{bio,medical} informatics
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The New York Times
Genetic Link Seen in Cancer Drug's Power
[requires 'free' registration]
"Stories about such rescues from death's door have given hope to tens of thousands of cancer patients who have tried Iressa, made by the British company AstraZeneca. But, maddeningly, only about one in 10 of them benefit significantly. And doctors have been unable to predict which patients will win this rare reprieve.
Now two groups of scientists say they have the answer: The people who improve sharply have a genetic mutation in their tumors that makes their disease highly vulnerable to the drug."
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The New York Times
A Glimpse at the Future of DNA: M.D.'s Inside the Body
[requires 'free' registration]
"Scientists have developed what they say could become the world's smallest medical kit: a computer, made of DNA, that can diagnose disease and automatically dispense medicine to treat it.
The computer, so small that one trillion would fit into a drop of water, now works only in a test tube, and it could be decades before something like it is ready for practical use. But it offers an intriguing glimpse of a future in which molecular machines operate inside people, spotting diseases and treating them before noticeable symptoms even appear."
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The Oregonian
Mathematical supermodels refine epidemic predictions
"Most modern disease models were developed about 100 years ago, she said, in response to malaria epidemics. They use statistics and a series of equations to define in general terms how epidemics progress. In graphic form, Crandall said, the models draw smooth, continuous curves.
The Reed model is notably different. Technically speaking, it relies on parametric relationships and fractals, not differential equations and curves, Crandall said. Simply put, the new model is "discrete," not "continuous." It considers millions of interactions event by event -- as represented by each tiny green speck in the virtual forest fire.
The difference is notable in disease outbreaks."
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The Mercury News
First across the gene pool
"Judging by the number of books recounting the complete sequencing of the human genome, this feat of late-20th-century scientific and fundraising prowess surely rates with the discoveries of Copernicus and Darwin.
Certainly, the major players in the drama routinely aired this and other grand claims during the great race to unravel the genome in the late 1990s. And the media obligingly repeated them.
Now we have another book recounting this tale of ego, cash and discovery."
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Bio-ITWorld
The Changing Politics of Grid
"Last year we did a study on the market and asked some 50-plus multibillion-dollar corporations, the CIOs and others, about the issues or barriers to grid computing. One of the biggest barriers that we discovered was that there is a group of what we call non-technical issues related to grid computing, and effectively that turned out to be organizational issues or what we described as "the politics" of grid. The issue there is really that people are unwilling to share their resources."
In the case of politics, then, what happens is most people feel -- and this came out in our study last year and again this year -- is that the politics are a significant issue."
redux [03.19.04]
"The humble personal computer used to send e-mail or surf the Internet could quietly be finding a way to stop cancer, treat smallpox or counter a bio-terror attack with anthrax spores."
Novartis is among the growing number of drug makers using in-house grids to search for new drugs. It has 2,700 PCs linked up now and aims to boost that to between 20,000 and 25,000 within two years, said Manuel Peitsch, the head of informatics and knowledge management at its drug research labs."
redux [11.29.03]
[requires 'free' registration]
"Various software packages are designed to build and manage internal grids using an enterprise's own computing resources, the market leader being Grid MP(TM) from United Devices of Austin, Texas.
Such solutions may be robust and help mop up otherwise wasted computing resources, but they still require considerable expertise to run efficiently and ensure that jobs are scheduled correctly and meet agreed priorities. The major cost of a grid lies in managing the resources rather than in the hardware itself, says Atkinson. Therefore, the cost saved by utilizing spare computing resources may be more than outweighed by the cost of additional IT staff. For this reason alone, Atkinson expects many laboratories will make use of external grids."
redux [10.01.03]
"Using the computing power of 2.5 million PCs donated by volunteers from around the world, researchers have narrowed the search for a new treatment for smallpox, now seen as a possible terrorist weapon, to 44 drug molecules that may render the smallpox protein inactive.
The volunteered computing power, set up in a grid through grid.org, contributed more than 250,000 years of computing time in the eight-month Smallpox Research Grid Project, project leaders said. "
""When this project was first explained to me, I thought it was rather Jules Verne-ish," said Army Brig. Gen. Patricia L. Nilo, acting deputy assistant for chemical and biological defense."
