{bio,medical} informatics
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New Scientist
Prions may hold key to stem cell function
"The curative properties of stem cells may rely on prions, a new study suggests, the type of protein made infamous by mad cow disease.
Prions are a special class of protein that can change the shape and function of other proteins around them. While these are found throughout any mammal’s body, the understanding of their biological role is limited. What is known is that prions that become misshapen, through some unknown process, can result in BSE (bovine spongiform encephalopathy) – mad cow disease – and its equivalents in other animals.
Researchers at the Whitehead Institute in Cambridge, Massachusetts, US, have now found that adult stem cells in bone marrow gradually lose their ability to regenerate without their normal complement of membrane-bound prions."
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Bio-IT World
Microarrays Decipher Disease"Interstitial lung diseases represent both a diagnostic and therapeutic challenge because the clinical features of the disease are often nonspecific. “The classifications of the disease changes every few years so it’s very hard to diagnose,” says Naftali Kaminski, director of the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease (ILD) and associate professor of medicine, pathology, and human genetics at the University of Pittsburgh Medical Center.
Kaminski and Moises Selman from Mexico City set out to ascertain whether gene expression patterns could help determine differences between various interstitial lung disease types, including idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), and nonspecific interstitial pneumonia (NSIP)."
"Using custom oligonucleotide arrays designed by Eos Biotechnology and Affymetrix, Kaminski and Selman and their collaborators found a functional genetic signature to distinguish between IPF and HP. “We found that the genes that distinguish HP from IPF were genes related to inflammation,” says Kaminski."
redux [12.05.00]
"Basic science came to be dominated by molecular genetics. The discovery of DNA spawned new technologies that led to research into genetic engineering, genetic screening, and gene therapy. Naive investors, often ignorant about the wafer-thin credibility of the research they were paying for, poured millions into biotechnology companies. The result, according to Le Fanu, has been that "the impression of progress has not been vindicated by anything resembling the practical benefits originally anticipated."
Worse, gene therapy has largely turned out to be "not only expensive but useless." Why has the new genetics so far failed medicine? Le Fanu answers that "genetics is not a particularly significant factor in human disease." And, in any case, genes are "complex," "unpredictable," and "perverse." They are not amenable to easy understanding. Their involvement in disease is largely "incomprehensible.""
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive. "
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."redux [11.02.00]
"On both sides of the Atlantic, revolutionary claims have been made about the ultimate impact of genetics on clinical medicine. John Bell at Oxford has asserted that "within the next decade genetic testing will be used widely for predictive testing in healthy people and for diagnosis and management of patients.... The excitement in the field has shifted to the elucidation of the genetic basis of the common diseases." (1) And in the United States the director of the National Human Genome Research Institute, Francis Collins, has stated that the good that would come from mapping the human genetic terrain "would include a new understanding of genetic contributions to human disease and the development of rational strategies for minimizing or preventing disease phenotypes altogether." (2)
Statements like these clothe medicine in a genetic mantle. The result of efforts to identify genes that have a role in common diseases suggests a different picture: the genetic mantle may prove to be like the emperor's new clothes. In this article we argue that the new genetics will not revolutionize the way in which common diseases are identified or prevented. Mapping and sequencing the human genome will lead to the identification of more genes causing mendelian disorders and to the development of diagnostic and predictive tests for them. The development of safe and effective treatments, however, will usually lag behind, (3) although occasionally a treatment does precede the discovery of the disease-causing allele, as was the case for hemochromatosis. (4) Furthermore, only a small proportion of the population has mendelian disorders, and this will limit the ultimate impact of the Human Genome Project.
Our doubts stem from the incomplete penetrance of genotypes for common diseases, the limited ability to tailor treatment to genotypes, and the low magnitude of risks conferred by various genotypes for the population at large. Consequently, most people will have little interest in learning their genotypes."
