leave much time for blogging. My group is not presenting anything, so we can enjoy the 200 talks and 1000 posters. ISMBs are always a good occasion to meet people - yesterday I met a guy I had last seen 1991 during my first bioinformatics conference ever. This year, I am particularly interested in text mining - not that i want to start doing text mining myselft, but I am interested to see what resources based on text-mining efforts are available. Yesterday, I attended a tutorial called “automatic text analysis based on web services“, which looked just right for my interest. Although the presenter, EBI’s Dietrich Rebholz-Schuhmann, did quite... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=749717 Sun, 22 Jul 2007 22:45:03 +0100 749717 http://suicyte.wordpress.com/2007/07/14/interesting-papers-july07-edition/ I am currently too busy to write the posts that are on my to-do list, which includes i) the next part of my soul searching series, ii) a text discussing if bioinformatics should be considered a science or a black art, iii) talking about a very blatant example of bad bioinformatics in a recent Cell paper, and finally two provocative pieces on v) what I don’t like about open access publishing and vi) why I think that most of junk DNA is actually junk. I am looking forward to being publicly ridiculed for the last one. Today, I just want to mention that the last few months have been a very good time for ubiquitin research. Here are a few papers that have appeared recently, which I consider to be must-reads: E3-Independent Monoubiquitination of Ubiquitin-Binding Proteins from Ivan Dikic&... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=733972 Fri, 13 Jul 2007 23:56:35 +0100 733972 http://suicyte.wordpress.com/2007/06/29/response-from-go/ This is going to be my last post in the thread on gene ontology [one, two, three] . I don’t want to leave you with the impression that the GO curators don’t care - just because there are no comments from them. Actually, I received two replies from two GO administrators in charge of the annotation efforts. As they chose to e-mail me privately instead of posting a reply on my blog, I will refrain from re-posting parts of their mail here. In any case, I was pleasantly surprised that the GO annotators take the problems serious. Here are few things I learned from the two response letters: Several of the problems mentioned in the blog are known at GO and are being worked on. This applies e.g. to the cytokine definition problem. Maybe I should look at my examples in one year time and... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=705802 Fri, 29 Jun 2007 20:23:31 +0100 705802 http://suicyte.wordpress.com/2007/06/26/more-thoughts-on-go/ In the last few days, I have written two posts on the Gene Ontology project (GO), the first and rather polemic one on the problems I encountered when using GO, the second one making some suggestions on how to improve GO. Now, I am having second thoughts on whether it was a good idea to criticize a resource that takes so much effort to create and maintain, but nevertheless is free for all. It is clearly a kind of work that is useful for many scientists, and also something most people (including myself) wouldn’t want to do on their own. So after all, we should be thankful that this project exists. Nevertheless, after pondering this question for the last day, I think that some amount of constructive criticism is warranted. For one thing, there is no shortage of reports on how great GO i... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=698191 Tue, 26 Jun 2007 23:01:25 +0100 698191 http://suicyte.wordpress.com/2007/06/26/making-a-better-go/ This is a follow-up to my recent post on the shortcomings of the current Gene Ontology (GO) database. As you might have noticed, my last contribution was written in a moment of frustration, caused by attempt to use GO for something useful in the real (biological) world. Today, I have calmed down a bit, and would like to use this occasion to discuss a few possibilities for improving GO. Here are some general factors that contribute to the problems with GO, as perceived by me and maybe others. GO might have been designed with something else in mind, differing from what GO is typically being used for (mainly annotation of gene lists, and gene set enrichment analysis). Many GO terms are virtually useless for this kind of application, although they might be very important for a more philosophi... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=695416 Tue, 26 Jun 2007 00:22:58 +0100 695416 http://suicyte.wordpress.com/2007/06/24/why-go-sucks/ Please excuse the rude title of this post - it is crafted after a number of recent blog postings on the shortcomings of Wikipedia. I for myself have been a very late adaptor of wikipedia and had never expected much from this resource - whenever I am using it now, I am pleasantly surprised how useful it is, even for most scientific topics. Obviously, you cannot believe everything you find in Wikipedia, and I am quite concerned about the growing number of young students,  who apparently learn biochemistry from Wikipedia rather than from textbooks - this is certainly not the way to go. However, for a quick look-up of the formula of orlistat (tetrahydrolipstatin, “alli“) and stuff like that, Wikipedia is much more convenient than any other resource I know of. And, as has been said... Suicyte Notes blogs http://www.medworm.com/rss/comments.php?id=692648 Sun, 24 Jun 2007 01:24:50 +0100 692648