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| Biology of Cloud Computing [Microarray and bioinformatics] Posted: 28 Oct 2008 05:47 PM CDT The world summit on Cloud Computing is on December 1-2/2008. Surprisingly Bioinformatics is mentioned only once . And only by cycle computing a company offering grid computing solutions. That apart there is no talk about lifescience space. Ofcourse cloud computing is buzz word for now, and will remain so for some time. It might event meet the same fate of bioinformatics industry has faced in initial years. But this time around there are amny Enterprise companies backing the concept, catiously though. From Amazon, Microsoft, Google, to Sun But according to according to research firm IDC the current economic crisis in the US may save IT companies that invest in cloud computing, as it will contribute to significant growth in that sector over the next five years. ofcourse there are concerns around data privacy and data security But Companies like Millenium Pharma re investing in technology provided by companies like WorkDay (SaaS HR started by former Peoplesoft founder). Earlier this year google announded that Genentech would use Google Apps While Cloud computing for scientist stil have wait, unless you are working in CERN or other research centre on high computing projects, after all they invented Grid Computing or atleast made the fiest steps       |
| Carnival of Carnivals [ScienceRoll] Posted: 28 Oct 2008 05:34 PM CDT Thanks to Alvaro Fernandez at SharpBrains, now we, organizers of biomedical carnivals, launched the carnival of carnivals, MetaCarnival. Here is the first edition. Alvaro collected the best submissions of several carnivals which means MetaCarnival is a collection of selected, quality articles about medicine, biology or medical informatics. I will host the 3rd edition on the 29th of December. A blog carnival can be a great way to make a compilation of articles, news and posts dedicated to a specific field of interest. Anyway, I’ve been running Gene Genie, the carnival of human genetics for almost 2 years now. If you would like to host an edition, let me know. Medicine 2.0 carnival focuses on the impact of web 2.0 on medicine and healthcare. While the Medicine 2.0 Microcarnival is a Friendfeed room with several links that can keep you updated about medicine and web.
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| Systems Biology for Human Healthcare: Webinar [ScienceRoll] Posted: 28 Oct 2008 05:24 PM CDT The Genetic Engineering and Biotechnology News is ready again to organize a webinar for all of us. This time, the topic is Systems Biology: New Approaches, New Tools, and Implications for Human Healthcare. Original Broadcast Date Thursday, October 30, 2008 Time 1:00 – 2:30 pm EST
You can register here.
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| Gene Genie #39 at Genetics & Health [ScienceRoll] Posted: 28 Oct 2008 04:11 PM CDT The 39th edition is up at Genetics & Health. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Grace Ibay, for hosting Gene Genie. Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine.
Don't forget to submit your articles via the official page. Let me know if you would like to host an edition. Here are all the issues of Gene genie:
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| Migrating Salmon Video [Bayblab] Posted: 28 Oct 2008 01:21 PM CDT  Ran into this video made of individual Chinook and Steelhead Salmon smolt migration in British Columbia. These individuals are tagged before they are released as stocked salmon in the Snake and Thompson Rivers. Their movements are monitored by an impressive system called the POST array. I don't really know much about the details, however, the punch line is there is an impressive monitoring system in place for these salmon and it makes a great video. Also if you are more interested here is the paper where they have some interesting survival data like survival /100km migrated and on places with and without hydroelectric dams. |
| You gotta love it! [The Gene Sherpa: Personalized Medicine and You] Posted: 28 Oct 2008 12:29 PM CDT It's mid-morning and the day is just getting moving. We had a round up today and talked about Brugada Syndrome. I think this is a wonderful topic and it was presented very nicely. It was also a... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Suicide linked to methylation in the brain [Mary Meets Dolly] Posted: 28 Oct 2008 11:58 AM CDT I am tired of politics so I am getting back to the subject I like: genetics. Researchers autopsied the brains of patients who committed suicide and those that died of other causes and found that the brains of those whose committed suicide had a ten-fold increase in methylation of a gene that regulates behavior. What is methylation? It is one way that the cell regulates what genes are turned on and off. If a gene is methylated it does not get expressed. See, it is not just about what genes you inherited, it is also about what genes are turned on. Expression of a gene is influenced by other factors than just the sequence of DNA. Scientists are discovering that the regulation of gene expression is influenced by many different factors like diet and exercise. This is a relatively new field of study called epigenetics. The ten-fold increase of methylation in those patients who committed suicide may lead to a better understanding of major depression and suicidal behavior. As someone who has suffered from postpartum depression and seasonal affective disorder most of my adult life, I was excited to read about this new development. From the BBC News:
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| Tomorrow's Table on Today's Table x 2 [The Tree of Life] Posted: 28 Oct 2008 11:09 AM CDT So - I was having breakfast with my daughter this morning and she was in a funky mood. She wanted some stories so to make life easy and not get up, I opened up the only thing near the table to read - a copy of Nature Biotechnology that I received for free in the mail (not sure why) - and was going to show her some pictures of things. And there was a review of my friend and colleague Pam Ronald's book "Tomorrow' Table." And so I told my daughter that this was a story about a book by my friend Pam and reminded her about how we had gone over to Pam's house and how she worked in the office next to mine. And then I asked my daughter if she wanted to see Pam's book, which I had in the office and she said yes. And so I got the book and then we told stories about Pam. So - here in living color is a picture of my daughter and Tomorrow's Table the book and the review of Tomorrow's Table on my table, today.