Collectively, the 2.5 million PCs running the grid screensaver constituted the world's largest supercomputer, said Todd S. Ramsey, IBM Corp.'s general manager for global government industry."
redux [07.17.03]
"The U.S. is falling behind Japan in the area of supercomputing, as federal research agencies have shifted their focus toward grid computing in the past decade, according to witnesses at a congressional hearing Wednesday.
The result is that U.S. companies have less access to supercomputing resources because demand from the U.S. government has traditionally driven the supercomputing industry in the U.S., critics of the government's efforts in high-performance computing told the U.S. House Science Committee."
redux [06.28.03]
""The language really matters, and confusion on language can be really damaging," Gage said. Citing Sun's experience with Java as an example, he warned developers about the dangers of hype and cautioned them that grid computing risks becoming a catch-all phrase that promises more than it ever can deliver."
"The term has been used to describe a myriad of computing scenarios, from harnessing the processing power in networked PCs build a vast, distributed "supercomputer," to an alternative architecture for the Internet that will provide the underpinnings for Web services and other distributed applications."
redux [05.21.03]
" The American Diabetes Association is using Gateway Inc.'s grid program to run a compute-intensive application designed to accelerate diabetes-related research.
The association, based in Alexandria, Va., is running the Archimedes software application, which Richard Kahn, chief scientific and medical officer for the ADA, called "the Sims City of health care." Using the program, the association can create an environment with any number of variables--such as doctors, hospitals, rooms, costs, patients and treatments--and run numerous what-if scenarios as a way of researching multiple aspects of diabetes care and running clinical studies."
redux [01.09.03]
"Clearly, grid computing means different things to different people, often at different times. To its most visionary pundits, grids symbolize the penultimate step in the evolution of computing architecture into a universal source of pervasive, utility-like computing power that companies can purchase as needed, much as they purchase electricity today. Most stalwart advocates believe that grids not only represent the IT environment of the future but also will ultimately eclipse in significance what the Internet is today."
"All hype aside, it is unlikely that grids will fundamentally change the way that scientific and technical computing is done in the near term, particularly in the private sector."
redux [09.13.02]
"A final obstacle that Stuart pointed out is of the self-inflicted variety: Grid, distributed, peer-to-peer, and other similar incarnations have become victims of their own hype. Increasing media coverage of these technologies has led to confusion in the marketplace, Stuart posited, "and when a prospect becomes confused, the easiest thing is not to do anything.""
"However, he added, there is a bright side to the publicity deluge. Citing the Gartner Group's annual "Hype Cycle of Emerging Technologies" report, which tracks new methods from the initial "tech trigger" period through the "peak of inflated expectations," the "trough of disillusionment," the "slope of enlightenment," and onto the final "plateau of productivity," Stuart noted that desktop grid computing might be working its way from the trough to the slope phase right now, largely because users are discovering which applications work best with the architecture."
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Wired News
Engineered Mice Have Two Mommies
"Men, your gender just took a hit in the animal kingdom. Scientists report they've created mice by using two genetic moms -- and no dad.
That's a first for any mammal. But don't look for this service at the corner fertility clinic. Experts say the mouse procedure can't be done in people for technical and ethical reasons."
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InformationWeek
Cream Of The Science Crop
"As Randal Bryant takes over as dean of the School of Computer Science at Carnegie Mellon University, one of the country's most prestigious IT training grounds, he might have to consider something his predecessors spent very little time worrying about: recruiting students."
"The computer-science school also needs to figure out how best to work with other departments, which increasingly see their futures tied to computer technology. The clearest example is the biology department, which five years ago approached the computer-science school about closer collaboration and started hiring computer-science Ph.D.s. Why? It recognizes that future discoveries in areas such as genomics will rely on computational biology.
But Bryant says the effect also will increasingly work the other way: Computer scientists will need to think like biologists to work in more-dynamic, less-stable network and data environments. "The interesting part is, biology will start driving a lot of computer science," he says."
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Nature: Science Update
Database lists human genes
"Researchers have compiled a comprehensive catalogue of over 21,000 human genes: as many as three-quarters of the total number of genes thought to be in our genome."
"Analysis of the gene set has already thrown up some interesting findings. It seems, for example, that the sequences at the beginning and end of genes tend to be longer than those in the middle, although no one yet knows why. "There's something funky going on at the front and back of genes," says Ewan Birney of the European Bioinformatics Institute in Hinxton, Britain."