"With advances in the human genome project and the increasing availability of DNA markers scattered throughout the genome such as simple sequence polymorphisms, variable number tandem repeats, and short sequence repeat polymorphisms, it has become increasingly possible to search for the genetic basis of complex human diseases using genomic wide screening methods. Linkage analysis using LOD score analysis in large pedigrees has been the traditional tool to identify gene loci for human disorders both for single gene disorders (e.g. Huntington) and for complex chronic diseases (e.g. bipolar disease). Recently, Risch and Merikangas have argued that the future of genetic studies of complex human disease may depend, to a large extent, on applications of new "association" type methods to family-based data. The main method of interest is the transmission disequilibrium test (TDT) in which alleles at a given locus for a person with a specific disease are compared with parental non transmitted alleles, to look for evidence of deviation from expectations in the absence of linkage. The TDT has been shown to be a valid test of linkage in the presence of linkage disequilibrium (which creates associations with specific alleles). They showed that the TDT has more power than traditional linkage analysis for disease genes with weak to moderate effects on disease risks.
In this paper, we argue that the future of the genetic study of complex disorders will rely increasingly on the classical epidemiologic "association" paradigm. We show that on the long run, improvements in study designs and in adjusting for population stratification using interviews and genetics markers will lead to a new era of population-based incident case-control studies that could have more power and lead to more detailed information not only on the presence or absence of a disease susceptibility gene but define the magnitude of risks and gene-environment interaction- a crucial first step to disease prevention and health promotion."
"As a result of the revolution in the biological sciences following the development of recombinant DNA technology and the sequencing of most of the human genome, the role of genetics in the pathogenesis of human disease now dominates biomedical research. There is every sign that the rapidly evolving technology of the post genome era will unravel the function of the human genome and explain how the 50 000 to 100 000 genes interact with one another and the environment to make us what we are.
The central question for the medical sciences is the extent to which it will be possible to relate events at the molecular level with the clinical findings or phenotypes of patients with particular diseases. This problem will permeate every aspect of medical research and practice in the future. It will dominate predictive genetics and genetic counselling. It will also be of major importance for clinical decision making as new and novel approaches to the treatment of disease become available, particularly those involving genetic manipulation. Further exploration of the genome may also provide information on some of the common killers of Western society, such as heart disease, stroke, diabetes, and psychiatric disease, leading to a new form of pharmacology in which drugs are tailored to an individual's genetic make up. Even more important, and certainly more complex, will be relating genotype to phenotype. Many of our most important diseases almost certainly reflect varying susceptibility, due to the action of many different genes and a wide variety of environmental factors and to the ill understood biology of ageing."
"Is there any way of guessing the likely levels of complexity that will be encountered as the genetic basis of disease is explored with the new technology?"
redux [07.13.00]
[requires 'free' registration]
"Genes may cause more than one-quarter of three major types of cancer, more than previously thought, a group of researchers says.
Scandinavian researchers concluded that genes account for 42 percent of the risk for prostate cancer, 35 percent for colorectal cancer and 27 percent for breast cancer.
The rest of the cases are caused by what people do, such as smoking and diet, or what happens to them, such as on-the-job hazards or viral infections, the researchers said."
"...the conclusion runs contrary to the widespread belief that scientists "will find solutions or cures to all diseases in the genes," Dr. Lichtenstein said. "That won't be the case."
redux [10.05.00]
"Simple genetic diseases, such as cystic fibrosis and thalassaemia are just that — simple. A single gene underlies them. Finding it is like climbing a steep hill — hard work but straightforward. Complex disorders, such as asthma and type 2 diabetes, by contrast, have many components, which makes finding a cause more like scaling Everest — far harder, requiring more specialist equipment and the strong possibility of failure.