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| Another Call for Submissions to Mendel's Garden #25 [evolgen] Posted: 28 Oct 2008 10:00 AM CDT
I will be hosting the next edition of Mendel's Garden on Sunday, November 2. If you have written any blog posts about genetics in the past few months, send me a link (evolgen[at]yahoo[dot]com). Also, if you've seen any good genetics posts on other people's blogs, let me know. For those not in the know, Mendel's Garden is the original genetics blog carnival. On the first Sunday of every month, the carnival plays host to the best genetics blogging of the past month. After a hiatus of a few months, the carnival is back. Read the comments on this post... |
| 5 Laboratory Sterilisation Methods [Bitesize Bio] Posted: 28 Oct 2008 06:21 AM CDT Effective sterilisation techniques are essential for working with isolated cell lines for obvious reasons – you don't want bugs from the environment growing in your nice culture medium, and equally, cultures must be sterilised before disposal. So what are the most common methods of sterilisation, and how do they work? Unsure? Read on… WET HEAT (Autoclaving) The method of choice for sterilisation in most labs is autoclaving; using pressurised steam to heat the material to be sterilised. This is a very effective method that kills all microbes, spores and viruses, although for some specific bugs, especially high temperatures or incubation times are required. Autoclaving kills microbes by hydrolysis and coagulation of cellular proteins, which is efficiently achieved by intense heat in the presence of water. The intense heat comes from the steam. Pressurised steam has a high latent heat; at 100degC it holds 7 times more heat than water at the same temperature. This heat is liberated upon contact with the cooler surface of the material to be sterilised, allowing rapid delivery of heat and good penetration of dense materials. At these temperatures, water does a great job of hydrolysing proteins… so those bugs don’t stand a chance. DRY HEAT (Flaming, baking) Dry heating has one crucial difference from autoclaving. You’ve guessed it - there’s no water, so protein hydrolysis can't take place. Instead, dry heat tends to kill microbes by oxidation of cellular components. This requires more energy than protein hydrolysis so higher temperatures are required for efficient sterilization by dry heat. For example sterilisation can normally be achieved in 15 minutes by autoclaving at 121degC, whereas dry heating would generally need a temperature of 160degC to sterilize in a similar amount of time. FILTRATION Filtration is a great way of quickly sterilizing solutions without heating. Filters, of course, work by passing the solution through a filter with a pore diameter that is too small for microbes to pass through. Filters can be scintered glass funnels made from heat-fused glass particles or, more commonly these days, membrane filters made from cellulose esters. For removal of bacteria, filters with an average pore diameter of 0.2um is normally used. But remember, viruses and phage can pass through these filters so filtration is not a good option if these are a concern. SOLVENTS Ethanol is commonly used as a disinfectant, although since isopropanol is a better solvent for fat it is probably a better option. Both work by denaturing proteins through a process that requires water, so they must be diluted to 60-90% in water to be effective. Again, a it’s important to remember that although ethanol and IPA are good at killing microbial cells, they have no effect on spores. RADIATION UV, x-rays and gamma rays are all types of electromagnetic radiation that have profoundly damaging effects on DNA, so make excellent tools for sterilization. The main difference between them, in terms of their effectiveness, is their penetration. UV has limited penetration in air so sterilisation only occurs in a fairly small area around the lamp. However, it is relatively safe and is quite useful for sterilising small areas, like laminar flow hoods. X-rays and gamma rays are far more penetrating, which makes them more dangerous but very effective for large scale cold sterilization of plastic items (e.g. syringes) during manufacturing. So those are some of the main methods for sterilization I can think of. Do you have any questions, comments or mistakes? Did I miss anything out? Hit the link below to chat with me about this article in the bistro. |
| Kill, kill, kill! [Mailund on the Internet] Posted: 28 Oct 2008 04:05 AM CDT Ok, so I notice that my CPU load is pretty high while the computer wasn’t really supposed to be doing much. I check out what is wrong and notice that I have a Totem process eating more than 80% of the CPU. Okay, I did watch a movie yesterday evening, so it is not that weird to have Totem running. Something must have gone wrong when I closed the program, but no worries, I’ll just terminate the process now. I send it a gentle HUP signal to let it know that I want it to shut down. That doesn’t work. Okay, no more mister nice guy; I send it kill -9. That still doesn’t work!?!! WTF? kill -9 means EAT FLAMING DEATH, PROCESS! It tells the OS to kill the process immediately. No questions asked. It doesn’t “inform” the process that it should terminate. There should be no way for a process to survive a kill -9, but my Totem process is running happily along. I had to reboot the machine to kill the process. That is just not right. What is going on here? Apparently I am not the only one with this problem, but I haven’t figured out what is causing this problem or how to avoid it :-( |
| Audio from PGP Press Conference on Public Data Release [The Personal Genome] Posted: 27 Oct 2008 02:31 PM CDT Harvard Medical School’s Office of Public Affairs has published an audio recording of the October 20th press conference where the PGP-10 discussed their individual decisions about public release of their genomic data. This posting includes an audio/video/photo media file: Download Now |
| Proposition 8 - My Vote [The Tree of Life] Posted: 26 Oct 2008 11:17 PM CDT I generally shy away from non sciency topics here but occasionally a few slip in. And as I was filling out my absentee ballot I just felt I had to post something about California's horrendous Anti-Gay-Marriage Proposition 8. Originally, I was going to post a picture of my no vote on my absentee ballot but then I read this New York Times article about how many states have laws that say something like "No person shall photograph, videotape, or otherwise record the image of a voted official ballot for any purpose not otherwise permitted under law."So instead of a picture I am going to simply put words here. And since a picture is worth 1000 words, here are mine. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. |
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