"The analysis also shows that about 4% of the human genome sequence is missing or misassembled, say the researchers. Professor Brookes added that the research supported the theory that much of our DNA has no function.
"The genome wasn't designed by a computer programmer, from top to bottom. It keeps evolving all the time. There are bits of the genome and RNA molecules that are probably not doing much. Maybe they did once, but they don't now. Or maybe they're evolving a function.""
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ScienceDaily
Researchers Substitute Whole Chromosomes To Speed The Search
For Genes In Common Diseases
"Medical researchers know that most common human diseases, such as hypertension and diabetes, have a large genetic component. Many genes, interacting with the environment, contribute to these diseases. For researchers, a major challenge is finding all the genes involved with a particular disease.
Researchers from Case Western Reserve University School of Medicine, the Whitehead Institute for Biomedical Research, and Baylor College of Medicine have developed a new method that they believe will revolutionize the search for these genes. In a new research paper, they report that by swapping one chromosome at a time in mice, they can more simply, yet thoroughly, detect the locations of genes involved with complex medical conditions."
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News-Medical.net
Free software helps capture the molecular signatures of
cells
"A new, free software package developed by the Broad Institute of MIT and Harvard makes it easier and faster for scientists to capture the molecular signatures of cells in a particular state--information that's crucial to disease diagnosis and prognosis."
"GenePattern addresses several hurdles facing biomedical research, particularly the need for interoperable tools that let researchers exchange one another's methods and data. Researchers can use GenePattern through a simple user interface or a powerful scripting language. Computational biologists can add a software module written in any language."
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The Buffalo News
A biotech match gone wrong?
"Two years ago, Jeffrey Skolnick arrived as the leader of the University at Buffalo's new bioinformatics center and the next great hope for the region's struggling economy.
Last week, UB issued a three-page news release announcing a restructuring and expansion of the bioinformatics center that includes a new executive director.
Skolnick's name did not appear anywhere in that document."
redux [03.29.04]
"Bioinformatics star Jeffrey Skolnick has created a stir at the University at Buffalo by criticizing his Dell supercomputer -- announced with fanfare in 2002 -- and switching his allegiance to rival IBM Corp.
The highly public flap has prompted UB administrators to come to the defense of Dell, a deep-pocketed research partner."
redux [03.25.04]
"The University at Buffalo Center of Excellence in Bioinformatics has installed an IBM Corp. supercomputer built on blades and also will work with IBM researchers who will provide algorithms to aid protein pattern and correlation discovery, the company and the center announced Thursday."
"The new supercomputer that will handle the intensive computational work will have a peak performance of more than 1.32T flops and will consist of a cluster of 266 IBM eServer BladeCenter HS20 systems running Red Hat Advance Server 2.1 Linux."
redux [12.08.03]
""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.
Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.
The bar's proprietor, Jim Daley Jr., was plenty aware of it.
"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""
redux [07.14.03]
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
"Scientists on the cutting edge of drug development were comparing notes in Buffalo Friday during a symposium aimed at introducing the city's developing bioinformatics center to the scientific world."
"In Buffalo, bioinformatics is viewed as perhaps the best hope to generate jobs lost with the demise of its steel and grain-milling industries. But with several other cities around the country also investing heavily in life sciences, the center's directors are well aware of the competition for staff and resources."
redux [03.02.03]
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
redux [07.26.02]
"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.
The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."
redux [05.01.02]
"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."
The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."
redux [12.07.01]
"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.
Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."
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Genomeweb
Where Are We One Year After the Completion of Human Genome
Project?
[requires 'free' registration]
"Today marks the one-year anniversary of the formal completion of the Human Genome Project and there are those who wonder where the benefits are from this feat of scientific investigation.
At a panel discussion sponsored by Rockefeller University last night, Francis Collins, director of the National Human Genome Research Institute, addressed public reaction to completing the first version of the human genome sequence. In response to those who expressed disappointment that the promised benefits have not yet arrived, Collins said that getting the sequence was a bit "like opening a closet with too much stuff inside; it all sort of fell on us.""
redux [04.13.03]
"This time it is the real thing, scientists promise - the complete sequence of human DNA, as perfectly rendered as it ever will be."
