Arizona's BioTech News Update

Moved to www.azbiotechnews.com

2006-09-15T13:56:00.000-07:00

We got our own server space and moved to AZ Biotech News at www.azbiotechnews.com. All of our olds posts are already transferred to their new location.

We'll be slowly deleting some of the posts here. Update your bookmarks.

12 Volunteers to Start Getting HIV Vaccine

2006-04-17T08:26:00.000-07:00

Human volunteers this week began signing up for an experimental HIV vaccine developed at Atlanta's Emory University.

Twelve people are expected to take part in the trial at four participating research centers _ St. Louis University, Vanderbilt University, the University of Maryland and the University of Alabama at Birmingham.

Volunteers should begin getting shots any day now, said Don Hildebrand, the chief executive of GeoVax Inc., the Atlanta biotechnology firm that licensed the vaccine.

It's a phase one trial, in which healthy, uninfected volunteers are given low doses in a check for safety and immune response, Hildebrand said Friday.

A second, higher-dose trial _ with 36 people _ is expected to begin in a few months.

If these trials are successful, future trials will be done to see if the vaccine actually prevents the virus from causing AIDS, he said.

The GeoVax product is one of more than 30 preventive AIDS vaccines in early stages of human clinical trials in approximately two dozen countries, according to the International AIDS Vaccine Initiative, a not-for-profit organization devoted to AIDS prevention.

One of the furthest along is a Merck & Co. vaccine, which tries to build immunity using a modified cold virus. About 3,000 people are being enrolled in Merck's phase two trial of the vaccine... HIV vaccine

Biotech event puts Arizona delegation on global stage

2006-04-16T23:18:00.000-07:00

Arizona got a chance to take its biotech efforts on an international road show last week. And state biotech leaders didn't have to leave the country to do it.

A 26-member delegation from the state traveled to Chicago for BIO 2006, one of largest annual gatherings of its kind in the world.

BIO represents more than 1,100 biotechnology companies, academic institutions, state biotechnology centers and related organizations across the United States and other nations. BIO members are involved in the research and development of health care, agricultural, industrial and environmental biotechnology products.

BIO 2006 organizers say the event is growing more international, with more than 60 countries represented. About one-third of the participants came from other countries.

That meshes with the latest findings from Ernst and Young's annual global biotechnology report titled, "Beyond Borders."

According to the report, biotechnology is growing worldwide. In Europe, biotech growth has increased by 28 percent over the past year; in Asia, it increased by 46 percent.

It's key to Arizona's biotech effort that the state thinks globally, said Micah Miranda, biosciences manager for the state Commerce Department.

International companies are looking to expand or relocate their bioscience operations... continue

Look out San Diego: Peoria and Phoenix are on your tail

2006-04-14T14:11:00.000-07:00

While San Diego, the Bay Area and the Boston area remain the country's dominant centers of biotechnology, other regions have popped onto the industry's map in the last four years, according to a study released yesterday at the Biotechnology Industry Organization's annual convention.

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In Phoenix, $50 million over five years from the Virginia G. Piper Charitable Trust has helped the city in its goal to attract 10 of the world's most distinguished leaders in the development of personalized medicine.

Pennsylvania is proposing to use $35 million annually in tobacco settlement dollars to create the $500 million Jonas Salk Legacy Fund to support bioscience faculty recruitment and facilities construction.

Northwestern University, the University of Chicago and the University of Illinois at Chicago have formed a consortium called the Chicago Community Trust. With up to $50 million in grants from the Searle Funds, they will try to build collaborations in biosciences.

More than 1.2 million people are employed in more than 37,000 bioscience facilities across the nation and Puerto Rico, according to the report prepared for BIO by the Battelle Technology Partnership. Biomedical research and testing labs were included in the figures, as were medical device companies, drug and pharmaceutical companies and agricultural and industrial biotech firms.

From 2000 to 2004, the years analyzed for the study, bioscience employment increased while overall employment nationwide declined by 0.7 percent, the study found.... continue

Gene Hunting in Canada

2006-04-13T08:22:00.000-07:00

Genizon is using the genetic homogeneity of French Canadians to find new drug targets -- and redefine human disease.

In the 17th century, 15,000 French immigrants bravely made their way to eastern Canada. Some headed further west, many returned to France, but a hardy few stayed in Quebec. Starting with a total of just 2,600 people between 1608 and 1760, this group would grow 800-fold over the next 10 or so generations, with little marriage outside the group. The result is the Quebec "founder" population -- a genetically homogenous group of individuals that is ideally suited to the genetic study of disease.

Geneticists have long taken advantage of founder populations -- so named because only a few ancestors founded the entire population -- such as the Ashkenazi Jews and Icelandic people. Members of these groups share long stretches of DNA, which simplifies genetic studies of disease by reducing the background noise of other genetic variations.

Today's best-known gene-hunting company, deCODE genetics, an Icelandic gene and drug discovery company, has identified genes for diabetes, heart disease, and asthma within the small Icelandic population. Now a biotech company, Genizon BioSciences, is finding similar success with the French Canadians of Quebec. Based in Quebec, the company is taking advantage of new advances in genomics to find disease genes that have been hard to detect with other methods.

Gene-hunting studies have traditionally focused on families in which some members are afflicted with a disease, a technique known as linkage analysis. Because families share so much DNA, scientists can survey the genome in relatively few spots to find a region that looks different in those with the disease. This technique is efficient at identifying genes that play a large role in rare diseases because it is easy to identify those individuals with the disease... gene hunting in Canada

Fossils fill gap in human lineage

2006-04-13T08:09:00.000-07:00

Fossil hunters have found remains of a probable direct ancestor of humans that lived more than four million years ago.

The specimens of this ancient creature are helping bridge a long gap during a crucial phase of human evolution.

Professor Tim White of the University of California, Berkeley, and colleagues unearthed the cache of fossils in the Middle Awash region of Ethiopia.

They describe the finds, which belong to the species Australopithecus anamensis, in the journal Nature.

Australopithecus is an important ancient genus of humanlike creatures, or hominids.

Our own genus, Homo, is widely thought to have evolved from this group. So the relationship of Australopithecus to even earlier bipedal hominids is crucial to understanding where we all ultimately come from.

When placed together with other fossils from the same general area of Ethiopia, the 4.1-million-year-old anamensis specimens appear to establish an evolutionary succession between earlier and later species... human fossil fill lineage

Evolution follows few of the possible paths to antibiotic resistance

2006-04-12T10:07:00.000-07:00

Bacteria gain resistance from only a handful of 120 possible five-step mutational paths in a key gene

Darwinian evolution follows very few of the available mutational pathways to attain fitter proteins, researchers at Harvard University have found in a study of a gene whose mutant form increases bacterial resistance to a widely prescribed antibiotic by a factor of roughly 100,000. Their work indicates that of 120 harrowing, five-step mutational paths that theoretically could grant antibiotic resistance, only about 10 actually endow bacteria with a meaningful evolutionary advantage.

The research is published in the journal Science.

"Just as there are many alternate routes one might follow in driving from Boston to New York, one intrinsic property of DNA is that very many distinct mutational paths link any two variants of a gene," says lead author Daniel M. Weinreich, a research associate in Harvard's Department of Organismic and Evolutionary Biology. "Although this fact has been recognized for at least 35 years, its implications for evolution by natural selection have remained unexplored. Specifically, it is of great interest to determine whether natural selection regards these many mutational paths equivalently."

Weinreich and colleagues generated a series of mutants found along all 120 possible mutational trajectories involving the gene coding for the enzyme beta-lactamase, which in altered form can serve to inactivate antibiotics including penicillin and cefotaxime. Analyzing how well each variant protected host Escherichia coli cells against treatment with various concentrations of antibiotic, the scientists found that only a very small fraction of these pathways confer ever-increasing resistance in pathogenic microbes, and are therefore relevant to natural selection.

Resistance-granting mutations of beta-lactamase occur in a five-step process, with the 120 possible mutational paths representing all the possible ways in which these five point mutations can occur. Fully 102 of the 120 trajectories are inaccessible to natural selection because they create intermediates that are no more fit than the original gene, and of the remaining 18 Weinreich and colleagues observed that only about half actually had a significant probability of evolutionary occurrence.

"To be followed by an evolving population, natural selection requires that antibiotic resistance increase with each mutation," Weinreich says. "In contrast, most mutational paths of the enzymatic variant we examined fail to continuously increase resistance. Importantly, this is not a reflection of the fact that many more mutations reduce biological function than improve it, because in the present case each mutational path is composed exclusively of mutations known jointly to improve resistance."

Weinreich argues that this finding likely applies to most protein evolution, not just the beta-lactamase enzyme.Although many mutational paths lead to favored variants, only a very small fraction are likely to result in continuously improved fitness and therefore be relevant to the process of natural selection.

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U.S. states battle for slice of biotech pie

2006-04-10T17:23:00.000-07:00

U.S. states squared off against each other on Monday in a battle to capture jobs and revenue generated by the burgeoning biotechnology industry.

A report released at the BIO 2006 conference here showed U.S. employment in biosciences reached 1.2 million in 2004. That was slightly more than a 1 percent increase since 2001, with workers earning an lucrative average annual wage of $65,775.

"These are good, well-paying jobs," said Walter Plosila, a vice president at Battelle Technology Partnership Practice, which co-sponsored the report.

The report also found that states are spending billions of dollars to support bioscience research and development. State governments are also using investment funds and tax incentives to attract large industry anchors, instead of solely focusing on launching and growing new bioscience ventures... read

Biotech progress overlooked

2006-04-10T17:19:00.000-07:00

At 30, America's biotech industry is growing, becoming more stable and nearing the elusive break-even point.

Since America's first biotech company, Genentech Inc., was formed April 7, 1976, it has developed into a $50 billion-a-year industry, with annual revenue growth that has ranged in the past three years from 16 to 19 percent.

At roughly 5 years old, Arizona's emerging biotech and bioscience industries show surprising signs of vitality and growth. The number of Arizona bioscience companies is growing, grant funding is sharply up and related employment grew 12 percent from 2000 to 2004 to about 72,000 total jobs.

Work on new drugs drew a record level of grants from the National Institutes of Health. Grants to researchers in the state rose 30 percent from 2001 to 2004 and now total more than $160 million.

Yet despite the strides Arizona has made toward becoming a major biotech hub, it remains unmentioned in national reports on biotech... continue

Novel Device Shows Great Potential in Detecting Oral Cancer

2006-04-10T17:14:00.000-07:00

Researchers supported by the National Institute of Dental and Craniofacial Research, part of the National Institutes of Health, report today their initial success using a customized optical device that allows dentists to visualize in a completely new way whether a patient might have a developing oral cancer.

Called a Visually Enhanced Lesion Scope (VELScope), this simple, hand-held device emits a cone of blue light into the mouth that excites various molecules within our cells, causing them to absorb the light energy and re-emit it as visible fluorescence. Remove the light, and the fluorescence of the tissue is no longer visible.

Because changes in the natural fluorescence of healthy tissue generally reflect light-scattering biochemical or structural changes indicative of developing tumor cells, the VELScope allows dentists to shine a light onto a suspicious sore in the mouth, look through an attached eyepiece, and watch directly for changes in color. Normal oral tissue emits a pale green fluorescence, while potentially early tumor, or dysplastic, cells appear dark green to black.

Testing the device in 44 people, the results of which are published online in the Journal of Biomedical Optics, the scientists found they could distinguish correctly in all but one instance between normal and abnormal tissue. Their diagnoses were confirmed to be correct by biopsy and standard pathology... read

ASU Biodesign chief Poste sets challenges

2006-04-08T11:13:00.000-07:00

As a drug-company executive for 17 years, George Poste knew the perils of slumping sales: less money for research, slower growth and possible layoffs.

Now, as head of the Biodesign Institute at Arizona State University, Poste wants his staff to face the same consequences.

Under him, each researcher must generate $225 in federal or private grants for each square foot of space he or she occupies or lose lab space and maybe points in a performance review. It's not the typical accountability measure in academe, but Poste makes no apologies.

"That is tragically the Darwinian model," Poste said. Those who can't compete shouldn't be carried by other researchers or the university, he said. "(Otherwise) it's a form of academic welfare. Dispense with it."

At 61 and headlong into a third career, Poste leads the most high-profile, ambitious effort launched at ASU under President Michael Crow. The Biodesign Institute is the flagship of ASU's effort to become a world-class research institution, applying its findings in biology, chemistry, physics, computing and other areas to better human health.

It recently opened a second building costing $79 million that will house up to 500 employees near the eastern edge of the Tempe campus.

Perhaps more than anyone, Poste embodies Crow's effort to inject corporate values and incentives into the university setting. He wants measurable results: grants, patents, high rankings, prestige.

"If you are competitive, you have a reputation," he said. "People want to work for the Fortune 500 companies. They want to play for the best sports teams."

A British native and naturalized U.S. citizen, Poste was lured out of retirement in north Scottsdale nearly three years ago to take the job. He came with experience as a research director, an adviser to the Defense Department on bioterrorism issues, and an author and speaker on genetics, health policy and personalized medicine.

He brings to the job a tireless curiosity, a penetrating intellect, and a force of will that wins admirers but comes off as arrogance to some faculty... biodesign chief George Poste

Lowly fly is selling point in a bio-high-tech world

2006-04-08T10:10:00.000-07:00

Presenters here for a conference promoting Arizona's biotechnology industry this week said the state has many things to offer the emerging industry — including state-of-the art flies for research.

For nearly 100 years, Drosophila, known as fruit flies to most of us, have done much of the heavy lifting in genetic studies, said Therese Ann Markow of the Arizona Research Lab. Markow is a Regent's Professor in the University of Arizona department of ecology and evolutionary biology.

Markow spoke Tuesday at a breakout session at BioSouthwest 2006, this year's edition of Arizona's statewide biotechnology conference, held at the Doubletree Hotel Tucson at Reid Park.

Markow said UA scientists have completed gene sequencing on two fruit-fly species and are working on others.

Drosophila, which are available from the UA's Tucson Drosophila Stock Center, are useful in many types of medical research, including studies of mental retardation, she said.

"Believe it or not," Markow said, "these little flies can learn."
She said that made them useful for studying human retardation.

Among the human-disease research being done using Drosophila, she said, is work on a number of fatal neurodegenerative diseases, including Huntington's disease. Although they may all look the same to most people, Markow said some of the flies have the ability to eat things that would be toxic to others. In many cases, those differences — mutations — can help in understanding human biology.

She said fruit flies, first used for genetic research in the early 1900s, have remained popular because they are easy to raise, have a small chromosome number and are not subject to the same regulations that govern work with vertebrate species... read

InNexus Biotechnology to Present at BIO 2006

2006-04-07T10:16:00.000-07:00

Dr. Morgan, President and Chief Executive Officer of InNexus Biotechnology, Inc., an innovative antibody-driven drug development company based on SuperAntibody™ Technologies, will be presenting at the BIO 2006 Annual International Convention Business Forum. The presentation will take place on Wednesday, April 12th at 12:00PM in Room A of McCormick Place South Convention Center, Level 3, Exhibit Hall A.

The world’s largest biotechnology event, BIO 2006, will be held April 9-12, 2006 in Chicago and hosts more than 18,000 industry executives from around the globe, and as an organization, represents more than 1,100 biotechnology companies, academic institutions, state biotechnology centers and related organizations across the United States and 31 other nations.

Decoding the Genetics of Common Disease

2006-04-07T07:30:00.000-07:00

Ten years after he returned to his native Iceland to build a biopharma company, Kari Stefansson says deCODE Genetics’ intense search for genes underlying common diseases is not only pushing promising new drug candidates into the clinic but is also revealing new insights into the very basis of common disease.

In a keynote address at Bio-IT World’s Life Sciences Conference + Expo Tuesday, Stefansson acknowledged, “There’s great enthusiasm for human genetics, but it has yet to deliver anything of great significance.” But he believes that “the genetics of common disease is the genetics of gene expression.”

Since 1996, deCODE has launched research programs to study 50 common diseases, mapping and isolating susceptibility genes for 30 diseases and turning nine of those into drug discovery and development programs. Three drugs are already in the clinic, a number Stefansson says will increase to five before the end of 2006.

Complex traits are confounded by environmental factors. Cases of lung cancer in Iceland are invariably triggered by smoking, but 10–15 percent of cancer deaths cluster in families, suggesting a genetic susceptibility that doesn’t penetrate until subject to an environmental trigger.

DeCODE’s search for the genetic causes of common disease have revealed several common themes. DNA sequence variants that predispose an individual to common disease rarely fall in the gene coding sequence; typically influence gene expression, e.g. alternative splicing; almost always provide a good drug target; and allow for the “intelligent design of clinical trials.”