In work published in the October issue of Nature Genetics, University of Chicago researchers have cleared a path to studying the genetic foundation of type 2, or non-insulin-dependent diabetes mellitus (NIDDM). In a study of a Mexican-American population and two white populations (Finns and Germans) they have found that small genetic variations, called single-nucleotide polymorphisms (SNPs), in a particular gene tend to occur more often in diabetics than in healthy relatives. Although finding a common genetic variation in family groups affected by simple genetic disorders is implicit, a gene implicated in a population with a complex disease could provide a potential new target for gene therapy. "Variation in this gene is associated with a threefold increased risk in the groups studied," explains lead researcher Graeme Bell. "
"The research does represent a shift in the landscape of genetic diseases. "Studies are not going to be easy," says Bell "but they are not impossible and each locus will present its own challenges." Kruglyak feels the path is clearer, if only because of the 'psychological factor' of showing it can succeed. How important it will be in the overall problem of diabetes, or how often this kind of success will occur in other diseases, will emerge in time. "
redux [08.31.00]
""Like any large construction project in the public domain, sequencing the human genome has been a subject of discussion and controversy. Major issues have been the cost of the project, its scientific merit, and the effects of the knowledge gained on human affairs. The concern about cost subsided as the project proved viable and attracted private funding. That leaves the other two questions: What will we learn from this sequence, and how will it affect our lives? With fame and fortune to be made in the genome business, one can only be skeptical of the wondrous claims made by the project's protagonists. The Triple Helix examines these questions from a critical and biologically informed angle."
"In Lewontin's triple helix, the genes are placed in their natural context, where history and geography shape the nature of organisms and the genes they contain. His differences with the most modern of molecular and cellular biologists are irreconcilable and reflect the ever-widening gulf between biologists who have an affinity for what goes on outside the laboratory and those for whom the differences between individuals and between species represent "an annoyance [to be] ignored whenever possible." In many laboratories, organisms are now studied under conditions in which genetic variation is eliminated and the environment held constant. It is only under these special conditions, where neither variation nor natural selection is tolerated, that the triple helix collapses into the double helix and genes appear to be paramount.""
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The Wall Street Journal
Prize for DNA Decoding Aims to Fuel Innovation
"When inventor Burt Rutan's SpaceShipOne soared 63.6 miles above the Earth in October 2004, he captured the $10 million X Prize and helped inaugurate the era of commercial human space flight.
The X Prize Foundation, a nonprofit-education organization, is looking to spur a new adventure -- into human genes.
The Santa Monica, Calif., foundation plans to offer a $5 million to $20 million prize to the first team that completely decodes the DNA of 100 or more people in a matter of weeks, according to foundation officials and others involved.
Such speedy gene sequencing would represent a technology breakthrough for medical research. It could launch an era of "personal" genomics in which ordinary people can learn their complete DNA code for less than the cost of a wide-screen television."
redux [01.03.06]
[requires 'free' registration]
"As next-generation sequencing technologies emerge on the market, some experts believe they will be used for projects other than medical sequencing. This notion was reinforced two weeks ago when scientists announced the first genome sequences from a wooly mammoth, which became extinct about 10,000 years ago.
"Now some scientists say this project could signal the start of a sequencing trend in paleogenomics --- as well as a potential new market for emerging sequencing technologies, which enabled the wooly mammoth research, published in the Dec. 22 issue of Science."
redux [10.24.05]
"Gene sequencing -- the process of unlocking an individual's DNA -- could one day revolutionize medicine, allowing doctors to quickly identify someone's genetic makeup and craft individual treatments for such diseases as cancer and tuberculosis. But first, there has to be a way to speed the cumbersome, slow and expensive sequencing process."
"The genome-sequencing technique from 454 Life Sciences was selected as the Gold winner in The Wall Street Journal's 2005 Technology Innovation Awards competition. Innovative technologies from around the world were eligible for awards in categories including biotechnology, software, security, energy and the environment, among others."
redux [08.05.05]
"A thousand dollars can buy a lot of things. Scientists hope to soon add an individual's genetic sequence to that list. Full-genome DNA decoding, estimated to now cost $20 million, could soon be done for about $2.2 million, experts say, and will continue to drop in price as researchers develop new ways to conquer the task. A report published online yesterday by the journal Science suggests one such method: a technique that used off-the-shelf instruments and reagents to successfully sequence the E. coli genome."