"Now, there are no substantial holes left in the string of three billion base units that make up our chromosomes and determine our biology. There are still parts that are technically unsequenceable, says Collins, "but it's only about 1.5 per cent. That's what we called the finishing line when we began this enterprise, and now we've actually done it.""
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Guardian Unlimited
Eureka! Scientists map the moment
"Neuroscientists in the United States have identified the brain region involved in that glorious "Eureka!" moment, when a solution to a puzzle suddenly appears from nowhere.
Mark Jung-Beeman and Edward Bowden of Northwestern University, and John Kounios of Drexel University, report in the Public Library of Science journal Biology today that the so-called "Aha!" moment is accompanied by a burst of telltale neural activity in the right hemisphere of the brain."
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The New York Times
After the Double Helix: Unraveling the Mysteries of the State
of Being
[requires 'free' registration]
"Sitting at lunch on the patio of his home here one muggy day last June, Francis Crick was expounding on the mind-body problem and the thorny subject of the human "self."
Where is the line between mind and matter? he asked. Aside from the neurons in our brains, the human body contains tens of millions of neurons in the enteric nervous system, which extends into the stomach and intestines. "When you digest your lunch is that you?" Dr. Crick asked."
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The Scientist
Bioinformatics for the Linux-Curious
[requires 'free' registration]
"If you've been intrigued by Linux but want to avoid the hassle of repartitioning your hard drive, Bioknoppix (bioknoppix.hpcf.upr.edu) may be just what you need. A bioinformatics-themed version of Knoppix, Bioknoppix, unlike most Linux distributions, does not install to the hard drive; instead it runs from a CD."
" But bioknoppix is not the only Knoppix-based Linux distribution customized for bioinformaticians."
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Chicago Tribune
Bioterror detectors go high-tech
"Government analysts have begun scanning the U.S. daily for the first signs of a bioterror attack by monitoring enormous databases that include over-the-counter drug sales and common ailments reported in hospital emergency rooms."
"Although supporters of the effort, including top Bush administration officials, believe stepped-up surveillance is crucial, critics say the concept is largely untested and likely to impose new burdens on an already over-stretched public health system."
redux [10.28.04]
"Prompted by the US anthrax attacks of October 2001, most of the new surveillance systems are designed to pick up early warning signs of a bioterror attack, such as a hike in fevers or rashes. They use sophisticated algorithms to filter computerized health data for unusual peaks.
But the systems are untested as yet by bioterror agents - so researchers are teasing other information from them. "These data have all sorts of uses," says Julie Paulin, an expert in preventive medicine at the Walter Reed Army Institute of Research in Silver Spring, Maryland."
redux [04.17.03]
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."
redux [01.22.03]
[requires 'free' registration]
"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."
redux [11.25.02]
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."
redux [10.31.02]
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."
redux [02.18.02]
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."
redux [06.29.01]
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
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Guardian Unlimited Books
Keep the Bunsens burning
"In a provocative comparison, Patricia Fara declares that "Official accounts of Soviet Russia avoided mentioning Josef Stalin. In contrast, women have not been written out of the history of science: they have never been written in." Women may have been excluded from the traditional historical record, but it is simply not the case, Fara demonstrates, that they were excluded from scientific activity in the 18th century. Pandora's Breeches presents so many examples of women active in science that the pronouncements of those who declared women were unscientific seem less like an injunction than a desperate attempt to lock the door after the horse has bolted."
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News.Com
Japan
expands supercomputer cluster
"Supercomputer maker Linux Networx has sold a system with 278 dual-processor servers to Japan's National Institute of Advanced Industrial Science and Technology, the Bluffdale, Utah-based company said Wednesday. The Linux system will be used for bioinformatics and nanotechnology research. It will also perform some calculations previously handled by another system, the Tsukuba Advanced Computing Center SuperCluster."
"The cluster addition and SGI storage together cost about $3 million, Linux Networx said. The Linux Networx machine uses 3.06GHz Intel Xeon processors and the company's Linux cluster management software."
"BM on Tuesday began selling prepackaged clusters of low-priced computers designed to offer supercomputer-type capabilities to company and university departments for less than $200,000."
"The clusters consist of IBM servers loaded with Linux or Windows, powered by Intel or Advanced Micro Devices Inc. chips, plus a management server and network connections."
"IBM is also working on preloading commonly used high-performance-computing software programs to create clusters tailored for applications such as bioinformatics or computational fluid dynamics."