DeCODE’s data mining relies on three key criteria – phenotype, genealogy, and genome data. “Genealogy is important in quality control and is the key to success in genome-wide association studies,” said Stefansson. Stefansson proudly noted how his personal genealogy tree extends back 1000 years to one Egil Skallagrimmson – “A great poet, great warrior, and said to be the ugliest man alive.”

Testing Times
DeCODE’s genotyping programs typically involve screens of 300–500,000 SNPs, but that raises the statistical problem of multiple testing. DeCODE’s standard practice is to test any Icelandic gene variants in a second population. “Every single discovery we report is done after we have replicated it in at least several other populations,” said Stefansson... read

Cervical cancer vaccine holds up

2006-04-06T21:54:00.000-07:00

A vaccine protecting against two types of viruses that cause cervical cancer has demonstrated unusual staying power, new research shows.

In a follow-up study to a randomized clinical trial, researchers found antibody levels in the study subjects remained steadfast for up to four and a half years. Researchers say the results confirm the success and safety of the vaccine Cervarix, which is designed to guard against two cancer-causing human papillomaviruses, HPV 16 and 18.

"This is the most significant advance in cancer prevention in the last 50 years," said lead author Diane Harper, director of Gynaecologic Cancer Prevention Research at Dartmouth Medical School. "We now have a vaccine that's 100 percent effective," she added.

She also emphasized the vaccine does not prevent cancer -- it prevents the virus that causes cervical cancer, the second most common malignant disease in women worldwide.

The research, conducted by Harper and several investigators, appears online Thursday in the British journal Lancet.

Around 800 women from the original clinical trial were included in the follow-up, conducted between 2003 and 2004. The women, who come from 32 sites around the world, represent a racially and ethnically diverse group, possibly the only global study with a planned longterm follow-up, Harper said.

Not only did the vaccine still appear strong after four years, the women encountered no vaccine-related diseases, Harper said. In other studies of HPV vaccines, the duration of effect, as it's called, was only three years. In general, vaccine duration varies greatly: some are needed only once-in-a-lifetime, and others last 10 years, as with tetanus. Researchers do not yet know the booster requirements for cervical cancer vaccines, or if boosters are even required.

Two cervical cancer vaccines are currently being developed: GlaxoSmithKline's Cervarix, which targets only HPV 16 and 18, and Merck's Gardasil, which prevents HPV 16, 18, 6 and 11; the latter two viruses cause genital warts. Cervarix could be released on the market as early as spring 2007, months after Gardasil's expected debut in fall 2006, Harper said.

HPV 16 and 18, in the same family of viruses as skin warts, are contracted through sexual activity, although genital contact alone can also spread the virus. These viruses are also very common: 80 percent of people will have an HPV genital infection in their lifetime. To develop cervical cancer, the virus must stay in the cervix long enough to change its cell structure.... cervical cancer vaccine

Cancer's "World Wide Web"

2006-04-05T23:02:00.000-07:00

A lung image database is breathing life into "medical grid" vision.

For several years, clinicians and computer scientists in the U.S. and abroad have been trying to improve cancer care—from diagnosis to treatment—by building vast, interconnected databases full of patient information. They call these repositories "medical grids" and envision the day when a physician in Strasbourg or New Delhi can see, for example, that an indecipherable image of a patient's lung is very similar to that of a San Francisco patient, whose case history could inform the decision to perform a biopsy.

These nascent databases include not only patients' medical histories, including such data as MRIs and CT scans, but also information about how they have responded to drugs. But the benefits of these under—construction grids have been slow to come, partly because of technical problems and partly because federal privacy rules make data sharing difficult. Now, a National Cancer Institute project could test a multihospital system for comparing lung cancer images as early as this year—a clear move toward putting grids to use.

Kenneth H. Buetow, director of the institute's Center for Bioinformatics in Bethesda, MD, calls it a crucial first step toward "a World Wide Web of cancer research."

In the past year or so, Buetow and his team have collected more than 50,000 images of lung cancers obtained from medical trials and archived them in a secure electronic repository at NCI. Their effort is part of a three-year, $60 million pilot project launched in 2004, which involves 50 cancer centers and more than 600 researchers. The archive is now available on the Internet at http://ncia.nci.nih.gov. In addition to other imaging projects, it contains a large collection of lung cancer cases followed throughout their therapy.

With the database now largely in place, testing is imminent. The image collection is intended to encourage and facilitate research into new software that can automatically compare images of lungs with those already in the database. In such software, algorithms will search for commonalities and build a directory of the likeliest matches. Clinicians in offices and hospitals will be able to contrast the resulting lung images with the scans they need to evaluate.

In the past year or so, Buetow and his team have collected more than 50,000 images of lung cancers obtained from medical trials and archived them in a secure electronic repository at NCI. Their effort is part of a three-year, $60 million pilot project launched in 2004, which involves 50 cancer centers and more than 600 researchers. The archive is now available on the Internet at http://ncia.nci.nih.gov. In addition to other imaging projects, it contains a large collection of lung cancer cases followed throughout their therapy.... cancer lung images online

Blind Mice Recover Visual Responses Using Protein from Green Algae

2006-04-05T20:23:00.000-07:00

Nerve cells that normally are not light sensitive in the retinas of blind mice can respond to light when a green algae protein called channelrhodopsin-2 (ChR2) is inserted into the cell membranes, according to a National Institutes of Health (NIH)-supported study published in the April 6, 2006 issue of the journal Neuron. The study was conducted with mice that had been genetically bred to lose rods and cones, the light-sensitive cells in the retina. This condition is similar to the blinding disease retinitis pigmentosa (RP) in humans.

Vision normally begins when rods and cones, also called photoreceptors, respond to light and send signals through the retina and the optic nerve to the visual cortex of the brain, where visual images are formed. Unfortunately, photoreceptors degenerate and die in some genetic diseases, such as RP. Both mice and humans go progressively blind because with the loss of rods and cones there is no signal sent to the brain.

This study, funded by the National Eye Institute (NEI) of the NIH, raises the intriguing possibility that visual function might be restored by conveying light-sensitive properties to other surviving cells in the retina after the rods and cones have died. Principal investigator Zhuo-Hua Pan, Ph.D., of Wayne State University School of Medicine, and his colleagues, using a gene-transfer approach, introduced the light-absorbing protein ChR2 into the mouse retinal cells that survived after the rods and cones had died. These cells became light sensitive and sent signals through the optic nerve to the visual cortex.

“This innovative gene-transfer approach is certainly compelling,” said Paul A. Sieving, M.D., Ph.D., director of vision research at the NIH. “This is a clever approach that offers the possibility of some extent of vision restoration at some time in the future.” In addition to RP, there are many forms of retinal degenerative eye diseases that possibly could be treated by gene-based therapies... blind mice recover vision

Arctic fossils mark move to land

2006-04-05T20:18:00.000-07:00

Fossil animals found in Arctic Canada provide a snapshot of fish evolving into land animals, scientists say.

The finds are giving researchers a fascinating insight into this key stage in the evolution of life on Earth.

US palaeontologists have published details of the fossil "missing links" in the prestigious journal Nature.

The 383 million-year-old specimens are described as crocodile-like animals with fins instead of limbs that probably lived in shallow water.

'Missing link'

Before these finds, palaeontologists knew that lobe-finned fishes evolved into land-living creatures during the Devonian Period.

But fossil records showed a gap between Panderichthys, a fish that lived about 385 million years ago which shows early signs of evolving land-friendly features, and Acanthostega, the earliest known tetrapod (four-limbed land-living animals) dating from about 365 million years ago.

In 1999, palaeontologists Professor Neil Shubin, from the University of Chicago, and Professor Edward Daeschler, from the Academy of Natural Sciences in Philadelphia, set out to explore the Canadian Arctic in an attempt to find the "missing link" that would explain the transition from water to land.

After several years of searching with very little success, they hit the jackpot in 2004.

"The really remarkable find came when one of the crew found a snout of a flat-headed animal sticking out of the side of a cliff - that is totally what you want to find because if you are at all lucky the rest of the skeleton is back in the cliff," said Professor Shubin... land-sea animal gap

US biotechnology firms move closer to breaking even

2006-04-05T08:10:00.000-07:00

The biotechnology industry is finally getting closer to an elusive goal: breaking even.

Despite its reputation for developing lifesaving drugs and providing high-paying jobs, the industry has lost tens of billions of dollars since Genentech, the first genetic engineering company, was founded 30 years ago this Friday.

Although the biotechnology giants Genentech and Amgen are now profitable, as are about four dozen smaller players, the overall industry has been kept afloat only by the willingness of investors to finance research and development.

"Investors have been very patient with the biotech industry, which has been one of the biggest money-losing industries in the history of mankind," Arthur Levinson, the chief executive of Genentech, told analysts last month. "The cumulative loss by this industry from its inception in 1976 is nearing US$100 billion."

But perhaps the tide is turning. Publicly traded US biotechnology companies lost only US$2.1 billion last year, down from US$4.9 billion in 2004, according to the latest annual scorecard compiled by Ernst & Young, the accounting and consulting firm.

More important, the firm said, the loss last year was equivalent to only 4 percent of the US$47.8 billion in combined revenue from the 329 public companies in the biotech industry. That is the first time that figure has ever been below 5 percent.

"We still feel pretty bullish that profitability for the entire industry, at least in the United States, will occur by the end of this decade," said Donn Szaro, leader of the global biotechnology practice for Ernst & Young. The prediction is for profitability on a yearly basis, not an erasure of three decades of cumulative losses.

For investors, of course, what matters most is what happens to the share price, not profits. Even shares of unprofitable companies can rise substantially -- at least for a while -- based on prospects for new drugs.

The stock of New River Pharmaceuticals, for instance, has more than quadrupled since its initial offering in 2004, propelled by hopes that the company's experimental drug for attention deficit hyperactivity disorder will be safer than alternatives. The stock closed Monday at US$33.51, up US$0.30.

Moreover, investors generally seek out particular stocks, not the industry as a whole, and big hits can pay off well. Amgen and Genentech, the two largest biotech companies, have market values of more than US$85 billion, exceeding those of many of the traditional pharmaceutical companies.

At the end of last year, the market capitalization of those two companies alone accounted for nearly half the total US$410 billion for all publicly traded US biotech companies. And much of the improvement in the industry's bottom line last year came from an increase of US$1.8 billion in the combined net profit of Amgen and Genentech... biotech industry breaking even

Redmond Forms Biotech Alliance

2006-04-05T07:58:00.000-07:00

Microsoft partners with pharma and biotech companies to accelerate drug development.

Microsoft formed an alliance of biotech, pharmaceutical, software, and hardware companies Tuesday in an effort to accelerate drug discovery and development.

The BioIT Alliance aims to create a stronger link between technology and science in order to develop personalized medical treatments.

Other companies in the alliance include Accelrys Software, Affymetrix, Amylin Pharmaceuticals, Applied Biosystems, Digipede Technologies, Discovery Biosciences, Geospiza, Hewlett-Packard, InterKnowlogy, Scripps Research Institute, Sun Microsystems, and VizX Labs.

The initiative appears to be an outgrowth of Microsoft Chairman Bill Gates’ interest in funding innovative ways to treat diseases like malaria that ravage the developing world. The Bill and Melinda Gates Foundation is one of the world’s largest donors to such programs.

The BioIT Alliance formed by the Redmond software giant plans to create multidisciplinary teams of experts from various industries who will share biomedical data and collaborate. The initial project is a data management system called the Collaborative Molecular Environment that will focus on improving the efficiency of drug research and personalized medicine... microsoft biotech alliance

Einstein Researchers Identify Genetic Variants That Lend Clues to Living Longer

2006-04-04T13:21:00.000-07:00

Many studies show that tweaking a single gene can extend life span in animal models. In a new study, Drs. Gil Atzmon and Nir Barzilai at the Albert Einstein College of Medicine of Yeshiva University have found that people harbor alleles—alternative forms of a gene—that confer the same sort of longevity advantage.

The researchers looked for genetic clues to longevity in a group of 214 Ashkenazi Jews who have passed or nearly reached 100 years of age. In the April 4 issue of PLoS Biology, they report that a specific genetic profile, or genotype, was associated with longevity as well as cardiovascular health, lower incidence of hypertension and healthy insulin metabolism.

“Since centenarians typically escape cardiovascular disease, diabetes, and other age-related disorders, we suspected these most senior of senior citizens might possess gene variations that help them reach a ripe old age,” said Dr. Nir Barzilai, director of the Institute for Aging Research at Einstein and senior author on the paper. “If so, then these genotypes should occur with higher frequency in centenarians than in the rest of us.”

Dr. Barzilai and his colleagues recruited Ashkenazi Jews for the study, because this population--descended from a founder group of just 30,000 or so people—is more genetically uniform than other groups, simplifying the challenge of associating a genotype with its physical manifestation (phenotype).

When studying centenarians, finding an age-matched control group is obviously difficult. But since longevity runs in families, the researchers were able to get around this problem by recruiting children of the centenarians and matching them against a control group consisting of other Ashkenazi Jews the same age.

more at http://www.aecom.yu.edu/home/news/PRdetails.asp?isPR=1&id=299

Avian flu modeled on supercomputer, explores vaccine and isolation options for thwarting a pandemic

2006-04-04T13:15:00.000-07:00

Using supercomputers to respond to a potential national health emergency, scientists have developed a simulation model that makes stark predictions about the possible future course of an avian influenza pandemic, given today’s environment of world-wide connectivity. The research, by a team of scientists from Los Alamos National Laboratory in New Mexico, the University of Washington and the Fred Hutchinson Cancer Research Center in Seattle, is presented in the Proceedings of the National Academy of Science online the week of April 3-7, and in the print issue of April 11.

The large-scale, stochastic simulation model examines the nationwide spread of a pandemic influenza virus strain, such as an evolved avian H5N1 virus, should it become transmissible human-to-human. The simulation rolls out a city- and census-tract-level picture of the spread of infection through a synthetic population of 281 million people over the course of 180 days, and examines the impact of interventions, from antiviral therapy to school closures and travel restrictions, as the vaccine industry struggles to catch up with the evolving virus.

“Based on the present work ... we believe that a large stockpile of avian influenza-based vaccine containing potential pandemic influenza antigens, coupled with the capacity to rapidly make a better-matched vaccine based on human strains, would be the best strategy to mitigate pandemic influenza,” say the authors, Timothy Germann, Kai Kadau, Ira Longini and Catherine Macken.

Longini is a biostatistician with the Fred Hutchinson Cancer Research Center and the University of Washington, while the rest of the team is at Los Alamos. Their collaboration is supported by grants from the Department of Homeland Security and the National Institute of General Medical Sciences MIDAS (Models of Infectious Disease Agent Study) program.

“It's probably not going to be practical to contain a potential pandemic by merely trying to limit contact between people (such as by travel restrictions, quarantine or even closing schools), but we find that these measures are useful in buying time to produce and distribute sufficient quantities of vaccine and antiviral drugs,” said Germann of Los Alamos’ Applied Physics Division.

via http://www.lanl.gov/news/index.php?fuseaction=home.story&story_id=8171

Cancer Virus Protein Needed for Successful Infection

2006-04-03T08:38:00.000-07:00

ew research shows that a protein made by a cancer-causing virus that was thought to be unimportant for its replication is in fact critically needed by the virus to initiate an infection and to reproduce.

The study examined the human T lymphotropic virus type 1 (HTLV-1) and a protein it makes called p13. The protein is one of the virus' so-called accessory proteins, proteins that earlier studies done in laboratory-grown cells suggested that the virus could live without.
Mike Lairmore

But this new study – done using an animal model that the virus can infect – suggests that HTLV-1 needs the p13 protein to successfully infect the body and reproduce.

The research, published in the April 1 issue of the Journal of Virology, was led by scientists with The Ohio State University Cancer Program and OSU College of Veterinary Medicine.