"Unlike the 454 approach, the method developed by Church and colleagues is a form of DNA resequencing – that is, it requires a reference sequence with which to compare the new sequence, because each fragment of DNA sequenced is so short. Nevertheless, many likely lab applications – from genotyping haplotypes in a disease study, searching for mutations in cancer resistance, or as in the Science paper, identifying microbial strain variants – would fall into this category."
redux [08.01.05]
"When Jonathan Rothberg's son was born six years ago, the baby was sent to the infant intensive care unit. Rothberg worried all night that something might be wrong with his child, and he found himself wishing he could just read the boy's genome to find out.
At the time that was impossible: it cost tens of millions of dollars and took more than a decade to decipher the first complete human genome, published in 2001 in Nature. But Rothberg's parental panic and frustration inspired him to design a faster, cheaper sequencing technique. Now Rothberg and his co-workers at the 454 Life Sciences Corporation, which he founded, report their success. "
[requires 'free' registration]
""What they have done here is very significant," Dr. Ronaghi said, noting that the company had already sequenced 50 microbial genomes. "This is the first step toward $1,000 human genome sequencing," he said."
"Jonathan Rothberg, board chairman of 454 Life Sciences, said the company was already able to decode DNA 400 units at a time in test machines. It was working toward sequencing a human genome for $100,000, and if costs could be further reduced to $20,000 the sequencing of individual genomes would be medically worthwhile, Dr. Rothberg said."
redux [10.03.02]
"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Wouldn't you, too, like your genome decoded?
Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."
"Tonight's plenary panel discussion at GSAC, "The Future of DNA Sequencing: Advancing Toward the $1,000 Genome," hosted by Craig Venter and Gerald Rubin, quickly turned into a genomics version of the game show "The Price is Right."
"I had to do a little better than the thousand-dollar genome," said VisiGen Biotechnologies CEO Susan Hardin, one of the panelists, about her company's efforts to develop a single-molecule sequencing method using both a modified polymerase and nucleotides. "So we're going for the $995 genome.""
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New Scientist
Banknote tracking helps model spread of disease
"Tracking the movements of hundreds of thousands of banknotes across the US could provide scientists with a vital new tool to help combat the spread of deadly infectious diseases like bird flu."
"The researchers noticed that the bills' move according to two mathematical rules, each known as a power law. One describes the distance travelled in each step of the journey, the other the length of time spent between journeys."
redux [08.03.05]
"Experts from U.S. universities and Thailand's Ministry of Health used a computer model to simulate an outbreak in rural Southeast Asia—the most likely place for a new, more deadly avian influenza strain to emerge."
"Anthony Fauci directs the National Institute of Allergy and Infectious Diseases at the National Institutes of Health in Bethesda, Maryland. He called the model valuable but noted that "any model is only as good as the assumptions put into that model, and these really are only assumptions.""
" In the scientists' computer model, a single resident of a rural village in Thailand was infected with a mutated H5N1 virus capable of human-to-human transmission. Scientists say that an avian flu pandemic would likely begin in southeast Asia, and the researchers chose Thailand because the type of national data they needed was easily accessible. Using information on past influenza pandemics, they calculated the number of secondary cases that would occur from the original infected individual, the normal incubation period of the illness, and the speed with which the pandemic would spread.
They then added demographic information such as regional and national population size and age; numbers of households, schools and large companies; and distances that people travel to work and school. This gave them a map of how the virus might spread."
redux [04.28.04]
"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."
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 [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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connected.telegraph
The mind's 'Enigma machine'
"In all the ballyhoo that greeted the sequencing of the entire human genetic code, one inconvenient detail was often overlooked: scientists may have found that it takes 25,000 genes to build and run a human being, but they had no idea how these components worked together.
Now a remarkable effort has shown how the proteins described by 200 of these genes make a fundamental piece of the machinery of thought, revealing the human brain is at least 1,000 times more powerful than previously estimated and providing profound new insights into mental illness."
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Guardian Unlimited
Closer to man than ape
"They already use basic tools, have rudimentary language and star in TV commercials, but now scientists have proof that chimpanzees are more closely related to humans than other great apes.
Genetic tests comparing DNA from humans, chimps, gorillas and orang-utans reveal striking similarities in the way chimps and humans evolve that set them apart from the others.
