The DNA Network

Department of redundancy department [genomeboy.com] Posted: 10 May 2008 05:43 PM CDT Six. That’s how many times I was asked to repeat my name, social security number and date of birth to the technicians at the American Red Cross today. This is how we protect blood recipients?

The 21st Century in Medicine: What will it look like? [ScienceRoll] Posted: 10 May 2008 04:37 PM CDT Jeffrey Dach used one of my recent posts (Personalized Medicine: Real Clinical Examples!) as a reference in his article describing the future of medicine. It’s a quite detailed and comprehensive essay about several fields of medicine and he doesn’t forget to mention personalized medicine and its impact on the future of healthcare: Personalized Medicine is the combination of these two new powerful forces, Orthomolecular Medicine and Genetic Testing. In the future, Personalized Medicine will expand and ultimately play a dominant role in medicine. Example: Warfarin Genetic Testing allows improved calibration of coumadin dosage to avoid bleeding complications. Drug metabolism testing allows for personal modification of drug dosage. Orthomolecular and personalized medicine together? We will be able to sequence the entire genome of an individual human in milliseconds. The cost will be minimal and within the means of the average person. Individuals will have ability to reprogram our own sperm and eggs. One will be able to buy new genes on the internet based on desired traits and features, and use these genes to make one’s own children as easily as buying a copy of Microsoft office. My comment: If the government gets involved, then this sounds a lot like Aldous Huxley’s, Brave New World. Example of this new biotechnology: Human genes are inserted into microbes to make insulin. We will see a dramatic increase in gene therapies and treatments. Well, I think and hope many of these will never come true, but it’s interesting to see how others predict the future. This fantastic video tries to show us some plans and projects that can really shape this century: If you would like to know more about the future, check out some of the presentations at TED or follow CNN Future Summit

My Medical Career: Serving Medical Students [ScienceRoll] Posted: 10 May 2008 04:00 PM CDT My 5th year exam period is just about to begin, and I still need one more year to graduate from medical school as medical education takes 6 years in Hungary. I’ve been studying genetics for years and I’ve been trying to find good opportunities through my blog for more than a year now so I really know how hard it is to build a medical career. A new Australian service now aims to help medical students: My Medical Career is an online career planning portal for Australian medical students and junior doctors. Our goal is to guide you through the process of selecting and achieving a career which best suits your interests, skills and lifestyle needs. You start with Self-assessment through personality tests Specialty profiles: it helps you decide which medical specialty should be your choice Options: activities that can be undertaken during your student and junior doctor years Career plan: how to write a résumé, what to expect in an interview News and conferences in your field of interest Useful resources: websites, blogs, forums, etc. And a whole community is ready to answer your questions. The idea is fantastic, I can’t wait to see something similar in Europe as well.

What's wrong with these figures? [T Ryan Gregory's column] Posted: 10 May 2008 01:34 PM CDT Those of you who have been reading Genomicron for some time will have seen most of these already, but it seems worthwhile reviewing them here at the new blog. The game is simple: identify what is wrong with these figures which have been published in science magazines or scientific journals.

Complete Neanderthal Genome Sequenced - Differs from CRS at 133 Positions [The Genetic Genealogist] Posted: 10 May 2008 08:22 AM CDT GenomeWeb Daily News published a story on Friday entitled “En route to Neandertal Genome, Researchers Analyze Its Complete Mitochondrial Genome” which revealed the results of recent Neanderthal mtDNA analysis. On Thursday May 9th, Svante Pääbo spoke at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Pääbo’s group, along with 454 Life Sciences, is currently engaged in a project to sequence the Neanderthal genome. The researchers have been able to sequence the complete Neanderthal mtDNA genome with 35-fold coverage. The genome is approximately 16 kilobases long and differs from the CRS at 133 positions. From what I’ve been able to find online, it doesn’t appear that the actual sequencing results have been released to the public. Given current estimates of mtDNA mutation rates, the number of differences between human and Neanderthal mtDNA suggests that the branches diverged approximately 600,000 years ago. Although there have been accusations that Neanderthal sequencing is often contaminated by human DNA, the concerns have been addressed by Pääbo’s group. From the article: Pääbo mentioned that about 10 percent of the DNA library they initially sequenced – data they published in late 2006 – consisted of modern human DNA. But over the last two years, they have been guarding against contamination by generating DNA libraries in a clean room and by barcoding the Neandertal DNA. The ISOGG has a page devoted to Neanderthal DNA for more information.

Bad quotes about evolution and genomics. [T Ryan Gregory's column] Posted: 10 May 2008 07:15 AM CDT I hesitate to single out colleagues for what is attributed to them in the media, because often what one says in an interview is not entirely what appears in print.