“It is important to understand the function of these accessory molecules so we know if they should be incorporated into vaccines or targeted by new drugs as a way to prevent infection,” says principal investigator Michael Lairmore, professor and chair of veterinary biosciences and a member of the OSU Comprehensive Cancer Center.... cancer causing virus

Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes

2006-04-03T08:29:00.000-07:00

Just as protein sequences change over time, so do gene structures. Over comparatively short evolutionary timescales, introns lengthen and shorten; and over longer timescales the number and positions of introns in homologous genes can change. These facts suggest that the intron–exon structures of genes may provide a source of evolutionary information. The utility of gene structures as materials for phylogenetic analyses, however, depends upon their independence from the forces driving protein evolution. If, for example, intron–exon structures are strongly influenced by selection at the amino acid level, then using them for phylogenetic investigations is largely pointless, as the same information could have been more easily gained from protein analyses. Using 11 animal genomes, Yandell et al. show that evolution of intron lengths and positions is largely—though not completely—independent of protein sequence evolution. This means that gene structures provide a source of information about the evolutionary past independent of protein sequence similarities—a finding the authors employ to investigate the accuracy of the protein clock and to explore the utility of gene structures as a means to resolve deep phylogenetic relationships within the animals... large scale evolution trends

Discovery of HIV protein opens up new drug production

2006-04-01T13:34:00.000-07:00

Scientists have discovered the existence of a HIV accessory protein that disables host immunity via receptor-protein intermediary in a discovery that points to possible novel ways to fight AIDS, immune disorders and sepsis.

"With additional study this research may provide approaches for designing new drugs to fight AIDS, as well as for inflammatory disorders," said David Weiner, associate professor of Pathology and Laboratory Medicine,

"This research also gives us a new way to think about the relationship between immune activation and sepsis, and it may have implications ultimately for our understanding of novel approaches to prevent sepsis."

Researchers at the University of Pennsylvania School of Medicine discovered that an HIV-1 accessory protein called Vpr, which destroys the host cell's ability to survive by binding to a host receptor.

This, in turn, keeps an important enzyme from activating the cell's immune system.

These findings refine an earlier understanding of Vpr HIV pathogenesis and imply new approaches to treating AIDS, inflammatory diseases such as rheumatoid arthritis, and possibly sepsis.

Weiner's group found that Vpr binds to the glucocorticoid receptor, but it remained unclear whether the GR pathway was required for Vpr to commandeer the host cell's machinery... HIV protein drug production

Genetically improving memories?

2006-04-01T13:30:00.000-07:00

Mice can be genetically engineered to remember a hidden platform in a water maze for several weeks.

Scientists from the Blanchette Rockefeller Neurosciences Institute (BRNI) in West Virginia have located a gene that is a powerful regulator of long-term memory, according to a research article titled "Enhancement of long-term memory retention and short-term synaptic plasticity in cbl-b null mice" that appears in the March 28 issue of the Proceedings of the National Academy of Sciences.

Daniel L. Alkon, M.D., is scientific director at the BRNI and a co-author of the article along with Dong-Ping Tan, M.D., Ph.D. According to Alkon, the mice were genetically engineered to remove the cbl-b gene. They also discovered that this gene controls enhancement of synaptic signaling in the brain.

The research compared the abilities of genetically engineered mice to the abilities of normal mice to locate a hidden platform in a water maze. "In normal mice, there was no measurable long-term memory for this particular water maze task," Alkon said. "However, the mice without this gene were able to remember the water maze six weeks later - a very long time for a mouse."

This finding is of particular interest to Alzheimer's disease researchers, Alkon said, because it provides an important opportunity to trace the molecular pathways for long-term memory and the critical physiological changes that play a role in its formation. "We can now begin to see what molecular changes this gene controls and how these molecular changes affect the physiology of the brain.

"Alzheimer's disease affects the brain's ability to transfer short-term memories into long-term memories," he continued. "This research leads us to new targets for research and potential new targets for Alzheimer's disease drug therapy."

The next step in capitalizing on this discovery, Alkon said, will be to screen for genomic and proteomic changes in the brain that are regulated by this gene. "In this animal model, the molecular changes were also accompanied by robust synaptic changes in the animal's brain. These synaptic changes also appear to be critical for long-term memory formation." ... continue

Engineers Building 'Erasible' Detectors, 'Nanobrushes' and DNA 'Highrises'

2006-04-01T13:28:00.000-07:00

Advances described in designing bio-detectors and structures scaled in the millionths and billionths of a meter

A Duke University engineering group is doing pioneering work at very diminutive dimensions. Their basic studies could lead to genetically engineered proteins that can form erasable chemical detectors; self-grown forests of molecular "bottlebrushes" that keep themselves contamination-free; and auto-assembled DNA "towers" that could become anchors for the tiniest of devices.

Professor of biomedical engineering Ashutosh Chilkoti of Duke's Pratt School of Engineering described such advances in designing bio-detectors and structures scaled in the millionths and billionths of a meter in a Wednesday, March 29, 2006, talk at the American Chemical Society's 231st national meeting in Atlanta.

He spoke at a session beginning at 8:30 a.m. in the Juniper Room in Atlanta's OMNI at CNNCenter. His group's work is supported by the National Science Foundation, the National Institutes of Health and Duke's Center for Biologically Inspired Materials and Materials Systems.

The proposed erasable detectors are made of artificial elastin-like polypeptides (ELPs), which are short segments of proteins normally soluble in water. Crafted through genetic engineering with the aid of bacteria, such ELPs have the useful property of coming out of a solution to form a solid whenever a slight temperature increase or other alterations to the water induces a phase change.

Chilkoti's group reported in the November 1999 issue of the journal Nature Biotechnology that an ELP could also be chemically linked with another protein so that both "fusion proteins" leave solution together after such phase changes.

Following that discovery, for which Duke has applied for a patent, Chilkoti's team reported in the February 2003 issue of Analytical Chemistry that this method could be used to create a "reversible" protein sensor on a glass slide... nanobrushes, dna highrises

Understanding the Degradation of Hominid Gene Control

2006-04-01T13:22:00.000-07:00

Recently, two groups have examined the level of sequence constraint in noncoding DNA flanking mammalian genes, and appear to have found conflicting results. By comparing 500-bp blocks in mice and rats, we found that mean nucleotide divergence within 2 kb of the start and stop codons of protein-coding genes is substantially lower than that of introns, and decreases when approaching the coding sequence. If nucleotide changes within introns are largely free from selection, this implies that noncoding blocks close to genes evolved under selective constraints, presumably because they contain gene expression control regions. In contrast, we find that upstream sequences in hominids do not evolve slower than introns, while downstream regions are under about half of the constraint seen in murids.

By analysing a similar set of noncoding DNA sequences, Bush and Lahn also found that the mean level of selective constraints in upstream regions between humans and chimpanzees is very low. However, their slightly more complex main analysis was to search for 16-bp sequences within upstream regions that are strongly conserved between humans, mice, and either dogs or chickens. They then examined the divergence between humans and chimpanzees at the flanking nucleotides, finding substantially reduced divergence compared with the genomic mean. This demonstrated selective constraints at certain upstream sequences in hominids. An analogous analysis of mouse–rat sequences showed that the selective constraints are about twice as strong in murids as in hominids... continue

The intelligent search engine for biomedical specialists

2006-03-31T10:14:00.000-07:00

“GoPubMed is a sort of an intelligent Google for biomedical specialists,” explains Dr Michael Alvers, CEO and Co-founder of Transinsight. “The search engine saves time and so accelerates research significantly.”

Founded in November 2005, Transinsight is a software company focused on the life sciences that provides products and solutions for intelligent search technologies. Their main product, GoPubMed, was partly developed during the IST project, Biogrid, by Professor Michael Schroeder and his research team from the Biotechnology Centre at the Technical University of Dresden.

“Biomedical researchers have to be familiar with a huge number of publications,” notes Schroeder, Transinsight’s Chief Scientific Officer and Co-founder. “The PubMed database currently contains 15 million biomedical publications that have to be assessed by research groups.”

“Researchers in the biotech and pharmaceutical industries spend an average of 12.4 hours a week searching for relevant information,” adds Alvers.

GoPubMed can search literature repositories, websites, intranets and desktops. It indexes results and thus allows users to explore a large body of results in a structured manner.

In contrast to classical search engines, GoPubMed can answer questions using its background knowledge in molecular biology, medicine, drug development and food science. To illustrate this point, a search for ‘aspirin inhibits’ on a classical search engine returns a large number of unstructured results that do not answer the user's original question. On the other hand, a search with GoPubMed reveals that the most frequently mentioned pathway for ‘aspirin inhibits’ is the cyclooxygenase pathway.

Schroeder stresses, “[GoPubMed] is intelligent and presents the search results in a way that is specifically linked to the interests of a particular research group.”

Thanks to its groundbreaking and competitive product, the young company has already won its first corporate customer – Unilever in the UK. Explaining why Unilever decided to purchase the software, Dr Cecilia Eyre remarks “GoPubMed helps us to quickly screen the vast literature for hidden gems and to discover trends in science.”

With exciting commercial prospects, the start-up company has also been quick to attract investment. This past January, it was announced that Transinsight had received €500,000 of seed funding from Germany’s recently established High-Tech-Gründerfonds and a further undisclosed sum from a private investor in Hamburg.

Indeed, such are the high expectations for Transinsight, that the firm was very recently crowned as one of only three ‘Lighthouse projects of the High-Tech-Gründerfonds’ by Michael Glos, German Federal Minister for Economic Affairs and Technology... read

SBA ruling hurts future of biotech companies

2006-03-31T10:07:00.000-07:00

In his 2006 State of the Union address, President Bush declared: "With more research in both the public and private sectors, we will improve our quality of life and ensure America will lead the world in opportunity and innovation for decades to come."

Unfortunately, the Small Business Administration in Washington, D.C., is not heeding those wise words. In fact, the SBA has imposed a regulatory ruling that is negatively impacting the future of our small biotech and biomedical research companies.
The SBA decision jeopardizes the development of critical breakthroughs and possible cures for America's patients and their families by cutting off a crucial avenue for our hometown labs to secure much-needed funding from the National Institutes of Health and other federal agencies.

The SBA decision disqualifies many of our small companies — those firms receiving more than 51 percent of their financial backing from venture capital or other outside interests — from the Small Business Innovation Research grant program.
It's clear the SBA simply doesn't understand how small biotech and biomedical firms must rely on outside funding to stay competitive while working to get their ideas off the ground and into the marketplace.

The good news is there is a solution.

While in Washington last week, I was joined by more than 200 of my colleagues from 35 other states also involved with cutting-edge research and innovation in calling on Congress to pass the Save America's Biotechnology Innovative Research Act this year... future of biotech companies

CpG Island Methylation Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

2006-03-31T10:03:00.000-07:00

CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is normally unmethylated, but a sizeable fraction is prone to become methylated in various cell types and pathological situations. The goal of this study is to show that a computational epigenetics approach can discriminate between CpG islands that are prone to methylation from those that remain unmethylated. We develop a bioinformatics scoring and prediction method on the basis of a set of 1,184 DNA attributes, which refer to sequence, repeats, predicted structure, CpG islands, genes, predicted binding sites, conservation, and single nucleotide polymorphisms. These attributes are scored on 132 CpG islands across the entire human Chromosome 21, whose methylation status was previously established for normal human lymphocytes. Our results show that three groups of DNA attributes, namely certain sequence patterns, specific DNA repeats, and a particular DNA structure, are each highly correlated with CpG island methylation (correlation coefficients of 0.64, 0.66, and 0.49, respectively). We predicted, and subsequently experimentally examined 12 CpG islands from human Chromosome 21 with unknown methylation patterns and found more than 90% of our predictions to be correct. In addition, we applied our prediction method to analyzing Human Epigenome Project methylation data on human Chromosome 6 and again observed high prediction accuracy. In summary, our results suggest that DNA composition of CpG islands (sequence, repeats, and structure) plays a significant role in predisposing CpG islands for DNA methylation. This finding may have a strong impact on our understanding of changes in CpG island methylation in development and disease... CpG methylation correlated with DNA sequence

Understanding the Basis for Down Syndrome Phenotypes

2006-03-31T10:00:00.000-07:00

Down syndrome is a collection of features that are caused by trisomy for human Chromosome 21. While elevated transcript levels of the more than 350 genes on the chromosome are primarily responsible, it is likely that multiple genetic mechanisms underlie the numerous ways in which development and function diverge in individuals with trisomy 21 compared to euploid individuals. We consider genotype–phenotype interactions with the goal of producing working concepts that will be useful for approaches to ameliorate the effects of trisomy.

Introduction

Trisomy 21 occurs in 1/750 live births. The frequency of Down syndrome (DS) is much higher at conception, given that up to 75% and 50% of DS fetuses identified during the first and second trimester, respectively, are lost before term [1,2]. Trisomy for some other autosomes occurs more frequently than trisomy 21, nearly always resulting in prenatal loss [3]. The relatively high frequency of postnatal survival for trisomy 21 is thought to be principally a function of the small number of genes on human Chromosome 21 (Hsa21), the smallest and least gene-dense of the autosomes.

Phenotypes

The clinical presentation of DS is complex and variable. A few features occur to some degree in every individual with trisomy 21, including characteristic facial dysmorphology, a small and hypocellular brain, and the histopathology of Alzheimer disease, which is present by the fourth decade. Individuals with DS are invariably cognitively impaired, though the severity is highly variable. Hypotonia occurs frequently in newborns, and most have atypical dermatoglyphic features, though the specific subset of these is again individually variable.

Trisomy 21 is also a risk factor for a number of diseases. For example, it is among the leading causes of congenital heart disease (CHD), some form of which occurs in 40%–50% of those with DS [4]. The incidence of childhood onset leukemia and Hirschsprung disease are both significantly elevated in individuals with trisomy 21. Health-care guidelines for individuals with DS include more than 80 clinical features that occur more frequently than in the population at large [5]. Three critical points for this discussion arise from these basic observations: (1) the incidence of most phenotypes seen in DS is variable; (2) the severity of a given feature is highly variable; and (3) none of the features diagnosed in DS is unique to people with trisomy 21. For “DS features” that also occur in euploid individuals, we assume that there is some commonality of etiology regardless of ploidy, but this must be proven for any specific case... down syndrome phenotypes

UofA's BIO5 organizes next stem cell conference in Tucson

2006-03-30T08:23:00.000-07:00

Scientists, politicians, and business and regulation experts come together for “The Promise of Stem Cells: Tissue Engineering and Regenerative Medicine,” a free, one-day conference on Wednesday, April 5, 2006 from 8:45 a.m. to 5:30 p.m. in DuVal Auditorium, University of Arizona (UA) College of Medicine, 1501 N. Campbell Ave. in Tucson. The public is welcome. Presentation topics include cells and cancer, transplantation, cardiology, vision, neurology, bioengineering, and diabetes; as well as the business, politics, and applications of non-embryonic/non-fetal stem cells in Arizona.

Stem cells are one of the most fascinating areas of medical research today. Research on stem cells is advancing knowledge about how an organism develops from a single cell and how healthy cells replace damaged cells in adult organisms. This promising area of science is leading scientists to investigate the possibility of cell-based therapies to treat injuries or disease, which is often referred to as regenerative or reparative medicine. Arizona is committed to growing its biosciences industry and has developed a detailed plan articulated in the Biosciences Roadmap that can “fast track” Arizona on a path to achieve national bioscience stature and a diversified economy. National prominence in stem cell research could be a core component in achieving this objective... more

TGen, Pa. clinic find gene tie to epilepsy

2006-03-30T08:17:00.000-07:00

In what was described as a major breakthrough, the Translational Genomics Research Institute said Wednesday that it has joined a Pennsylvania-based clinic in identifying a genetic cause for epilepsy, which could lead to development of medicines to treat both epilepsy and autism.

“This is the first step” in finding a cure for the childhood-onset diseases, said Dr. Dietrich Stephan, director of the neurogenomic division of Translational Genomics Research Institute, or TGen, the Phoenix based research group that focuses on treatments and cures for genetically related illnesses.

“It allows us to better understand what causes the diseases. That is the first step in developing new medicines to treat the diseases,” Stephan said.

Medications are currently available to treat epilepsy, but about 40 percent of the varying types of epilepsy do not respond to them, he said. For autism, the only treatment is behavioral therapies — working with kids extensively on a daily basis to teach them life skills, he said... tgen epilepsy

H5N1 Avian Flu Virus Vaccine Induces Immune Responses in Healthy Adults

2006-03-30T08:15:00.000-07:00

Results from a clinical trial demonstrate that high doses of an experimental H5N1 avian influenza vaccine can induce immune responses in healthy adults. Approximately half of those volunteers who received an initial and a booster dose of the highest dosage of the vaccine tested in the trial developed levels of infection-fighting antibodies that current tests predict would neutralize the virus. The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, funded the study, published in the current issue of The New England Journal of Medicine. Preliminary results from this trial were first disclosed late last summer.

“These findings represent an important step forward in the nation’s efforts to prepare for the possible emergence of a human pandemic of H5N1 avian influenza,” notes NIH Director Elias A. Zerhouni, M.D.