The finding adds weight to a controversial proposal to scrap the long-used chimp genus "Pan" and reclassify the animals as members of the human family. The move would give chimps a new place in creation's pecking order alongside humans, the only survivor of the genus Homo."
redux [09.27.05]
"When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins.
But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests."
redux [08.31.05]
"Scientists unleashed a torrent of studies comparing the genetic coding for humans and chimpanzees on Wednesday, reporting that 96 percent of our DNA sequences are identical. Even more intriguingly, the other 4 percent appears to contain clues to how we became different from our closest relatives in the animal kingdom, they said."
"The researchers said the results confirmed the common evolutionary origin of humans and chimpanzees. Out of the 3 billion base pairs in the DNA coding for chimps and humans, about 35 million show single-base differences, and another 5 million DNA sites are different because of insertions or deletions of genetic code. Waterston estimated that 1 million of those coding changes are responsible for the functional differences between humans and chimps — thus defining our humanness."
redux [05.26.04]
"What is the difference between a chimp and a human? There could be a lot more to the answer than scientists thought, according to the first accurate DNA sequence of a chimp chromosome."
"Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case."
redux [04.05.04]
"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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Bio-IT World
The End of Relational Databases?
"Nathan Myhrvold has been doing the rounds recently. One month after he was interviewed by Bio·IT World, there he was again, popping up in Technology Review. In that interview, he made one particularly provocative statement, that heavy reliance on relational databases like Oracle, SQL, and DB2 within the field of proteomics and genomics is "completely boneheaded."
Myhrvold did not elaborate, and as an entrepreneur he might not want to comment further. But let us suppose that his assessment is largely correct. What are some of the implications?"
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The New York Times
Science Blogs as a Vehicle for Upscale Ads
[requires 'free' registration]
"Seed Media, which produces science publications in print and online, is seeking to broaden its audience - and its appeal to advertisers - by introducing on Monday a network of blogs, or Web journals, devoted to science and science-related subjects. The network is to be made available on a Web site, scienceblogs.com, that is now operating in beta, or test, mode."
"The blog network is a sign of the growing interest among media companies and advertisers in using new media for an old purpose: selling."
redux [08.02.05]
"Even more exciting is this: How about a blog after every scientific paper published? Here scientists could debate results in real-time right on a journal's homepage. "The idea is being kicked around," says Lowe, "and it's a hell of a good idea." Nobody is there yet, but Lowe, Tyrelle, and Zemlo all hope this will soon become a reality.
Overall, science blogs run by scientists and industry insiders are just getting started. "This whole thing is still very immature," says Gerritsen. This may be due to scientists' caution about retribution, unfamiliarity with the technology, or not grasping the potential impact yet. Nevertheless, people should be jumping on blogs, says Gerritsen. "I expect to see this within the next year."
The spark that might really get things going is a blog by a famous scientist, which could add a great deal of credibility and insight (similar to what Bob Lutz did for CEO blogs). "If James Watson had a blog," says Bizzaro, "I'd read it, and I think a lot of other scientists would too.""
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The Wall Street Journal
In Switch, Scientists Share Data to Develop Useful Drug Therapies
"From Alzheimer's and diabetes to cancer, schizophrenia and even baldness, the list of ailments that elude cure marches on. The crisis in "translational science," or turning basic discoveries into therapies, has been brewing for years, but it hit a depressing nadir in 2005, when just 20 new drugs won approval from the Food and Drug Administration.
"Basic scientists and clinical investigators haven't had enough to do with each other," says endocrinologist William Crowley, director of clinical research at Massachusetts General Hospital. The resulting "bench-to-bedside block has been of great concern throughout academic medicine. But now we're starting to see things that hopefully will overcome it.""
redux [08.14.03]
""The concept can work if it's a really integrated center," says Michael Liebman, director of computational biology at the Abramson Family Cancer Research Institute at the University of Pennsylvania. He likes the disease focus because it makes more sense from a clinical standpoint - starting from the disease and its effect in patients and stripping that down, layer by layer, to understanding "how genomics and proteomics can help differentiate between subtypes of disease" - than starting with genomics and working up from genes."
redux [05.17.02]
"An unprecedented wealth of biological data has been generated by the human genome project and sequencing projects in other organisms. The huge demand for analysis and interpretation of these data is being managed by the evolving science of bioinformatics. Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology. Bioinformatics is essential for management of data in modern biology and medicine. This paper describes the main tools of the bioinformatician and discusses how they are being used to interpret biological data and to further understanding of disease. The potential clinical applications of these data in drug discovery and development are also discussed."