Debugging fun [Mailund on the Internet] Posted: 10 May 2008 06:11 AM CDT Yesterday I got a simulator from Garrett Hellenthal that I need to simulate some genetics data (combined “panel” and “tagSNP” data, if you want to know). The program didn’t work for me. On the example data provided with the code, it complained about invalid input. Right! Naturally, I expected that Garrett had given me test data that was in some way outdated. It happens quie often that the test data isn’t updated when new features are added to a program, and that test examples no longer function the way they should. I make that mistake a lot, anyway. So I got hold of Garrett, and yes the test example was incorrect and he sent me an updated test. It didn’t work either. We emailed back and forth a bit, and this time it was a bit of a puzzle. Everything worked fine at Garrett’s end, but the program just wouldn’t eat the input on my computer. I didn’t have the time to figure out why, yesterday, as I had a plane to catch, but I had another look at it today. I first grep’ed for the error message I got: “CV frequencies must be between 0 and 0.50″. That line occurred a few places in the code, so I annotated the code with some output before each and that pinpointed this test as the problem: if ((allelefreq[count] < epsilon[count]) || (allelefreq[count] > (0.50-epsilon[count]))) { printf("CV frequencies must be between 0 and 0.50\n"); exit(1); } Ok, so on Garrett’s machine, the test was false and on mine it was true, but the input files were the same. First I tested if the input was read in correctly (Garrett’s IO code is a bit of a mess, excuse me for saying it). allelefreq[count] was supposed to be 0.4 — and it was — and epsilon[count] should be 0.1 — and it was. That’s when I spotted the problem. Do you see it? Clearly 0.4 ≥ 0.1 and 0.4 ≤ 0.5-0.1 so the test should evaluate to false, but it doesn’t. The thing is, floating point numbers aren’t real numbers (as you probably know). And for one thing, 0.1 cannot be represented in a finite number of bits (as a binary number) so it is approximated in the computer. So 0.5-0.1 is not 0.4 (although they could be represented by the same bit-patter as 0.4 is represented as). Whether 0.4 ≤ 0.5-0.1 or 0.4 > 0.5-0.1 on the computer depends on the way the numbers are represented. Garrett was running his program on a 64 bit architecture (where the numbers were represented using 128 bits) and I on a 32 bit architecture (with 64 bits per number). That made all the difference. Fun, eh?

Magnet Lab researchers make observing cell functions easier [Think Gene] Posted: 10 May 2008 04:32 AM CDT Now that the genome (DNA) of humans and many other organisms have been sequenced, biologists are turning their attention to discovering how the many thousands of structural and control genes — the "worker bees" of living cells that can turn genes on and off — function. To do that, they need to develop new techniques and tools. Scientists in the Optical Microscopy group at the National High Magnetic Field Laboratory at Florida State University, working in collaboration with researchers from the University of Alberta in Canada and the University of California, San Diego, have done just that, and in the process have produced back-to-back articles in the prestigious journal Nature Methods. In the first paper, magnet-lab biologists Michael Davidson and Kristen Hazelwood worked with researchers from the University of Alberta to create two new fluorescent-protein biosensors, molecular "beacons" that can tell if there is activity within a cell. The biosensors can be used simultaneously to monitor two separate dynamic functions in a single cell — a key to understanding how different proteins and enzymes (the biomolecules that cause chemical reactions) work together to complete the daily chores that help cells grow and divide. Knowing how cells work together can help researchers learn a great deal more about tumors and developmental biology, among many other things. The researchers improved a powerful technique used to monitor cellular dynamics called fluorescence resonance energy transfer, or FRET. The technique is used to examine a new class of biosensor molecules that tether two fluorescent proteins together through an intervening peptide (which is like a polymer). Several hundred of these new biosensors have been developed over the past few years and are being used by scientists around the world to study a variety of functions, including programmed cell death, carbohydrate metabolism, cell division, hormone stimulation, acidity changes — just about any cellular process that can occur. "In FRET, two molecules that are fluorescent act as 'molecular beacons' under the microscope, transferring energy between each other if they interact in the living cell," said Davidson, who directs the magnet lab's Optical Microscopy program. "With FRET, we can see that happen, but until now, we have only been able to monitor one biosensor at a time." The new technique, called Dual FRET, is outlined in the paper "Fluorescent Protein FRET Pairs for Ratiometric Imaging of Dual Biosensors." http://www.nature.com/nmeth/journal/v5/n5/abs/nmeth.1207.html Further expanding the capabilities of optical microscopy, Davidson and his team worked with collaborators from the University of California, San Diego to create a new screening method for fluorescent proteins that makes them more stable under the microscope. These proteins are sensitive to light, which can bleach them out after a certain period of time. By making the proteins more stable, microscopists can observe live cell dynamics for longer periods of time. The paper describing their work, "Improving the Photostability of Bright Monomeric Orange and Red Fluorescent Proteins," was published in the May 4 online edition of Nature Methods. http://www.nature.com/nmeth/journal/v4/n9/full/nmeth1083.html Taken together, the new technique and tool are expected to speed up experiments and expand the utility of optical microscopy by allowing two dynamic processes inside a cell to be observed at once — and for longer periods of time. Source: Florida State University