“We are working hard to address the many challenges that remain with regard to the development of an H5N1 vaccine,” adds NIAID Director Anthony S. Fauci, M.D. “For example, potentially protective immune responses were seen most frequently at the highest dose of this vaccine. We are investigating other options that may allow us to reduce the dosage — for example, adding an immune booster, or adjuvant, to the vaccine — so we can achieve a more practical immunization strategy.” In addition, the U.S. Department of Health and Human Services is pursuing other approaches to an H5N1 vaccine, including vaccines made in cell cultures rather than grown in eggs.

H5N1 avian influenza viruses are of enormous concern to public health officials worldwide. The potential for a human avian flu pandemic looms large, say experts, as daily reports indicate an increasing spread of infection in bird populations in Southeast Asia, Europe, the Middle East and Africa. According to the World Health Organization, as of March 24, 2006, 186 people had been infected with avian flu viruses, and more than half of them had died... H5N1 avian flu vaccine

Proteins' Baby Pictures

2006-03-29T16:52:00.000-07:00

A technique for imaging freshly made proteins is giving researchers a unique window on the working of genes and cells.

For the first time, scientists have made movies of the birth of individual proteins in single cells. The ability to track protein production with such precision in vivo may make it easier to study the expression of important genes with low activity levels such as those that turn other genes on and off.

Led by Sunney Xie, professor of chemistry and chemical biology at Harvard University, the scientists studied real-time protein production in two ways. In one set of experiments, they genetically engineered a gene for a fluorescent protein that moves to cells' membranes and becomes immobile; since the protein is still, the researchers could take its picture. In a second set of experiments, they created a microfluidic device with a series of holding chambers that they used to capture fluorescent molecules expelled from cells.

Imaging individual proteins inside cells has traditionally been difficult because all cells have a small amount of background fluorescence, and cameras cannot track a single moving fluorescent protein over this faint glow.

"The cool thing about these experiments is that the tools they developed allow the measurement of transcription levels [gene expression] with single molecule accuracy," says Alexander van Oudenaarden, systems biologist and associate professor of physics at MIT. "You can count single protein molecules."

Counting single proteins is powerful because many genes are not very active, and their products are effectively invisible using conventional techniques for studying gene expression. The gold standard in the field, the DNA microarray, is very good for studying genes with high activity levels but is less useful in looking at low-activity genes. Much of the genome, however, is not highly active. In his experiments, Xie could see very low levels of genetic activity across populations of living cells and in individuals... imaging new forming proteins

DNA gene vaccine protects against harmful protein of Alzheimer's disease

2006-03-29T16:46:00.000-07:00

Doses of DNA-gene-coated gold particles protect mice against a protein implicated in Alzheimer's disease, researchers at UT Southwestern Medical Center have found.

By pressure-injecting the gene responsible for producing the specific protein — called amyloid-beta 42 — the researchers caused the mice to make antibodies and greatly reduce the protein's build-up in the brain. Accumulation of amyloid-beta 42 in humans is a hallmark of Alzheimer's disease.

"The whole point of the study is to determine whether the antibody is therapeutically effective as a means to inhibit the formation of amyloid-beta storage in the brain, and it is," said Dr. Roger Rosenberg, the study's senior author and director of the Alzheimer's Disease Center at UT Southwestern.

The gene injection avoids a serious side-effect that caused the cancellation of a previous multi-center human trial with amyloid-beta 42, researchers said. UT Southwestern did not participate in that trial. In that earlier study, people received injections of the protein itself and some developed dangerous brain inflammation.

The new study is available online and appears in an upcoming issue of the Journal of the Neurological Sciences.

The researchers used mutant mice with two defective human genes associated with Alzheimer's, genes that produce amyloid-beta 42. "By seven months, the mice are storing abundant amounts of amyloid-beta 42," said Dr. Rosenberg.

While the mice were young, the scientists coated microscopically small gold particles with human amyloid-beta 42 genes attached to other genes that program cells to make the protein. The particles were then injected with a gene gun into the skin cells of the mice's ears using a blast of helium.

After receiving 11 injections over several months, the mice showed a high level of antibodies to amyloid-beta 42, and a 60 percent to 77.5 percent reduction of plaques in their brains... DNA gene vaccine against Alzheimer's

Affymetrix announces new ChIP-On-Chip array range

2006-03-29T16:42:00.000-07:00

Affymetrix introduces its new ChIP-On-Chip array product line that its designers hope will provide drug researchers with new whole-genome tools to assist scientists discover DNA-Protein interactions.

Laboratory researchers can use the GeneChip tiling arrays to map sites of DNA-protein interaction in chromatin immunoprecipitation (ChIP)-on-chip experiments to discover new RNA transcripts or investigate global epigenomic changes like methylation or acetylation.

Affymetrix tiling arrays interrogate all of the non-repetitive portions of the various genomes. For example, the human tiling arrays interrogate nearly 90 million data points at regular 35 base pair intervals across the human genome.

The complete tiling array systems include an assay kit, analysis software and an integrated browser that enables researchers to compare experimental results to computational results.

Affymetrix has also released a tested and qualified assay protocol for chromatin immunoprecipitation experiments.

The tiling array products to be made available include the Human Tiling 2.0R Array Set, a seven-array set designed for ChIP-on-chip experiments (A-G arrays also available separately)

The Human Promoter 1.0R Array is an array comprised of more than 4.6 million probes tiled to interrogate more than 25,500 human promoter regions, enabling researchers to easily identify thousands of regulatory sequences... affymetrix chip-on-chip

Chapel Hill bio launches human trials for gene therapy

2006-03-29T16:34:00.000-07:00

Asklepios Biopharmaceutical Inc. has ushered its lead product candidate into the first human gene therapy trial in the United States for a particular type of muscular dystrophy.

A clinical trial is under way at Columbus Children's Hospital in Ohio to test the safety and effectiveness of Biostrophin as a treatment for Duchenne muscular dystrophy. The therapy was developed over two years at the University of North Carolina at Chapel Hill and the University of Pittsburgh and is licensed to Chapel Hill-based AskBio.

In the trial launched Wednesday, six boys with Duchenne muscular dystrophy will receive replacement genes for an essential muscle protein.

After several weeks, an analysis of the muscle tissue's microscopic appearance, as well as testing of the boys' health and strength, will provide results on whether gene therapy for the disease is safe and effective.

Muscular dystrophies are disorders that cause progressive muscle degeneration and weakness that begin with microscopic changes in the muscle tissue.

Currently, the best available medical therapy for Duchenne muscular dystrophy can only slow the disease's progress... source

RNA Interference Genetic Screen Suggests New Targets for Cancer Therapies

2006-03-29T16:24:00.000-07:00

Researchers at the National Cancer Institute (NCI), part of the National Institutes of Health, have developed a new method to identify genes that keep cancer cells active and that could be potential targets of anticancer therapies.

The method uses RNA interference (RNAi), a technology for silencing genes, to screen cancer cells for genes that, when silenced, cause cancer cells to die or stop dividing. These genes are essential for the survival of cancer cells and represent potential therapeutic targets, but they might not contain mutations or other alterations typically associated with the disease.

“This method could be used to identify a new class of oncogenes beyond the ones traditionally identified as mutated or otherwise deregulated in cancer,” said lead researcher Louis M. Staudt, M.D., Ph.D., of NCI’s Center for Cancer Research (CCR). The method is described in a study to be published online in Nature* on March 29.

“The traditional way of approaching cancer biology is to identify genes in cancer cells altered by mutations or in their functions,” explained Staudt. “This method identifies additional genes that are not necessarily mutated or altered but that are nonetheless required for the cancer cell’s survival. These additional genes could provide a range of therapeutic targets beyond the small set of genes we have already identified.”

The researchers used the method, technically called a loss-of-function RNA interference genetic screen, to identify three genes not previously linked to cancer. These genes turn on a cellular process, or pathway, that is continuously activated in a type of lymphoma cell. Lymphoma is a cancer of the lymph nodes. The genes could become targets of therapies for a type of lymphoma called activated B cell-like diffuse large B-cell lymphoma (DLBCL)... RNA interference

"Accelerated Evolution" Converts RNA Enzyme to DNA Enzyme In Vitro

2006-03-28T13:22:00.000-07:00

Scientists at The Scripps Research Institute have successfully converted an RNA enzyme (ribozyme) into a DNA enzyme (deoxyribozyme) through a process of accelerated in vitro evolution. The molecular conversion or transfer of both genetic information and catalytic function between these two different genetic systems, which are both based on nucleic acid-like molecules, is exactly what many scientists believe occurred during the very earliest period of earth's existence.

This "evolutionary conversion" provides a modern-day snapshot of how life as we understand it may have first evolved out of the earliest primordial mix of RNA-like molecules—sometimes referred to as the "pre-RNA world"—into a more complex form of RNA-based life (or the "RNA world") and eventually to cellular life based on DNA and proteins. Nucleic acids are large complex molecules that store and convey genetic information, but can also function as enzymes.

While the transfer of sequence information between two different classes of nucleic acid-like molecules—between RNA and DNA, for example—is straightforward because it relies on the one-to-one correspondence of the double helix pairing, transferring catalytic function is significantly more difficult because function cannot be conveyed sequentially. The present study demonstrates that the "evolutionary conversion" of an RNA enzyme to a DNA enzyme with the same function is possible, however, through the acquisition of a few critical mutations.

The study is being released in an advance online version of the journal Chemistry & Biology.... RNA to DNA in vitro

Bioinformatics in Structure-Based Drug Design

2006-03-28T12:36:00.000-07:00

Bioinformatics plays an important role in the design of new drug compounds. In this month’s article, we’ll explore one approach in drug design that benefits from the availability of bioinformatics applications in the cancer research community.

Rational Drug Design (RDD). Rational drug design is a process used in the biopharmaceutical industry to discover and develop new drug compounds. RDD uses a variety of computational methods to identify novel compounds, design compounds for selectivity, efficacy and safety, and develop compounds into clinical trial candidates. These methods fall into several natural categories – structure-based drug design, ligand-based drug design, de novo design and homology modeling – depending on how much information is available about drug targets and potential drug compounds. We’ll focus on structure-based drug design in this article and describe a few of its salient features.

Structure-Based Drug Design (SBDD). Structure-based drug design is one of several methods in the rational drug design toolbox. Drug targets are typically key molecules involved in a specific metabolic or cell signaling pathway that is known, or believed, to be related to a particular disease state. Drug targets are most often proteins and enzymes in these pathways. Drug compounds are designed to inhibit, restore or otherwise modify the structure and behavior of disease-related proteins and enzymes. SBDD uses the known 3D geometrical shape or structure of proteins to assist in the development of new drug compounds. The 3D structure of protein targets is most often derived from x-ray crystallography or nuclear magnetic resonance (NMR) techniques. X-ray and NMR methods can resolve the structure of proteins to a resolution of a few angstroms (about 500,000 times smaller than the diameter of a human hair). At this level of resolution, researchers can precisely examine the interactions between atoms in protein targets and atoms in potential drug compounds that bind to the proteins. This ability to work at high resolution with both proteins and drug compounds makes SBDD one of the most powerful methods in drug design.

Let’s consider how SBDD methods have been used in designing drugs for a well known cancer-related protein complex. Two protein targets that have been studied extensively in cancer research are p53 and MDM2. These two proteins form a single p53-MDM2 complex as part of a cell-signaling pathway that regulates cell division. Mutated forms of p53-MDM2 result in various forms of tumors and cancers. Several decades of research have been aimed at designing small-molecule compounds that restore the normal function of p53-MDM2, and consequently reduce or eliminate certain forms of cancer.

One well-known anticancer drug - “nutlin” - has been developed by Roche Pharmaceuticals to restore the normal functioning of MDM2. (Technically, “nutlin” goes by the name cis-[4,5-bis-(4-bromophenyl)-2-(2-ethoxy-4-methoxyphenyl)-4,5-dihydroimidazol-1-yl]- [4-(2-hydroxyethyl)piperazin-1-yl]methanone, but let’s not get into naming conventions!). SBDD methods played an important role in this development. Figure 1 shows the 3D structure of MDM2 as derived from x-ray crystallography studies. MDM2’s backbone structure and amino acid sidechains are shown in multicolored stick form. Five separate “nutlin” molecules are also shown docked along the protein’s surface and deeply embedded in hydrophobic pockets and cavities... structure based drug design

ASU Biodesign Creates Electricity from Bacteria

2006-03-28T12:31:00.000-07:00

Microorganisms 100 times smaller than the width of a human hair could help power America’s energy future, a professor at Arizona State University says.
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Bruce Rittmann, director of the Center for Environmental Biotechnology at the ASU Biodesign Institute, is experimenting with microbial fuel cells — devices that use bacteria to produce electricity.

Weird though it may sound, some bacteria that feed on organic waste such as sewage, feedlot manure, algae or crop waste, release electrons in the process, creating an electric current, he said.

At the ASU lab, Rittmann and his research team have created bacteria biofilms that coat the electrodes in a fuel cell, setting up an electrical circuit between the anode and cathode.

“Someday, we could use this electricity to run a car,” he said. “It also could be used eventually in a power plant.”

Theoretically, biopower has a lot of advantages. It uses a renewable fuel supply. Also, unlike traditional combustion, the electricity production takes place at room temperature and no energy is lost as heat. And there are no combustionrelated pollutants to contribute to global warming. In fact, the only byproduct is ultra-pure water, Rittmann said.

Microbial fuel cells also have advantages over conventional fuel cells that run on hydrogen, Rittmann said.

For the most part, hydrogen is obtained from nonrenewable fossil fuels like coal and natural gas, which leaves them tied to the escalating cost of fossil fuels. Hydrogen can be extracted from water, but that consumes more energy than it produces, he said.

According to the U.S. Department of Energy, converting the energy value in domestic sewage to electricity could save the U.S. the equivalent of 2 million barrels of oil each year, while capturing the energy value of feedlot manure could save 6 million barrels a year... bacteria to produce electricity

TGen, ASU Technopolis join forces for technology forum

2006-03-28T12:23:00.000-07:00

ASU Technopolis and the Translational Genomics Research Institute (TGen) have again joined forces to present the second annual Commercializing Arizona Life Sciences Forum April 20 – 21 at the Phoenix Airport Marriott.

The forum sessions are divided into two tracks, allowing investors and venture capitalists, as well as researchers and entrepreneurs, to receive information tailored to their respective needs.

Confirmed keynote speakers include Fred Craves, co-founder and managing director of Bay City Capital; Kerry Dance, managing director of Hamilton Bioventures; Mark Ferguson, founder and chief executive officer of Renovo of the United Kingdom; and Jack J. Florio, vice president and communications/board member of the San Diego Tech Coast Angels.

Registration is available online at (www.asutechnopolis.org).

Session highlights for investors and venture capitalists, featuring keynote speaker presentations and panelists, include:

The ABCs of investing in life science companies.
The status of the Arizona life science industry and company development.
A life science case study.
Arizona tax incentives for life science investors.
Tours of the Biodesign Institute at ASU and the Translational Genomics Research Institute (for investors and venture capitalists only).
An investor-only luncheon hosted by TGen.

Session highlights for researchers and entrepreneurs, featuring keynote speaker presentations and panelists, include:

Strategic partnerships and collaborations.
Commercializing life sciences with the government.
IP protection.
Commercialization and licensing.
Entrepreneurial start-up.
Arizona tax incentives for life science investors.
SBIR Phase I and Phase II proposal-writing workshop (with a certificate of completion).

asu technopolist and tgen

Scientists seek biotech answer to hunger

2006-03-27T14:54:00.000-07:00

...The goal is to turn sorghum -- a common U.S. row crop used in animal feed, cereals and industrial products -- into a plant that can not only weather devastating drought but also yield a rich blend of vitamins and minerals. Researchers believe such a combination could help combat the hunger and malnutrition ravaging parts of Africa.

"A lot of people have died on the African continent, quite unnecessarily," said Mehlo, a molecular biotechnologist who came to Iowa from South Africa in October. "We seek to have a crop that will enable us to survive during disasters and food shortages."

TWEAKING GENES

Mehlo is one of a team of African scientists who will be working in Iowa over the next three years, tinkering with the genes of sorghum seeds.

An estimated 300 million people in arid regions of Africa rely on sorghum as a food source along with other crops. But while conventional sorghum is already known to do well in drought conditions, it lacks certain key nutrients.

By taking genes from other crops as well as manipulating genes within the sorghum plant itself, scientists believe they can remake sorghum into a more easily digestible crop richer in vitamins A and E, iron, zinc and amino acids and protein.