"Complex diseases have complex phenotypes, and proper diagnosis requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genetic information. Signaling information is one aspect of a grander "biomedical informatics" approach advocated for a better understanding of a patient's medically relevant disease phenotype."
redux [04.17.02]
"Research into human genetics is being limited by a lack of knowledge in other areas of science, say delegates at the Seventh International Human Genome Meeting (HUGO) in China.
Professor Lap-Chee Tsui, HUGO's outgoing president, says that our poor understanding of even basic human anatomy means that the human genome project is not delivering cures for genetic diseases as was hoped."
redux [12.08.01]
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Bio-IT World
Google and Venter Mum on Collaboration Reports
"Google and the J. Craig Venter Institute are playing down highly publicized reports of a collaboration reported in a recently published book."
"“Google has been exploring applications of our technologies to various scientific fields, including biology. We have no products to announce or information to share at this time,” a Google spokesman wrote via e-mail.
“At the Venter Institute, there isn’t a project under way of that nature that ran in David Vise’s book, so we don’t have anything to contribute at this time,” said an institute spokeswoman."
redux [12.26.05]
"Google’s IPO has also made big news this year as their current stock position places the net worth of the company at an amazing USD 130 billion. This brings them close to the giants of the industry IBM and is only trailed by biggest like Intel and Microsoft. However, the Google guys are not resting on their laurels, as they believe that there is much more to be done and achieved.
"Brin said in a statement: “It’s clear there’s a lot of room for improvement, there’s no inherent ceiling we’re hitting up on. Google has a large computational infrastructure – that could be very useful for microbiology or computational biology. I don’t think we particularly restrict ourselves or have a 20-year vision or anything like that. I don’t think we’re averse to doing something new.”"
redux [11.29.05]
"SERGEY BRIN and Larry Page have ambitious long-term plans for Google’s expansion into biology and genetics through the fusion of science, medicine and technology."
"Over dinner and plenty of wine in February, Brin discussed the prospects for genetics with Craig Venter, the maverick biologist who decoded the human genome.
Despite millions of dollars in funding and thousands of hours of computing time from America’s federal Department of Energy, Venter needed more help to unlock the molecular mysteries of life. It seemed to him that Google’s mathematicians, scientists, technologists, and computing power had the potential to vault his research forward. He pressed Brin hard to get Google involved."
"Not long after the dinner, Brin and Page teamed up with Venter."
redux [11.08.05]
"By the end of next year, Google intends to open an engineering center in the Valley that will employ 600. The company has said it wants to be in a place with a strong quality of life for its employees, with access to public transportation and amenities."
"Downtown Phoenix offers perfect geography, housing and the public transit amenities that Google wants, said John Chan, deputy director of the downtown development office."
"Downtown is the Valley’s financial center and it also has a growing cluster of biotechnology companies. That may interest Google, since the company is said to be intrigued by bioinformatics, the use of computers to characterize the molecular components of living things."
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Wellcome Trust Sanger Institute
Around the World in 800 Billion Bases
"On Tuesday 17 January 2006 the Wellcome Trust Sanger Institute's World Trace Archive database of DNA sequences hit one billion entries. The Trace Archive is a store of all the sequence data produced and published by the world scientific community, including the Sanger Institute's own prodigious output as a world-leading genomics institution.
To grasp how much data is in the Archive, if it were printed out as a single line of text, it would stretch around the world more than 250 times. Printing it out on pages of A4 would produce a stack of paper two-and-a-half times as high as Mount Everest."
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The New York Times
Custom-Made Microbes, at Your Service
[requires 'free' registration]
"There are bacteria that blink on and off like Christmas tree lights and bacteria that form multicolored patterns of concentric circles resembling an archery target. Yet others can reproduce photographic images.