Magnet Lab researchers make observing cell functions easier [Think Gene] Posted: 10 May 2008 04:29 AM CDT Now that the genome (DNA) of humans and many other organisms have been sequenced, biologists are turning their attention to discovering how the many thousands of structural and control genes — the "worker bees" of living cells that can turn genes on and off — function. To do that, they need to develop new techniques and tools. Scientists in the Optical Microscopy group at the National High Magnetic Field Laboratory at Florida State University, working in collaboration with researchers from the University of Alberta in Canada and the University of California, San Diego, have done just that, and in the process have produced back-to-back articles in the prestigious journal Nature Methods. This image illustrates fluorescence resonance energy transfer works. With FRET, the illuminated yellow molecules come together, signaling that they are transferring energy in the living cell. Click here for more information. In the first paper, magnet-lab biologists Michael Davidson and Kristen Hazelwood worked with researchers from the University of Alberta to create two new fluorescent-protein biosensors, molecular "beacons" that can tell if there is activity within a cell. The biosensors can be used simultaneously to monitor two separate dynamic functions in a single cell — a key to understanding how different proteins and enzymes (the biomolecules that cause chemical reactions) work together to complete the daily chores that help cells grow and divide. Knowing how cells work together can help researchers learn a great deal more about tumors and developmental biology, among many other things. The researchers improved a powerful technique used to monitor cellular dynamics called fluorescence resonance energy transfer, or FRET. The technique is used to examine a new class of biosensor molecules that tether two fluorescent proteins together through an intervening peptide (which is like a polymer). Several hundred of these new biosensors have been developed over the past few years and are being used by scientists around the world to study a variety of functions, including programmed cell death, carbohydrate metabolism, cell division, hormone stimulation, acidity changes — just about any cellular process that can occur. "In FRET, two molecules that are fluorescent act as 'molecular beacons' under the microscope, transferring energy between each other if they interact in the living cell," said Davidson, who directs the magnet lab's Optical Microscopy program. "With FRET, we can see that happen, but until now, we have only been able to monitor one biosensor at a time." Kristin Hazelwood, National High Magnetic Field Laboratory biologist. Click here for more information. The new technique, called Dual FRET, is outlined in the paper "Fluorescent Protein FRET Pairs for Ratiometric Imaging of Dual Biosensors." http://www.nature.com/nmeth/journal/v5/n5/abs/nmeth.1207.html Further expanding the capabilities of optical microscopy, Davidson and his team worked with collaborators from the University of California, San Diego to create a new screening method for fluorescent proteins that makes them more stable under the microscope. These proteins are sensitive to light, which can bleach them out after a certain period of time. By making the proteins more stable, microscopists can observe live cell dynamics for longer periods of time. The paper describing their work, "Improving the Photostability of Bright Monomeric Orange and Red Fluorescent Proteins," was published in the May 4 online edition of Nature Methods. http://www.nature.com/nmeth/journal/v4/n9/full/nmeth1083.html Taken together, the new technique and tool are expected to speed up experiments and expand the utility of optical microscopy by allowing two dynamic processes inside a cell to be observed at once — and for longer periods of time. Source: Florida State University

DNA Video: Pimp My Genome! Google Tech Talk with Andrew Hessel [Eye on DNA] Posted: 10 May 2008 03:05 AM CDT Google Tech Talks May 3, 2007 ABSTRACT DNA is a programming language for living cells. The cell’s basic operating system, or genome, directs functions like growth and reproduction, energy utilization, and the production of useful compounds like ethanol or penicillin. With genetic engineering, new functions can be added to cells or broken metabolic pathways repaired. Until recently, genetic engineering has required the DNA molecule itself to be physically manipulated, a tedious and expensive process. Now, automatic DNA synthesis permits virtually any DNA code to be made from scratch, opening up genetic engineering to anyone with a computer and a credit card.

Fold it - Solve puzzles for science [My Biotech Life] Posted: 10 May 2008 12:28 AM CDT Jason from Free Genes pointed me in the direction of this cool project called Fold It that just caught my eye. It’s a game but it’s a game with serious impact. Based upon a similar concept of grid processing like the protein folding project (folding@home) or the search for ETs (SETI@home), this new approach makes the collective effort of players directly impact the processing. It’s as if Fold It is an upgraded version of folding@home with the extra special new feature called: human interaction. The concept is quite simple at the gaming point of view where you try to make the protein fold in the best way possible with points being given for stability through hydrogen bonding, compacting, hydrophobic and hydrophilic positioning of lateral protein chains, etc The “better” you fold your protein, the more points you achieve. These conformations are registered by the software and then processed furthermore thus contributing to the overall effort of predicting protein folding and therefore solving puzzles for science! Post from: My Biotech Life

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