Pioneer Hi-Bred International, a subsidiary of Dupont, is a key U.S. partner and the sole commercial player in the endeavor. Pioneer has donated $4.8 million in gene technology, and is lending manpower and facilities for visiting African scientists at its Johnston headquarters.

"Africa is a place where biotechnology is necessary," said Dean Oestreich, President of Pioneer Hi-Bred International Inc. "It would be a big step to take and make a food crop more nutritious for people in Africa."... biotech vs hunger

Banner brings foremost Alzheimer's expert to Arizona

2006-03-27T14:51:00.000-07:00

The state's largest health care system is creating a research arm to end Alzheimer's disease.

Called Banner Alzheimer's Institute, the new project also has attracted a world-renowned researcher as co-director.

Dr. Pierre Tariot, an Alzheimer's expert at University of Rochester Medical Center and an empty nester at home, has a dream to build a model Alzheimer's disease center where care is provided like nowhere else.

In pursuit of that vision, he visited 11 institutions around the country and had offers from about half of them. But when he met with Dr. Eric Reiman, head of Banner Health's new Banner Alzheimer's Institute, he was amazed at what was in the works. And that brought Tariot to Arizona.

"I chose the only one where I'm not the director because of my conviction that this environment is the one where we're most likely to succeed in a very ambitious undertaking," Tariot said. "The vision that the folks here had come up with independently exceeded my own."

As associate director of the institute, Tariot will serve as principal investigator of clinical trials.

Plus, he said, Reiman works collaboratively with Alzheimer's researchers around the state at several hospitals and at the Translational Genomics Research Institute... continue

Excess weight in Hispanics could mean a fatter Arizona

2006-03-27T14:45:00.000-07:00

If state and public health officials don't address obesity in its Hispanic population, Arizona could become fatter and experience more health problems than the rest of the country, researchers say.

...But researchers at the Translational Genomics Research Institute hope to stop the problem before the population puts on more pounds.

TGen's latest research found that eight of 10 Avondale adults are overweight or obese. Avondale and TGen have worked together for the past year to study residents' cardiovascular health, and the partnership received recognition last week from the federal Centers for Disease Control and Prevention.

Johanna Wolford, heading the TGen study, hopes the work will lead to culturally customized diets, educational materials and health plans that can curb the disturbing rate of cardiovascular disease within the ethnic group.

Wolford's study sampled about 500 people and focused on Avondale because its population of 60,000 is nearly half Hispanic.

If more Avondale residents are going up in belt sizes, the rest of Arizona might do the same and could quickly outpace the national figures, Wolford said... read

Pharmaceutical and Biotechnology Companies are Turning to Personalized Medicine to Help Improve the Drug Development Process of New Drugs

2006-03-25T10:21:00.000-07:00

Research and Markets has announced the addition of The Trend Toward Personalized Medicine to their offering.

In vitro diagnostics (IVD) and molecular diagnostics are multibillion-dollar industries. Together, they play critical roles in the trend toward personalized medicine. Pharmaceutical and biotechnology companies are turning to personalized medicine to help improve the drug development process and speed the approval of new drugs.

This Decision Resources report discusses the role of IVD and molecular diagnostics in personalized medicine, profile companies in the field, discuss key trends and issues, and ponder the future of personalized medicine.

Personalized medicine is a component of the molecular diagnostics market, which is the fastest-growing segment of the in vitro diagnostics (IVD) market. According to S.G. Cowen & Co., the IVD industry was a $26 billion industry in 2004. Within this industry, the molecular diagnostics market segment is expected to show the most robust growth, increasing from $1.8 billion in 2004 to $3.6 billion in 2009, representing an annual growth rate of 15%.

Personalized medicine will require more emphasis on IVD and greater cooperation between diagnostic and therapeutic companies in the development of new technologies and products; it will result in improved health care and business growth for both diagnostic and therapeutic companies. The beginnings of this increased cooperation are already evident in several diagnostic products and services directly guiding therapeutic decisions, notably in the areas of cancer and infectious disease.

Diagnostic assays that test the genetic basis for the metabolism of drugs, including toxicity, and define eligibility for targeted oncological therapies are already on the market. It is anticipated that the FDA will require the development of companion diagnostic tests before it approves some of the targeted therapeutic products in development.

Business models for diagnostic companies engaged in personalized medicine include major IVD manufacturers such as Roche (with a significant existing molecular diagnostics business), technology platform companies such as Affymetrix (with stand-alone products as well as partnering relationships with IVD manufacturers), and small specialized diagnostic companies such as DakoCytomation, which partners with pharmaceutical companies to develop and produce specific companion diagnostics.

Topics covered include:

The Role of IVD in Personalized Medicine
Targeted Cancer Therapies
Drug-Metabolizing Enzymes
HIV-Resistance Testing
Diagnostic Companies in Personalized Medicine
Key IVD Trends in Personalized Medicine
Combination Drug/Diagnostic Products
Increasing Use of Pharmacogenetic Tests
Multiplex Testing
Successful Business Models
Cost
Patients' Acceptance of Personalized Medicine

Companies mentioned in this report include:

Affymetrix
AstraZeneca
Corixa
DakoCytomation
Genentech
Genta
Genzyme Genetics
GlaxoSmithKline
Idec
Ilex Oncology
Millennium
Monogram Biosciences
Novartis
Pfizer
Promega
Roche Diagnostics
Zenyaku Kogyo
Schering AG
Third Wave Technologies
Virco Lab
Vysis
Wyeth/AHP

via

Junk DNA May Not Be So Junky After All

2006-03-24T10:45:00.000-07:00

Researchers at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins have invented a cost-effective and highly efficient way of analyzing what many have termed “junk” DNA and identified regions critical for controlling gene function. And they have found that these control regions from different species don’t have to look alike to work alike.

The study will be published online at Science Express March 23.

The researchers developed a new system that uses zebrafish to test mammalian DNA and identify DNA sequences, known as enhancers, involved in turning on a gene. In studying RET, the major gene implicated in Hirschsprung disease and multiple endocrine neoplasia (MEN2), the team identified DNA sequences that can control RET but had not been identified using standard methods. Hirschsprung disease, also known as congenital megacolon, is a relatively common birth defect marked by bowel obstruction. MEN2 is an inherited predisposition to neuroendocrine cancers.

The notion that mutations in enhancers play a role in human disease progression has been difficult to confirm because usually enhancers are located in the 98 percent of the human genome that does not code for protein, termed non-coding DNA. Unlike DNA sequences that code for protein, non-coding DNA, sometimes referred to as “junk” DNA, follows few rules for organization and sequence patterns and therefore is more difficult to study.

“The difficulty with human genetic approaches to common disease is that we lack the power to precisely localize DNA sequences that are associated with disease, often leaving us immense stretches of DNA to look at,” says one of the study’s corresponding authors, Andy McCallion, Ph.D., an assistant professor in the McKusick-Nathans Institute. Most often one is limited to looking in the most obvious places, which may not yield the best results. “Until now,” he says, “we’ve only been able to look under the lamplights for the car keys.”

Traditionally, DNA sequences are thought to have to look similar to function similarly; this is how scientists identify genes in other species, a strategy best used for studying similar species. From an evolutionary standpoint, the last common ancestor of human and zebrafish lived more than 300 million years ago. Because DNA sequences in each species have changed over time, traditional methods of comparing DNA sequences between humans and zebrafish have failed to identify any potential enhancers around the RET gene because the DNA sequences differ too much... analyzing junk DNA

DNA breakthrough promises crispier and tastier apples

2006-03-24T09:20:00.000-07:00

A stunning new red-fleshed apple, packed with health-promoting antioxidants, could soon redefine the way consumers and industry perceive the perfect fruit.

New Zealand-based fruit science company HortResearch today unveiled a new apple which carries the fruit’s traditional rosy colouring right to the core.

From the outside the apple looks like almost any other, but bite into or slice it and the fruit’s rich red flesh is revealed – given its unique colour by a high concentration of anthocyanin – an antioxidant known to offer human health benefits.

HortResearch’s work on new apple colours is well known in the science community, and while photographs of the fruit have appeared in scientific literature, little public information has been made available about how the fruit was created, or how close it may be to market.

HortResearch Chief Scientist Dr Ian Ferguson said the apple represents “the next level of achievement” for the company’s established breeding programme, which has already produced numerous successful new apples including the latest blockbuster variety Jazz™.

“Our breeders have built an enviable reputation for innovation and quality and this exciting new fruit is testimony to their skills and imagination,” he said.

Dr Ferguson explained that HortResearch began work in 1998, using apples that have naturally red flesh, but do not possess the external appearance, eating qualities or storage capability required to meet commercial standards.

Breeders crossed these apples with high quality white-fleshed apples, creating breeding lines with fruit that range from white/pink to full purple.

The red-fleshed breeding line has been singled out for immediate fast-track development mainly because the colour is so appealing and HortResearch reports excellent progress.

In the past, taking a new fruit trait from this early stage to full commercialisation has often taken decades of breeding effort, but HortResearch says that by applying the latest genomic science techniques, it could be offering growers the new trees in as little as 5-6 years.

Scientists at the company’s Auckland research campus are now endeavouring to speed up the breeding effort by unlocking the apple’s genetic code. Researchers there have already identified over 150,000 apple ESTs – Expressed Sequence Tags – portions of an entire gene that can be used to help locate and identify unknown genes.... apple DNA

BRCA Genetic Mutation Test Yields False Negatives For Breast Cancer Patients With Family History Of Breast, Ovarian Cancer

2006-03-24T09:00:00.000-07:00

A commonly used genetic test to determine a person's risk of breast cancer failed to identify the BRCA1 and BRCA2 genetic mutations -- thought to increase risk of the disease -- in about 12% of people who have been diagnosed with breast cancer, who have a family history of breast or ovarian cancer and who previously tested negative for the mutation, according to a study published in the March 22 issue of the Journal of the American Medical Association, the New York Times reports . About one in 400 people are believed to carry either the BRCA1 or BRCA2 mutation, both of which are believed to increase the chance of developing breast and ovarian cancers. The only commercially available BRCA test in the U.S. is made by Salt Lake City-based Myriad Genetics at a cost of about $3,000.

According to the Times, Myriad Genetics "has long been the focus of controversy because its patents give it a monopoly on the test" and some critics believe the "monopoly has slowed development of better testing". Thomas Walsh of the University of Washington's departments of Medicine and Genome Sciences and colleagues examined 297 women and three men who had tested negative for the BRCA mutations, been diagnosed with breast cancer at some point in their lives and were members of families that have had at least four individuals with breast or ovarian cancer . Researchers tested the patients using various techniques including one known as MLPA, which is not commercially available in the U.S., the Milwaukee Journal Sentinel reports. The study finds that 52 of the participants had some type of genetic mutation, including 35 -- or about 12% -- who had the BRCA1 or BRCA2 genetic mutation. The MLPA test was developed by Amsterdam, Netherlands-based Microbiology Research Center-Holland... continue

New research reveals oxygen’s contributions to evolution

2006-03-23T22:51:00.000-07:00

It’s common knowledge that humans and other animals couldn’t survive without oxygen. But scientists are now learning a good deal more about the extent of our evolutionary debt to a substance that was once a deadly poison.

New research at Lawrence Livermore National Laboratory (LLNL) and Boston University shows that many of the complex biochemical networks that humans and other advanced organisms depend on for their existence could not have evolved without oxygen.

“You could call it the ‘oxygen imperative,’ ” said LLNL postdoctoral researcher Jason Raymond. “It’s clear that you need molecular oxygen to evolve complex life as we know it.”

“Researchers have spent decades putting together maps of how the building blocks of life connect to each other,” added Daniel Segrè of Boston University, who holds a joint appointment in LLNL’s Biosciences Directorate. “It turns out that whole regions in this map may not have existed without oxygen.”

Raymond and Segrè used computer simulations to study the effect of oxygen on metabolic networks – the biochemical systems that enable organisms to convert food and nutrients into life-sustaining energy. Their analysis shows that the largest and most complex networks – those found in humans and other advanced organisms – require the presence of molecular oxygen. The research is reported in the March 24 issue of the journal Science.

“We wanted to look at how the availability of oxygen changed the types of chemical reactions,” Raymond said, “both with respect to metabolites (metabolism byproducts) and to the enzymes needed to carry out metabolism.”

Raymond and Segrè calculated the number of possible combinations of the thousands of enzymes and chemicals involved in all known metabolic reactions across the tree of life, and came up with a “virtually limitless” number – ten to the 16,536th power. Simulating that many networks would be an impossible task even for LLNL, which houses the world’s most powerful supercomputers.

To make the project manageable, the researchers used a statistical technique called Monte Carlo to randomly sample and simulate about 100,000 networks. “We found that all the different types of networks fell into four different clusters of increasing size and connectivity, and in networks within the largest clusters, molecular oxygen was always present,” Raymond said... oxygen’s contributions to evolution

Gold Nanoparticles and Cancer Treatment

2006-03-23T21:12:00.000-07:00

Cancer is a disease caused by genetic mutations, so it should be no surprise that cancer researchers and clinical oncologists alike are eager for new, inexpensive methods that would enable them to rapidly and accurately identify mutations associated with cancer. Using gold nanoparticles, two groups of investigators have each developed gene-identification methods that may fill this need.

Research teams headed by Lloyd Smith, Ph.D., at the University of Wisconsin-Madison, and Robert Corn, of the University of California-Irvine, each published papers in the journal Analytical Chemistry that detail the two new approaches to rapid, quantitative gene identification. Both of the new techniques identify single-nucleotide polymorphisms (SNPs), the most frequent type of human genetic variation, with the help of DNA microarrays. In each case, sample DNA is added to a gene chip containing known sequences of DNA. Each of these known sequences corresponds to a known SNP associated with a disease. After any DNA in the sample binds to its chip-immobilized complement, the chip is washed to remove any unbound DNA.

In the Wisconsin team's method, the DNA chip is then treated with an enzyme that degrades the ends of the bound DNA, leaving a free, reactive phosphate group that over the course of two subsequent biochemical reactions is labeled with a gold nanoparticle. Because of the techniques the researchers used, only those places on the DNA chip where a piece of sample DNA had been bound to a SNP-identifying DNA probe become labeled with gold nanoparticles. When the chip is then viewed under an electron microscope, the gold nanoparticles appear as white pinpoints on a black background. Commercial software can readily analyze the electron micrograph, providing an accurate tally of any SNPs that were present in the original sample.

The investigators note that their methodology improves labeling efficiency by as much as 15-fold over conventional analytical methods. In addition, the signal-to-noise ratio – a measure of how strong the analytical signal is compared to background signal – is some 4-fold higher using gold nanoparticles as the detection reagent.

The UC-Irvine group took advantage of the extreme optical brightness of gold nanoparticles to generate its highly sensitive SNP detection scheme. When irradiated with light, gold nanoparticles generate bright light of a different frequency by a process called plasmon surface resonance. In their method, Corn and his colleagues take the washed DNA chip and use an enzyme that attaches a short piece of DNA linked to a gold nanoparticle to the ends of the sample probe wherever it has bound to complementary pieces of DNA from the sample. Again, gold nanoparticles end up only where the DNA chip has identified the presence of a specific SNP in the original sample.

Using a plasmon resonance scanner, the investigators can easily spot which of the chip-based probes bound to sample DNA. To test their method, the UC-Irvine team successfully identified DNA containing point mutations, or SNPs, in the BRCA1 gene that are associated with breast cancer.

The Smith group's work was detailed in a paper titled, "Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging." An abstract of this paper is available through PubMed.
View abstract.

The work from the Corn group was detailed in a paper titled, "Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions." This paper was published online in advance of print publication. An abstract is available at the journal's website.

Human Cells Have a Natural Defense Against HIV

2006-03-22T07:46:00.000-07:00

Scientists here have discovered a previously unknown mechanism that cells use to fight off the human immunodeficiency virus (HIV), the cause of AIDS.

The findings indicate that two proteins that normally help repair cellular DNA can also destroy the DNA made by HIV after it enters a human cell. This HIV DNA is essential for the virus to survive and reproduce.

The findings could lead to a possible new strategy for treating HIV infection and AIDS, one that might complement current therapies and would probably be less susceptible to viral drug resistance – an increasingly urgent dilemma for patients and doctors.

Currently, doctors treat people with AIDS using combinations of drugs that target the virus itself. These drugs do not eliminate HIV from the body, but they do block its ability to reproduce and spread, and they restore most people with AIDS to good health.

In time, however, HIV can develop mutations that render those drugs ineffective.

“Our findings identify a new potential drug target, one that involves a natural host defense,” says principal investigator Richard Fishel, professor of molecular virology, immunology and molecular genetics and a researcher with the OSUCCC

“HIV treatments that target cellular components should be far less likely to develop resistance.”