"The turnkey system "Apple Workgroup Cluster for Bioinformatics," being presented today at ClusterWorld Conference and Expo in the San Jose Convention Center, is an all-inclusive system with everything a non-technical bench scientist needs to set up, operate, and maintain a small, computational cluster with little or no support required from IT departments."
"Bench scientists, with little or no assistance from their IT department, can deploy iNquiry on the Xserve via a unique self-deployment method that uses an external firewire drive as a cluster installation and configuration device -- in an average of 30 minutes."
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BBC
New
light shed on chimp genome
"A comparison of the chimp and human genomes casts new light on why the two species are so different despite having very similar genetic code."
"One of the leading scientists on the project says the answer lies in the process that orchestrates the genes as the chimpanzee is developing."
"The latest experimental results have solidified evidence of a roughly 10% difference in gene expression from several regions of the brain."
"The researchers have confirmed their findings in four regions of the cerebral cortex, and in the cerebellum and the caudate nucleus. On the other hand, evidence relating to the linear accumulation of differences over time means "we are coming to believe that these are not all functionally relevant," Paabo added."
redux [12.12.03]
[requires 'free' registration]
"In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.
A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear."
"Another group of selected genes is involved in brain development."
redux [12.10.03]
"Researchers today released a draft version of the genetic sequence of our closest relative, the chimpanzee Pan troglodytes .
The differences between the chimp's genetic code and ours should reveal what makes us human, scientists hope. The disparities might, for example, lie in genes that control the development of the brain and language, or of human-specific diseases such as Alzheimer's, AIDS and malaria."
redux [05.20.03]
"Scientists from the Wayne State University, School of Medicine, Detroit, US, examined key genes in humans and several ape species and found our "life code" to be 99.4% the same as chimps.
They propose moving common chimps and another very closely related ape, bonobos, into the genus, Homo, the taxonomic grouping researchers use to classify people in the animal kingdom."
redux [04.29.03]
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."
"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.
redux [03.04.03]
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
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New Scientist
Rat genome reveals supercharged evolution
"Roughly 200 years after being tamed, bred and adopted as science's favourite laboratory animal, the brown Norway rat has had its genome sequenced. It is only the third mammal after humans and mice to have its genetic plan read."
"Comparisons between the genomes is also yielding tantalising insights into how each species evolved. The analysis has already shown, for example, that rats have been evolving faster than both humans and mice. "We find that rodent evolution is an order of magnitude faster than in humans," says Richard Gibbs of the Baylor College of Medicine in Houston, Texas, and head of the sequencing effort."
""Sequencing the rat genome represents much more than an odometer moment," said Francis Collins, director of the Human Genome Research Institute, during a press conference on Wednesday in Washington, D.C. "It gives the opportunity for triangular comparison -- three is vastly better than two.""
"Studies on the rat genome have already led to significant discoveries, said Howard Jacob, a senior author on the paper and researcher at the Medical College of Wisconsin. For example, scientists had been unable to find the gene that caused polycystic kidney disease by using patient samples. Researchers mapped a region of the rat's genome where they suspected the gene was located and noticed the same sequence of letters (A, C, T and G, which represent the nucleotides that make up all DNA: adenine, cytosine, thymine and guanine). By lining up these two sections of DNA, they were able to pinpoint the human gene responsible for polycystic kidney disease."
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Innovations Report
Stoned sea-squirts
"The genome of the sea- squirt was recently sequenced, revealing a cannabinoid receptor gene in an invertebrate for the first time. This means that these receptors were present in the common ancestor of the chordates, much further back on the evolutionary timescale than previously thought.
As Dr. Elphick will report on Thursday 1st April 2004 at the annual SEB meeting in Edinburgh [session A1.7], the sea-squirt cannabinoid receptor gene is expressed in tissues outside the nervous system, raising interesting questions about the functions of this evolutionarily conserved signalling system. "
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"And no, this is not an April Fool's joke."
"Elphick's research focuses on the molecular biology and functions of the cannabinoid receptor. Previously, he has demonstrated that the cannabinoid system "is a fundamental signalling system in the central nervous system of vertebrates, where it plays a role in movement, pain, and learning and memory," according to SEB. "In invertebrates such as the sea-squirt, however, the system may have very different functions, perhaps indicating how and why the system evolved in the first place.""
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