These are not strange-but-true specimens from nature, but rather the early tinkering of synthetic biologists, scientists who seek to create living machines and biological devices that can perform novel tasks.
"We want to do for biology what Intel does for electronics," said George Church, a professor of genetics at Harvard and a leader in the field. "We want to design and manufacture complicated biological circuitry."
redux [12.01.05]
"Setting -- (Dude is squatting close to a river of cells) little amorphous, faceless, bacterial cells burbling along replicating and racing from the distant past into the distant future (let's call this the River of Life?). The first half of Hardy's poem Heredity about the "family face" sets the mood. Sally and Dude stand overlooking the burbling river of replicating cells. Dude wants to get the cells to do something. Sally does too, but she's feeling more circumspect about taking responsibility for the consequences of success."
redux [08.17.05]
[requires 'free' registration]
""You can sit down at a computer, and you can design experiments, and you can see the performance of this thing, and then you can figure out why it's done what it's done," Dr. Ellison said. "You're not going to recognize the full return of the biological revolution until you can simulate a living organism."
In the past few years this fantasy has become plausible and now Dr. Ellison is part of an international team of biologists who are now trying to make it a reality. They have chosen to recreate Escherichia coli, the humble resident of the human gut that has been the favorite species for biology experiments for decades."
redux [11.14.03]
"For now, "this is basic science at the most basic level with lots of unknowns".
But he added: "The ability to construct synthetic genomes may lead to extraordinary advances in our ability to engineer micro-organisms for many vital energy and environmental purposes"."
[requires 'free' registration]
"Venter also said during the press conference that his team would not commercialize PCA, nor would he file patents on it. "We'd rather wait till the next stage when there's a clear cut application: for instance if we have something that produces hydrogen that might hold some value." Asked how the PCA technology will be made available to other scientists he said "By reading our paper."
redux [11.26.02]
[requires 'free' registration]
"Craig Venter's "minimal genome" project announced Wednesday is not about creating a new life form and probably doesn't pose much of a biowarfare threat, researchers say. The high-profile project was just funded by the US Department of Energy (DOE) with $3 million going to the Institute for Biological Energy Alternatives (IBEA), one of the non-profit research institutes Venter founded after leaving the newly profit-minded Celera Genomics early this year.
According to some scientists, the new project won't even define the minimal genomethe basic gene set required for lifebecause there can be no single minimal genome."
"Several years ago, Venter first looked at this mycoplasma as the best such model, because the organism is a record-holder of sorts: the self-replicating life form with the smallest known complement of genetic material. Unlike the human genome with its 30,000 to 50,000 genes, M. genitalium gets by with only 517. But remarkably, nearly half of even that minimal set is extra baggage. Under some laboratory conditions, as few as 300 of the genes can fulfill its definition as a lifeform that feeds and divides.
As it turns out, what is the definition of life itself? and also exactly what is its minimal genetic set? have been hotly contested. Gene size is one of the main limits to what could be the final and minimal cell size, and thus may set a limit on possible targets for creating life from scratch.
But what structures are too small or too simple to be considered "life"?"
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The New York Times
Gene Increases Diabetes Risk, Scientists Find
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"Scientists have discovered a variant gene that leads to a sizable extra risk of Type 2 diabetes and is carried by more than a third of the American population.
The finding is being reported today in the journal Nature Genetics by researchers at Decode Genetics, a company in Reykjavik, Iceland, that specializes in finding the genetic roots of human diseases. Decode Genetics first found the variant gene - one of many different versions that exist in the human population - in Icelanders and has now confirmed the finding in a Danish and an American population."
redux [06.08.04]
"Researchers on a hunt for the causes of obesity are looking for clues in the genetic makeup of 3,000 inhabitants of the Micronesian island of Kosrae in the western Pacific.
Gene hunters from Rockefeller University announced Monday that they will use gene chips developed by Affymetrix in Santa Clara to look through hundreds of thousands of variations in the genetic code of the Kosrae population to discover why most of them are seriously overweight -- and why others on the island are not."