Fishel's laboratory colleague and first author Kristine Yoder discovered the role of the cellular repair proteins while trying to answer a different question.
“Our findings identify a new potential drug target, one that involves a natural host defense. HIV treatments that target cellular components should be far less likely to develop resistance.”

Before HIV infects a cell, it carries its genetic material in the form of RNA, or ribonucleic acid. Once inside a cell, the virus makes a copy of its genes in the form of DNA. This DNA copy – known as cDNA – then travels to the cell nucleus. There, it becomes inserted, or integrated, into the cell's DNA. There it is known as a provirus, and it will generate new HIV in an infected patient and eventually cause AIDS... human defense against HIV

Life's diversity 'being depleted'

2006-03-22T07:40:00.000-07:00

Virtually all indicators of the likely future for the diversity of life on Earth are heading in the wrong direction, a major new report says.

The Global Biodiversity Outlook (GBO) is published as national delegates gather in Brazil under the UN Convention on Biological Diversity.

The Convention commits governments to slow the decline in the richness of living systems by 2010.

The GBO says "unprecedented efforts" will be needed to achieve this aim.

It sets out 15 indicators of progress towards the 2010 target, ranging from trends in the extent of wildlife habitats to the build-up of nutrients such as nitrogen which can harm aquatic life.

Only one of the 15 - the area of the world's surface officially protected for wildlife - is moving in the right direction for biodiversity.

Even here, however, most areas still fall far short of targets to protect 10% of each region with distinctive combinations of species.

The other indicators point to an accelerating decline, which has seen the rates of species extinctions surge to their highest levels since the demise of the dinosaurs 65 million years ago.

Forests continue to be lost at a rate of six million hectares a year - that's about four times the size of the English county of Yorkshire - and similar trends are noted for marine and coastal ecosystems such as coral reefs, kelp beds and mangrove forests... bio diversity

500th post of Arizona Biotech News Update

2006-03-22T07:36:00.000-07:00

I've been updating this site since August 16th 2005 and this is the 500th post!!! Like the 1st post this one also doesn't contain any useful info. Anyhow, thank you for reading.

Italians find gene key to fab wine

2006-03-21T07:49:00.000-07:00

Cracking pinot grape's life code compared to first moonwalk

Italian scientists have uncovered the 'life code' of the pinot noir grape plant, a breakthrough destined to change the future of wine-making .

On Monday experts from the San Michele all'Adige Agrarian Institute presented the results of six years of research, in which they decoded the plant's genome - the complex molecular chains that constitute each organism's unique genetic heritage .

The institute says the development will make it possible to create new, more resistant grape plants that can produce superior wines .

"Today's event is agriculture's equivalent of the first moonwalk," said Riccardo Velasco, the head of the team that decoded the DNA sequences, at Monday's press conference .

"Agriculture will never be the same again" .

Pinot noir, which is known as pinot nero in Italy, is the first fruit and only the second food crop, after rice, to have its genetic material laid completely bare... italians decode gene for wine

A balancing act between the sexes

2006-03-21T07:44:00.000-07:00

Genetic differences between males and females might be evened out at the rim of the nucleus

Recent research at the European Molecular Biology Laboratory [EMBL] reveals new insights into how cells achieve equality between the sexes. A new link discovered between the membrane surrounding the nucleus and the male X-chromosome in fruit flies may play a crucial role in determining how active certain genes are. The study, which appears in the current issue of the journal Molecular Cell, may help researchers understand how male and female cells manage to produce the same quantities of certain proteins.

"The problem arises because the females of many species from insects to humans have two X-chromosomes whereas males have only one", says Asifa Akhtar whose group carried out the project at EMBL. "Since genes contain the recipes for proteins this would normally lead female cells to produce twice as many of the proteins encoded by the X-chromosome as males. Balance is achieved through the activity of an assembly of proteins, called the dosage compensation complex [DCC]."

In flies the DCC hyperactivates the male X-chromosome to double the amount of proteins it produces. Investigating how this hyperactivation is brought about Akhtar's group discovered that the DCC interacts with molecules that sit in the nuclear membrane where they form gateways to the nucleus. This interaction seems to play an important role in dosage compensation, because when the pore proteins are removed from a cell the hyperactivity of the Xchromosome is lost.

"We have found a complex with striking similarities to the fly DCC in human cells", says Sascha Mendjan from Akhtar's group. "This leaves room for speculations about its role in dosage compensation in mammals. Unlike flies, mammals inactivate one of the female X-chromosomes to match the protein contents between the sexes. But the fact that the machinery is evolutionary conserved suggests a common molecular basis from which the different mechanisms evolved."... continue

H5N1 Has Evolved Into Two Different Forms

2006-03-21T07:33:00.000-07:00

Researchers from the US Centers for Disease Control and Prevention (CDC) have discovered that there are now two different forms of the virulent H5N1 bird flu virus strain. It appears that the new variant evolved last year and has infected humans in Indonesia.

This will make it more difficult to develop an effective vaccine.

The researchers looked at 300 samples taken from birds and humans during 2003 - 2005. Scientists had thought there was only one type of H5N1 strain. However, as the virus spreads geographically it is also undergoing genetic diversity expansion. Dr. Rebecca Garten said “Back in 2003 we only had one genetically distinct population of H5N1 with the potential to cause a human pandemic. Now we have two."

The researchers stressed that neither of the two H5N1 types has the ability to spread easily among humans.

Currently, scientists around the world are working on a vaccine for humans. The problem is we cannot come up with an effective finished product until we know what the finally evolved virus is like, i.e. we have to wait until we know the exact form of the pandemic virus.

In the USA, research is now underway on creating a vaccine to protect from both forms of the H5N1 strain. A vaccine for one form of the virus would also offer some protection against the other, say researchers... H5N1 evolved into two strains

Gene discovery offers hope for eczema and asthma sufferers

2006-03-20T09:42:00.001-07:00

The gene that causes dry skin and predisposes people to eczema and asthma has been identified by scientists.

The discovery could lead to new treatments for conditions that affect millions of people.

According to researchers at the University of Dundee, the gene is the one whose job it is to create the protein filaggrin, which is normally found in the outermost layers of the skin.

The protein is vital to ensure that the skin forms a barrier to keep water in and foreign organisms out.

All genes come in pairs, so the degree of disability depends on whether people have a single defective copy or two. About 10per cent of the population carry a single defective copy, and have dry and flaky skin. But those with two defective copies -- about 1 in 500 people -- make no filaggrin and have a severe and persistent disease called ichthyosis vulgaris.

Common observation over many years has suggested a strong link between eczema, allergies and asthma. Children who have one tend to have the others, and doctors call the combination of symptoms atopic disease. Believing the likely cause to be a malfunction of the immune system, scientists in the past have looked for a common factor in immune system genes, but without complete success... eczema and asthma genes

Muscular Dystrophy Association Funds Large-Scale Gene Screening Project to Find ALS Clues

2006-03-20T09:31:00.000-07:00

TGen to Scan 1,000 Patient Samples in Year-long Study

The largest screening of genes that may be involved in causing, exacerbating or increasing vulnerability to amyotrophic lateral sclerosis (ALS, or Lou Gehrig's disease) has been funded by the Muscular Dystrophy Association (MDA), the organization announced today.

MDA will provide $650,000 to the non-profit Translational Genomics Research Institute (TGen) in Phoenix, to scan the genomes of 1,000 patient samples collected from several clinical sites around the country to identify ALS-causing genes.

The one-year project is focused on identifying regions in the human genome that harbor genes that predispose individuals to sporadic ALS. Much insight has been gained into other forms of ALS, but there is still little understanding of the common causes of ALS, which occur with no prior history.

"We are optimistic that this study will enable us to identify those genes that contribute to sporadic ALS. That knowledge will bring us a step closer to developing a diagnostic test and hopefully improved therapeutics for battling ALS," said Dr. Dietrich Stephan, head of TGen's Neurogenomics Division and project director.

ALS is a progressive, degenerative disease of the nervous system that usually begins in middle or late adulthood, causes total paralysis, and most often leads to death within five years. It's called Lou Gehrig's disease after the famed New York Yankees baseball player who died of the disease in 1941. Since 1993, scientists, many of whom have received funding from MDA, have uncovered a few genes that, when flawed, can directly cause ALS, and have suspected several others of increasing vulnerability to the disorder or accelerating its course.

Projects funded by MDA that are smaller in scope have provided researchers with several hunches concerning biochemical pathways that are likely to contribute to ALS, but this is the first project that will scan the entire human genome (full set of human genes) for variants that may be more common in the ALS population than in the general population.... MDA funds Tgen

Minor Mutations in Avian Flu Virus Increase Chances of Human Infection

2006-03-18T21:36:00.000-07:00

Scientists at The Scripps Research Institute, the Centers for Disease Control, and the Armed Forces Institute of Pathology have identified what the researchers described as a possible pathway for a particularly virulent strain of the avian flu virus H5N1 "to gain a foothold in the human population."

The H5N1 avian influenza virus, commonly known as "bird flu," is a highly contagious and deadly disease in poultry. So far, its spread to humans has been limited, with 177 documented severe infections, and nearly 100 deaths in Indonesia, Vietnam, Thailand, Cambodia, China, Iraq, and Turkey as of March 14, 2006, according to the World Health Organization.

"With continued outbreaks of the H5N1 virus in poultry and wild birds, further human cases are likely," said Ian Wilson, Scripps Research professor of molecular biology and head of the laboratory that conducted the recent study. "The potential for the emergence of a human-adapted H5 virus, either by re-assortment or mutation, is a clear threat to public health worldwide."

Of the H5N1 strains isolated to date, the researchers looked at A/Vietnam/1203/2004 (Viet04), one of the most pathogenic H5N1 viruses studied so far. The virus was originally isolated from a 10-year-old Vietnamese boy who died from the infection in 2004. The hemagglutinin (HA) structure from the Viet04 virus was found to be closely related to the 1918 virus HA, which caused some 50 million deaths worldwide.

Using a recently developed microarray technology—hundreds of microscopic assay sites on a single small surface—the study showed that relatively small mutations can result in switching the binding site preference of the avian virus from receptors in the intestinal tract of birds to the respiratory tract of humans.These mutations, the study noted, were already "known in [some human influenza] viruses to increase binding for these receptors."

The study was published on March 16, 2006 by ScienceXpress, the advance online version of the journal Science... bird flu human infection

NIH Provides $24 Million to Support Research Network

2006-03-18T21:30:00.000-07:00

Funding Will Enable Refinement of Multi-Site Neuroimaging Tools

The National Center for Research Resources (NCRR), a part of the National Institutes of Health (NIH), announced today it will provide $24.29 million over five years to the University of California, Irvine (UCI) for continued support to the Biomedical Informatics Research Network (BIRN). Currently a consortium of 28 universities and 37 research groups, BIRN is leveraging and sharing distributed tools, software applications, techniques, data, and expertise that extend beyond the boundaries of individual laboratories. This major NCRR initiative, involving both basic and clinical investigators, is initially concentrating on research involving neuroimaging, but the tools and technologies developed will ultimately be applicable to other disciplines.

UCI is leading the part of the project known as Function BIRN that brings together researchers at 14 institutions for the common purpose of developing and testing interdisciplinary techniques for integrating efforts in functional Magnetic Resonance Imaging (fMRI) across multiple sites. The award will allow the Function BIRN team to improve calibration of imaging equipment across sites, develop robust protocols for cognitive assessment, formulate methods for analysis of resulting data, and develop a scalable technology toolkit to support such complex studies. A test project will interpret fMRI datasets from more than 200 subjects scanned at facilities across the country.... NIH support for research network

Chandler, Arizona looks to attract biotech

2006-03-18T21:24:00.000-07:00

With Chandler already established as a semiconductor hub, economic development officials are looking to add biosciences to the city’s high-tech mix.

The economic development department is studying the feasibility of setting up a biotech incubator that would provide offices and lab space for new bioscience companies and help them become established, said Chris Mackey, an economic development specialist for the city.

“There is a tremendous need for biotech startup company space,” she said.

During her research, Mackey said she could find only one wet lab available in a Valleywide market of 228 million square feet of retail, industrial and office space.

Biotechnology is being promoted as one of the most promising sectors for job growth in Arizona.

Several important private and public projects have been launched in the past three years, including the Biodesign Institute at Arizona State University, the Translational Genomics Research Institute and the collaborative biomedical campus for ASU and the University of Arizona in downtown Phoenix.

In addition to public support, the Virginia G. Piper and the Stardust charitable trusts have announced initiatives totalling $150 million for bioscience research.

But economic development specialists say a lack of wet labs is hampering efforts to attract private-sector biotech businesses to Arizona.

“Someone needs to invest more in wet lab space so these companies can move here,” said David Drennon, a spokesman for the Arizona Department of Commerce.

A wet lab offers researchers the ability to use liquids and gas and requires special plumbing, air-handling systems, waste disposal facilities, water purification capacity, etc.

Surprise and Chandler are among the municipalities that might fill the gap, according to Barry Broome, president of the Greater Phoenix Economic Council, a Valley economic development group. Because of the risks, private developers are often reluctant to build space aimed at developmental-stage companies, which means that government will have to play a role, he said.

“We need some communities to step up,” he said.

Mackey said Chandler officials have not yet determined how they would finance a biotech incubator.

Typically cities that have built such projects have done them in partnerships with universities or private benefactors, she said.

“You really need someone who fully understands startup companies and what they need,” she said. “A community usually is not in the best position to determine that.”

In any event, such a building wouldn’t be cheap. Space for biotech companies typically costs about $250 to $300 a square foot to build, compared with $60 for standard industrial space and $100 to $110 for office space, she said... Chandler for biotech

UK scientists launch big genetic database project

2006-03-17T13:05:00.000-07:00

A major project to collect DNA samples and medical data from 500,000 people was launched on Wednesday to study how genes, lifestyle and environment affect the risk of disease.

The UK Biobank, the world's biggest genetic database, will hold millions of samples in a robotically controlled facility near Manchester, England.

The wealth of data that will be collected from men and women volunteers aged 45-69 will help scientists determine the genetic basis of diseases and why some people develop cancer, heart disease, diabetes, asthma or Alzheimer's and others don't.

"Nothing like this has been attempted before in such fine detail on such a vast scale," said Professor Rory Collins, chief executive of the Biobank.

"We will get very reliable information about the causes of disease," he told a news conference.

The 61 million pound ($100 million) Biobank will be funded by the Wellcome Trust, the world's largest medical research charity, the British government and other sources.

Some researchers have expressed concerns about the design and size of the project, which has been described as the world's biggest medical experiment, but Collins said it has been carefully planned for several years.

CONFIDENTIAL INFORMATION

Scientists will soon begin collecting blood and urine samples, as well as data on height, weight, body fat and respiratory function from the first volunteers.

Their health will be monitored over future decades to untangle the interaction of how genetics, lifestyle and environmental factors cause disease.

Scientists believe the project could improve prevention, diagnosis and treatment of diseases and help to explain why people react differently to medications... genetic database project

Biosouthwest 2006 Focuses on Regional Strengths, Arizona BioIndustry Will Benefit Everyday Lives

2006-03-17T12:55:00.000-07:00

BioSouthwest 2006, the premier biotech and bioscience conference with a regional focus is April 3 & 4 in Tucson. The region’s latest crop of startups and maturing companies will be featured as they respond to issues of our times.

Tucson, AZ (PRWEB) March 17, 2006 -- BioSouthwest 2006, the premier biotech and bioscience conference with a Southwestern regional focus, is April 3 & 4 in Tucson. The region’s latest crop of startups and maturing companies will be featured as they respond to the issues of our times. The consequences of an aging baby boomer generation, bioterrorism such as the Anthrax attacks post 9/11, and emerging infectious threats have all inspired diverse innovations.

While addressing the needs of aging populations, cutting-edge bioengineering will be presented. Exciting stem cell therapeutic approaches also will be described by Cord Blood Registry and Vet-Stem. This will provide an opportunity to learn about somatic stem cell sources and veterinary applications of cellular materials in regenerative medicine. The subject is so important to the region’s biotech scene, that the organizers have arranged a free, one day symposium on April 5 devoted to Stem Cells. More information about that special focus meeting is available at www.bio-sa.org... BioSouthWest 2006

Same Genes May Underlie Alcohol and Nicotine Co-Abuse

2006-03-17T12:46:00.000-07:00

Vulnerability to both alcohol and nicotine abuse may be influenced by the same genetic factor, according to a recent study supported by the National Institute on Alcohol Abuse and Alcoholism (NIAAA), part of the National Institutes of Health (NIH).

In the study, two genetically distinct kinds of rat — one an innately heavy-drinking strain bred to prefer alcohol (“P” rats), the other strain bred to not prefer alcohol (“NP” rats) — learned to give themselves nicotine injections by pressing a lever. Researchers found that P rats took more than twice as much nicotine as NP rats. Their findings were reported recently in the Journal of Neuroscience.

"Our findings suggest that the genetic factor underlying the high alcohol consumption seen in P rats may also contribute to their affinity for nicotine," said lead author A.D. Lê, Ph.D., a NIAAA-supported researcher at Toronto's Centre for Addiction and Mental Health and University of Toronto.

Researchers have known for some time that people who smoke are more likely to drink alcohol than non-smokers. Similarly, smoking is three times more common in people with alcoholism than in the general population. Since previous studies have also determined that genetics plays an important role in both alcohol and nicotine addictions, researchers have hypothesized that the same gene or genes may influence the co-abuse of these substances.

Investigating this hypothesis in human studies is stymied by the possibility that alcohol use leads to nicotine use, and vice versa. However, in the current study, researchers showed that the P rats’ affinity for nicotine could be demonstrated before the animals were ever exposed to alcohol.

P rats were also found to be more vulnerable to nicotine relapse than NP rats. Researchers withheld nicotine from the rats until their lever pressing occurred infrequently. Then, both P and NP rats were given a single nicotine injection. P rats, but not NP rats, resumed pressing the lever previously associated with nicotine infusions.

The researchers also showed that the P rats’ apparent genetic vulnerability to alcohol and nicotine does not appear to extend to other drugs of abuse. When P and NP rats learned to press a lever to receive cocaine, each group took about the same amount of that drug. The authors note that the lack of a difference in cocaine self-administration indicates that the difference between P and NP rats in nicotine self-administration is not due to a general “reward deficit” in NP rats... alcohol nicotine gene

Gene Influences Antidepressant Response

2006-03-16T20:02:00.003-07:00

Whether depressed patients will respond to an antidepressant depends, in part, on which version of a gene they inherit, a study led by scientists at the National Institutes of Health (NIH) has discovered. Having two copies of one version of a gene that codes for a component of the brain’s mood-regulating system increased the odds of a favorable response to an antidepressant by up to 18 percent, compared to having two copies of the other, more common version.

Since the less common version was over 6 times more prevalent in white than in black patients — and fewer blacks responded — the researchers suggest that the gene may help to explain racial differences in the outcome of antidepressant treatment. The findings also add to evidence that the component, a receptor for the chemical messenger serotonin, plays a pivotal role in the mechanism of antidepressant action.

The study, authored by National Institute of Mental Health (NIMH) researchers Francis J. McMahon, M.D., Silvia Buervenich, Ph.D., and Husseini Manji, M.D., along with collaborators at several other institutions, was posted online March 8 and will appear in the May, 2006 American Journal of Human Genetics.

“This discovery brings us closer to the day when clinicians will be able to offer treatment options and medications that are tailored and personalized to be optimally effective for individual patients,” said NIH Director Elias A. Zerhouni, M.D.

However, the findings cannot yet guide treatment decisions... gene antidepressant interaction

Arizona Biomedical Collaborative building groundbreaking day

2006-03-16T16:19:00.000-07:00

The UA and ASU will break ground today on the Arizona Biomedical Collaborative building, which will anchor a research complex in downtown Phoenix alongside TGen and the UA's College of Medicine expansion.

The Arizona Biomedical Collaborative, or ABC, building will sit between the renovated Phoenix Union High School buildings that will form the core of the UA College of Medicine's Phoenix campus and the Translational Genomics Institute, or TGen. The $17.2 million, 85,600-square-foot building is scheduled to be finished in April 2007.
"It's a fascinating combination of different structures for different purposes, but it's just the start," said Dr. Keith Joiner, dean of the College of Medicine. "We think the excitement that will be generated by all these will be very catalytic to getting the support to getting the rest of this biomedical campus built out."
Joiner said the collaboration is the wave of the future for the state's biomedical enterprise. "Research that crosses institutions and integrates institutions is what we need to do," he said.

The 9 a.m. groundbreaking ceremony will include UA President Peter Likins, ASU President Michael Crow, Arizona Board of Regents President Christina Palacios, Gov. Janet Napolitano and Phoenix Mayor Phil Gordon.

"Things are on schedule for every part of this equation," Joiner said. "The development of the curriculum, the hiring of the faculty, the arrangements for all of the ancillary services — are all moving on a very rapid but appropriate pace."
The ABC project is the first building that will be shared by the University of Arizona and Arizona State University and is the first public research building in the city of Phoenix. Funding came as part of $440 million the Legislature approved in 2003 for new research facilities at the state's three universities... Arizona Biomedical Collaborative

Old-World Primates Evolved Color Vision to Better See Each Other Blush, Study Reveals

2006-03-15T20:53:00.000-07:00

Your emotions can easily be read by others when you blush--at least by others familiar with your skin color. What's more, the blood rushing out of your face when you're terrified is just as telling. And when it comes to our evolutionary cousins the chimpanzees, they not only can see color changes in each other's faces, but in each other's rumps as well.

Now, a team of California Institute of Technology researchers has published a paper suggesting that we primates evolved our particular brand of color vision so that we could subtly discriminate slight changes in skin tone due to blushing and blanching. The work may answer a long-standing question about why trichromat vision (that is, color via three cone receptors) evolved in the first place in primates.

"For a hundred years, we've thought that color vision was for finding the right fruit to eat when it was ripe," says Mark Changizi, a theoretical neurobiologist and postdoctoral researcher at Caltech. "But if you look at the variety of diets of all the primates having trichromat vision, the evidence is not overwhelming."

Reporting in the current issue of the journal Biology Letters, Changizi and his coauthors show that our color cones are optimized to be sensitive to subtle changes in skin tone due to varying amounts of oxygenated hemoglobin in the blood.

The spectral sensitivity of the color cones is somewhat odd, Changizi says. Bees, for example, have four color cones that are evenly spread across the visible spectrum, with the high-frequency end extending into the ultraviolet. Birds have three color cones that are also evenly distributed in the visible spectrum.

The old-world primates, by contrast, have an "S" cone at about 440 nanometers (the wavelength of visible light roughly corresponding to blue light), an "M" cone sensitive at slightly less than 550 nanometers, and an "L" cone sensitive at slightly above 550 nanometers.

"This seems like a bad idea to have two cones so close together," Changizi says. "But it turns out that the closeness of the M and L cone sensitivities allows for an additional dimension of sensitivity to spectral modulation. Also, their spacing maximizes sensitivity for discriminating variations in blood oxygen saturation." As a result, a very slight lowering or rising of the oxygen in the blood is easily discriminated by any primate with this type of cone arrangement... evolution of color vision

Researchers simulate complete structure of virus–on computer

2006-03-15T09:24:00.000-07:00

When Boeing and Airbus developed their latest aircraft, the companies’ engineers designed and tested them on a computer long before the planes were built. Biologists are catching on. They’ve just completed the first computer simulation of an entire life form – a virus.

In their quest to study life, biologists apply engineering knowledge somewhat differently: They “reverse engineer” life forms, test fly them in the computer, and see if they work in silico the way they do in vivo. This technique previously had been employed for small pieces of living cells, such as proteins, but not for an entire life form until now.

The accomplishment, performed by computational biologists at the University of Illinois at Urbana-Champaign and crystallographers at the University of California at Irvine, is detailed in the March issue of the journal Structure.

Deeper understanding of the mechanistic properties of viruses, the researchers say, could not only contribute to improvements in public health, but also in the creation of artificial nanomachines made of capsids – a small protein shell that contains a viral building plan, a genome, in the form of DNA or RNA.

Viruses are incredibly tiny and extremely primitive life forms that cause myriad diseases. Biologists often refer to them as particles rather than organisms. Viruses hijack a biological cell and make it produce many new viruses from a single original. They’ve evolved elaborate mechanisms of cell infection, proliferation and departure from the host when it bursts from viral overcrowding.

For their first attempt to reverse engineer a life form in a computer program, computational biologists selected the satellite tobacco mosaic virus because of its simplicity and small size.

The satellite virus they chose is a spherical RNA sub-viral agent that is so small and simple that it can only proliferate in a cell already hijacked by a helper virus – in this case the tobacco mosaic virus that is a serious threat to tomato plants.

A computer program was used to reverse engineer the dynamics of all atoms making up the virus and a small drop of salt water surrounding it. The virus and water contain more than a million atoms altogether.

The necessary calculation was done at Illinois on one of the world’s largest and fastest computers operated by the National Center for Supercomputing Applications. The computer simulations provided an unprecedented view into the dynamics of the virus.

“The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,” said co-author Peter Freddolino, a doctoral student in biophysics and computational biology at Illinois. “Nevertheless, they elucidated the key physical properties of the viral particle as well as providing crucial information on its assembly.”... virus simulation

genetically modified mosquitoes stop dengue virus replicating

2006-03-15T09:17:00.000-07:00

Mosquitoes can be genetically modified to resist being infected by the virus that causes dengue fever, say researchers.

It is the first time that scientists have bred mosquitoes that not only resist 'type 2' dengue virus — the most prevalent strain — but also pass this resistance on to their offspring.

Dengue fever is spread through the bite of the Aedes aegypti mosquito. Each year, the virus kills about 20,000 of the 50 million people it infects across the developing world.

The researchers say that releasing the genetically modified (GM) mosquitoes could help prevent people from catching the disease as the mosquitoes would no longer be able to transmit the virus.

They add, though, that much more research is needed before this can happen.

The team, led by Ken Olson of Colorado State University in the United States, published their findings yesterday (13 March) in Proceedings of the National Academy of Sciences.

Olson and colleagues modified Aedes aegypti mosquitoes to trigger a mechanism that destroys the virus when it enters their midgut.

If the approach could be reproduced in wild mosquitoes, the incidence of dengue fever in humans could be reduced as fewer insects would transmit the virus... genetically modified mosquitos

NHGRI Announces New Sequencing Targets

2006-03-15T09:12:00.000-07:00

Comprehensive Strategy Seeks to Identify Structural Variation in Human Genome

Bethesda, Maryland — The National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), today announced its latest round of sequencing targets, with an emphasis on enhancing the understanding of how human genes function and how genomic differences between individuals influence the risk of health and disease.

The National Advisory Council for Human Genome Research, which is a federally chartered committee that advises NHGRI on program priorities and goals, recently approved three plans to specify the targets as part of its comprehensive strategy for NHGRI’s Large-Scale Sequencing Research Network

“The goal of our sequencing program is to build the most powerful toolbox possible for advancing human health. By identifying and seeking to fill crucial gaps in our knowledge, these new sequencing plans represent yet another important step in that direction,” said NHGRI Director Francis S. Collins, M.D., Ph.D.

The plan given the highest priority is a project to identify structural variations in the human genome, which will characterize the most common types of structural variation in human DNA. The effort will use 48 human DNA samples donated for the recently completed International HapMap Project, which produced a comprehensive catalog of human genetic variation, or haplotypes, designed to speed the search for genes involved in common diseases. The HapMap identified neighborhoods of tiny changes in DNA — known as single nucleotide polymorphisms (SNPs) — that can be involved in human disease. The structural variation effort will seek to identify instances where larger segments of DNA have been deleted, duplicated or rearranged — all of which can cause disease by disrupting the structure and function of genes.

A recent analysis has shown that these large-scale structural variations are much more common than previously appreciated. In fact, the genomes of any two humans are thought to differ by several hundred insertions, deletions and inversions.

The second plan will add DNA sequence to existing draft sequences of a number of primate species and add additional sequence information in regions of high biological interest within those genomes. The increased coverage — a high-density genome sequence — will allow for an even better understanding of the factors contributing to the evolution of the human genome. The primates chosen for this “index species” effort are rhesus macacque (Macaca mulatta), marmoset (Callithrix jacchus) and orangutan (Pongo pygmaeus). In the future, NHGRI intends to add other organisms to the list of index species for which high-density genome sequences are desirable... new sequencing targets

Being Positive about Selection

2006-03-14T10:01:00.000-07:00

How has language developed in humans and what genetic changes underlie our unique cognitive abilities? Accounts of positive selection that lead to such abilities in humans fascinate us because of the insight they provide into our own evolution, and into the many genetic differences that distinguish us from other apes. The genes that became fixed in our lineage as a result of positive selection are, after all, the ones that make us human. But understanding which gene, or what proportion of a genome, is being driven to fixation by natural selection is of more fundamental biological importance because it can tell us about speciation and the very nature of adaptation.

Relatively recent advances in genomic sequencing and analysis tools have resulted in an explosion of papers on this topic. And as editors of a journal aiming to publish major advances in a field, we face the challenge of identifying standards of excellence in the face of this increasing interest. But the papers vary across many dimensions: they are based on different types of data in a variety of systems and taxa, they use increasingly sophisticated methods, and they address different questions—from targeting disease to understanding the nature of selection and reproductive isolation. Recognizing an advance in this rapidly changing field, where the quality and availability of data also differ substantially, is like trying to catch a moving target.

Detecting Selection

Most genomic regions are thought to be evolving neutrally; that is, they accumulate mutations (by random genetic drift) that do not influence the fitness of the organism. The traditional measure of whether a protein-coding gene deviates from this and is under positive selection is the relative rate at which nonsynonymous (amino acid–changing) and synonymous (silent) mutations are fixed in a population [1,2]—the Ka/Ks ratio... detecting selection

I started a new blog about nanotechnology

2006-03-13T17:16:00.000-07:00

Like I said in the title, my new blog is about nanotechnology. I find the area very interesting and ever evolving like biotechnology. In fact both fields have so much information to share that yet another interdisciplenary science has been created; called 'nanobiotechnology'. Hopefully I'll be updating it every day. I also will try to post a 'Nano Image of the Day' every now and then.

http://usnanotechnology.blogspot.com/

Biotech progress report for Arizona - part 2

2006-03-13T12:54:00.000-07:00

According to the Flinn Foundation's Arizona Bioscience Roadmap, there are four main strategies the state needs to focus on to develop a strong bioscience hub. Here are those strategies and how Arizona fared in the first quarter of 2006.
Strategy 1: Build research infrastructure

* Arizona's business leadership groups file papers with the state to create Science Foundation Arizona, a nonprofit entity that would build and strengthen the state's medical, scientific and engineering programs. SFA will be supported financially by the business community and led by Greater Phoenix Leadership, Southern Arizona Leadership Council and Flagstaff 40.

* Legislation to create a public/private fund to strengthen scientific research advances in the Arizona House of Representatives. The bill would establish the Arizona 21st Century Fund by providing $150 million over five years to be matched by private funds. The legislation builds upon a concept proposed by Gov. Janet Napolitano in her State of the State Address, and has evolved through support of legislators.

* The Virginia G. Piper Charitable Trust commits $50 million over the next five years to attract world leaders in the development of personalized medicine.

* Valley philanthropist Jerry Bisgrove, chairman of the Stardust Charitable Group, pledges $100 million over the next four years to advance the biosciences. The funds, administered through Science Foundation Arizona, would support research, attraction of internationally recognized scientists, creation of early-stage tech firms and related activities.

* A "virtual coalition" of statewide business and science leaders forms to help carry out the recommendations of Arizona's Bioscience Roadmap, the state's long-term plan to become competitive in the biosciences. The partnership involves groups from three categories... continue

Strategy 2: Build critical mass

Strategy 3: Enhance business environment

Strategy 4: Prepare work force, educate citizens

Biotech Progress Report for Arizona - part 1

Researchers Discover a Unique Molecular Profile for Lung Cancer

2006-03-13T12:52:00.000-07:00

A team of researchers has found that the expression pattern of certain microRNAs, or miRNAs, may predict tumor aggressiveness in some patients with lung cancer. These findings indicate that miRNAs may represent a new class of diagnostic and prognostic tools for lung cancer. The study is a collaboration among researchers at The Ohio State University Comprehensive Cancer Center, Columbus, Ohio; the Jikei University School of Medicine, Tokyo, Japan; National Cancer Center Research Institute, Tokyo, Japan; and the Center for Cancer Research at the National Cancer Institute (NCI), which is part of the National Institutes of Health. The study results appear in the March 13, 2006, issue of Cancer Cell*.

miRNAs are small segments of genetic material called ribonucleic acid, or RNA, and are thought to control gene expression. Their actions could change the expression of cancer-related genes within a cell and lead to malignancies.

The researchers identified two miRNAs — has-mir-155 and has-let-7a-2 — that could be used as prognostic indicators in patients with adenocarcinoma, a malignancy of the mucous glands in the lungs. High levels of has-mir-155 or low levels of has-let-7a-2 were associated with poor prognosis. Specifically, overexpression of has-mir-155, or the signalling of the miRNA to change the amount of a protein produced, was the most significant indicator of this prognosis, independent of tumor stage. Although these miRNAs have been identified in other cancers, this is the first evidence linking has-mir-155 to lung cancer.

A tumor with an overexpression of has-mir-155 or reduced expression of has-let-7a-2 would indicate the need for aggressive chemotherapy or radiation treatments. Other tumors that do not show high has-mir-155 or low has-let-7a-2 levels are less aggressive, and those patients might not require more therapy... NIH

Vaccines 'may block many cancers'

2006-03-13T12:45:00.000-07:00

Anti-viral vaccines have the potential to prevent one in ten cases of cancer in Britain, and as many as 25% in the developing world, a report says.

The Cancer Research UK study estimates there are more than 1.8 million new cases of virus-associated cancer world-wide each year.

The charity says just a handful of viruses are to blame.

It says greater investment in new vaccines could be a highly productive way to combat cancer.

Cancers linked to infection with particular viruses include:

* Cervix
* Stomach
* Liver
* Nasopharyngeal carcinoma (nasal passages)
* Lymphomas
* Leukaemia

The report stresses that only a small proportion of people infected with viruses linked to cancer go on to develop the disease.

However, it estimates that as many as 18% of new cases of cancer each year are linked to viral infections.

Lead researcher Professor Alan Rickinson, from the University of Birmingham, said: "Studying the association between infectious agents and human cancers is extremely important because, in such cases, infection represents one defined link in the chain of events leading to cancer development.

"Knowing this helps us to trace other links in the chain and to understand how the whole chain fits together.

"More importantly, if we can break the chain by preventing the infection through vaccination, then we can prevent the cancer developing."

Vaccine development is most well advanced in the case of cervical cancer, which is largely caused by infection with the human papilloma virus (HPV)... vaccines against cancer

Most human-chimp differences due to gene regulation--not genes

2006-03-12T12:22:00.000-07:00

The vast differences between humans and chimpanzees are due more to changes in gene regulation than differences in individual genes themselves, researchers from Yale, the University of Chicago, and the Hall Institute in Parkville, Victoria, Australia, argue in the March 9, 2006, issue of the journal Nature.

The scientists provide powerful new evidence for a 30-year-old theory, proposed in a classic paper from Mary-Claire King and Allan Wilson of Berkeley. That 1975 paper documented the 99-percent similarity of genes from humans and chimps and suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes could produce the wide anatomic and behavioral differences between the two.

Using novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously, this study shows that as humans diverged from their ape ancestors in the last five million years, genes for transcription factors--which control the expression of other genes--were four times as likely to have changed their own expression patterns as the genes they regulate.

Because they influence the activity of many "downstream" genetic targets, small changes in the expression of these regulatory genes can have an enormous impact.

"When we looked at gene expression, we found fairly small changes in 65 million years of the macaque, orangutan, and chimpanzee evolution," said study author Yoav Gilad, PhD, assistant professor of human genetics at the University of Chicago, "followed by rapid change, along the five million years of the human lineage, that was concentrated on these specific groups of genes. This rapid evolution in transcription factors occurred only in humans."... human chimp gene difference

Largest Study of Human INTERACTOME Reveals A Novel Way To Find Disease Targets

2006-03-11T13:55:00.000-07:00

Discoveries made during the first large-scale analysis of interactions between proteins in our cells hold promise for identifying new genes involved in genetic diseases, according to researchers at Johns Hopkins and the Institute of Bioinformatics (IOB) in Bangalore.

The findings, reported in the March issue of Nature Genetics, were made using a database of more than 25,000 protein-protein interactions compiled by the Hopkins-IOB team. The result is believed to be the most detailed human "interactome" yet describing the interplay of proteins that occur in cells during health and disease.

"Genes are important because they are the blueprints for proteins, but proteins are where the action is in human life and health," says Akhilesh Pandey, M.D., Ph.D., an assistant professor at the Institute of Genetic Medicine and the departments of Biological Chemistry, Oncology and Pathology at The Johns Hopkins University School of Medicine. "This ability to find links between sets of proteins involved in different genetic disorders offers a novel approach for more rapidly identifying new candidate genes involved in human diseases," he says.

The analysis included interactions among 1,077 genes coding for proteins linked to 3,133 diseases, the researchers report. Significantly, it showed that proteins encoded by genes that are mutated in inherited disorders were likely to interact with proteins already known to cause similar disorders. In addition, the researchers disproved the long-held belief among scientists that the relative importance of a specific protein is always reflected by the number of other proteins it interacts with in the cell... read

NYU Scientists Identify Key Factor in How Fruit Fly Color Receptor Cells Randomly "Decide" Their Type

2006-03-11T13:49:00.000-07:00

Biologists at New York University have identified a key factor that enables photoreceptor cells to decide their color sensitivity. The findings, which were uncovered by researchers in Professor Claude Desplan’s laboratory in NYU’s Center for Developmental Genetics, were published in the March 9th issue of the journal Nature.

The researchers used the fruit fly Drosophila as a genetic model system to study stochastic events like color sensitivity in photoreceptor cells. The eye of the fly contains some 800 optical units, called ommatidia. Each ommatidium contains six outer and two inner photoreceptors (R7 and R8); the inner receptors detect color, like cone cells in human eyes. Approximately 30 percent of the ommatidia are named “pale,” with sensitivity to blue light, and about 70 percent are called “yellow,” with sensitivity to green light. This ratio of 30 to 70 appears in a large number of diverse species of flies. However, these receptors are stochastically (or randomly) distributed.

Desplan, the corresponding author of the article, said, “The key question we explored was how each individual R7 and R8 receptor ‘decides’ to be either ‘pale’ or ‘yellow,’ and how this ‘decision’ contributes to the stochastic distribution of each type in the mosaic of color photoreceptors in the fruit flies’ eyes.”... fruit fly color receptor

U.S. firm gets Toshiba DNA chip license

2006-03-11T13:44:00.000-07:00

Toshiba Corp. said Friday it has signed a licensing agreement with U.S. firm Antara BioSciences Inc. to transfer its expertise on compact, low-cost DNA chips and DNA diagnostic equipment.

Antara will use the deal to develop similar products it aims to sell under its own brand in the United States after obtaining approval from the U.S. Food and Drug Administration.

Toshiba claims the accord with Antara is the first step toward establishing its proprietary technology for genetic diagnoses as a standard in the U.S.

A DNA chip consists of numerous nucleotide sequences attached to a substrate that serves as a probe to identify whether a test sample contains a particular DNA sequence.

Most existing chips are based on a technology that uses a laser to irradiate a sample and then measures the resulting fluorescence.

But the method requires large equipment and tends to be costly.

The Toshiba technology, which the company calls electrochemical detection, uses smaller machinery with a simplified, easy-to-operate mechanism. It also enhances testing accuracy and lowers costs, Toshiba said.

Antara BioSciences was established in December by Eurus Genomics, a Tokyo-based biotechnology equipment maker, to enter in vitro diagnostic services in the U.S.

The latest agreement with Toshiba covers the technology applied in in vitro diagnoses of diseases in humans... Toshiba DNA chip

Genetic disorders on the rise for India

2006-03-11T13:25:00.000-07:00

Genetic disorders are "enormous" in rural India and proper therapy for genetic problems is the need of the hour, Dr L Singh, Director of Centre for Cellular and Molecular Biology, Hyderabad, said.

Inaugurating a one-day Indo-Australian symposim on "Pharmacogenomics" here today,he said 5,000 genetic disorders have been detected in the country and changing lifestyles have been found to be the main cause for genetic diseases.

Variation in a particular gene or genes might influence a person's susceptibility to certain health problems, he said.

"Clinical practice as far as treating genetic disorders is concerned, would shift from the reactive to preventive mode," and DNA technology would also become cheaper in future, Singh said.

Dr Sheel Nuna,Director of Australian Education International (AEI), said the Australian Prime Minister during his recent visit to India had announced USD 20 million fund for joint research activities in science and technology including biotechnology and genomics. The government of India has also announced a matching grant for this. This seed fund would be utilised for joint research projects and scholarships, Singh said.

USD five million would be spent during the next five years, starting from June this year, for short time research which is expected to benefit about 500 scholars, he said. About 400 participants from India and Australia participated in the symposium... genetic disorders increase

Stardust donates $7.5M to Arizona bioscience research efforts

2006-03-10T11:09:00.000-07:00

As if pledging a donation of $100 million toward Arizona's bioscience effort isn't enough, The Stardust Foundation is donating $7.5 million to several local powerhouses to further research efforts.

Scottsdale Healthcare is getting $5 million, Translational Genomics Research Institute, TGen, is getting $1.5 million, while the Southwest Autism Research and Resource Center is getting $1 million.

Scottsdale Healthcare will use the money for cancer research and treatment at its Virginia G. Piper Cancer Center. TGen will use the money to fund research in bipolar disease and to help expand its overall infrastructure, including computational resources.

SARRC will fund the Bisgrove Autism Research Center, naming the center after Stardust's founder, Jerry Bisgrove.

"Arizona's effort toward building the necessary momentum to support a thriving biosciences community has reached a tipping point, and the moment to act is now," said TGen President and Scientific Director, Dr. Jeffrey Trent. "Support from the Stardust Foundation complements existing efforts, thereby accelerating TGen's mission to develop earlier diagnostics and smarter treatments, as well as foster collaborations between TGen and its many partners, including Scottsdale Healthcare and SARRC."

This most recent funding from Stardust comes just after Bisgrove offered to pump $100 million into the state's biotech sector if the Arizona Legislature approves $150 million in state funding for bioscience... stardust donate Arizona bioscience

Family may provide evolution clue

2006-03-10T09:22:00.000-07:00

Five siblings from Turkey who walk on all fours could provide science with an insight into human evolution, researchers have said.

The four sisters and one brother could yield clues to why our ancestors made the transition from four-legged to two-legged animals, says a UK expert.

But Professor Nicholas Humphrey rejects the idea that there is a "gene" for bipedalism, or upright walking.

A BBC documentary about the family will be shown on Friday 17 March.

Professor Humphrey, from the London School of Economics (LSE), says that our own species' transition to walking on two feet must have been a more complex process that involved many changes to the skeleton and to the human genetic make-up.

However, a German group says a genetic abnormality does seem to be involved in the siblings' gait... evolution clue from quadrupeds

Many human genes evolved recently

2006-03-08T10:30:00.000-07:00

Human genes involved in metabolism, skin pigmentation, brain function and reproduction have evolved in response to recent environmental changes, according to a new study of natural selection in the human genome.

Researchers at the University of Chicago, US, developed a statistical test to find genomic regions that evolution has favoured over the last 15,000 years or so – when modern humans dealt with the end of the last ice age, the beginning of agriculture, and increased population densities.

Many of the 700 genes the researchers identified – especially those involved in smelling, fertility, and reproduction – are also suspected of having undergone natural selection during the divergence of humans and chimpanzees millions of years ago.

But some of the newly identified genes fall into categories not previously known to be targets of selection in the human lineage, such as those involved in metabolism of carbohydrates and fatty acids.

Milk lovers
“It’s reasonable to suspect that a lot of these are adaptations in response to new diets and agriculture,” says team member Jonathan Pritchard.

For example, gene variants that improve the digestion of lactose have become more common, presumably since the domestication of cattle provided a ready source of milk. And in some Europeans, genes giving a lighter skin have increased in frequency, as populations have moved north to regions where there is less sunlight to generate vitamin D... recent human evolution

Genetic Evidence that Humans Have Pushed Orang-utans to the Brink of Extinction

2006-03-08T08:34:00.000-07:00

Humans' capacity to alter the environment has grown exponentially over the past century, challenging other species to adapt to a transfigured landscape. Over some 15,000 plants and animals face extinction, the overwhelming majority threatened by increasingly fragmented, polluted, and deteriorating habitats. These forces are most acute in Africa and Asia, where 25% of all primate species are threatened. Chimpanzees, bonobos, orang-utans, and gorillas could vanish from the wild completely within a matter of decades.

In Africa, deforestation, illegal hunting, and disease outbreaks are decimating chimp, bonobo, and gorilla populations. Orang-utans, the only non-African great ape, face similar threats, compounded by agricultural conversion of logged forests. But because orang-utans spend most of their time in trees and avoid open spaces, they may suffer most from deforestation. A new study by Benoit Goossens, Lounès Chikhi, Michael Bruford, and their colleagues shows that the case for orang-utans is in fact even more desperate than previously believed. Using computer simulations and the largest genetic dataset ever collected from wild orangutans, the authors build up a picture of alarming—and very recent—declines of orang-utan populations of over 95%.

Orang-utans, Malaysian for “man of the forest,” once ranged from Indonesia to southern China and northeastern India, but now struggle to survive in isolated forest patches in northern Sumatra and Borneo. Over 66% of the Sumatra orang-utan population was killed between 1993 and 2000; 33% of the Borneo population may have succumbed to drought and fire between 1996 and 1997 alone. When a 1987 study estimated that over 20,000 orang-utans persisted in Sabah, Malaysia, in the 1980s, it was challenged as too optimistic... genetic evidence orang-utan extinction

Insys moving to Arizona

2006-03-08T08:31:00.000-07:00

Insys Therapeutics, a Chicago-based biotechnology firm that specializes in rapid development and commercialization of drugs, said Tuesday it plans to move its corporate headquarters and research facilities to the Valley, creating 30 jobs within three to four years.

But the exact location in the Valley has not been determined and will depend on the company finding “wet lab” space to conduct its research, economic development officials said.

Because Insys, founded in 2002, is still in the startup stage, public funds may be needed to build research space for the company, said Barry Broome, president of the Greater Phoenix Economic Partnership, a private/public economic development group.

He said officials in Chandler and Surprise have expressed interest in developing lab space that could host the company, and a private developer also is planning biotech space in Tempe. “But private developers are usually more interested in companies that are publicly traded,” Broome said. “A company like this could take five to seven years to emerge. It’s going to need some type of philanthropic support — either public investment or a foundation... insys moving to AZ

Coffee-Gene Interaction Raises Heart Attack Risk

2006-03-08T08:27:00.000-07:00

...Caffeine is "the most widely consumed stimulant in the world" and has been implicated in the development of such cardiovascular diseases as acute MI, the authors noted.

But coffee contains a range of other chemicals and is associated with other lifestyle factors that cloud the link between consumed caffeine and unwanted cardiovascular outcomes, the researchers wrote.

They noted also that 95% of consumed caffeine is metabolized in the liver by cytochrome P450 1A2 (CYP1A2), which varies greatly in terms of activity among individuals. Specifically, a substitution - dubbed CYP1A2*1F -- in the CYP1A2 gene decreases its activity and carriers of the allele, whether homo- or heterozygous, are called "slow" metabolizers of caffeine.

By contrast, carriers of another variant -- CYP1A2*1A -- are called "fast" metabolizers of the stimulant, Dr. El-Sohemy and colleagues noted.... coffee gene interaction

Sex Chromosome Genes Influence Aggression And Maternal Behavior, Say Researchers

2006-03-07T08:42:00.000-07:00

It has been well documented that, across human cultures and in most mammals, males are usually more aggressive and less nurturing than females. It’s simple to blame male hormones, like testosterone, for male behavior such as aggression. But maybe it’s in our genes, too.

Indeed such social behavior also has a genetic basis, according to new research on mice by neuroscientists at the University of Virginia Health System. “The differences in sex chromosomes, XX versus XY, are also responsible for differences in adult behavior,” explained Emilie Rissman, PhD, a professor of biochemistry and molecular genetics at UVa, who studied aggression and maternal behavior in genetically engineered mice. “Sex chromosome genes may not be the whole story that determines how aggressive or motherly we are, but they are a partof it.”

Rissman’s work is published in the Feb. 22 issue of The Journal of Neuroscience, found online at www.jneurosci.org. Co-authors on the paper are scientists at the University of California Los Angeles and the National Institute for Medical Research in London, England.

Using mouse models, Rissman and the research team uncoupled the testis-determining gene Sry on the male Y chromosome from other sex chromosome genes. The presence of Sry leads to the development of the testes and high levels of androgens in males, which is partly responsible for aggression. Sry was deleted from the Y chromosome and replaced by a transgenic copy... sex chromosomes genes

A Map of Recent Positive Selection in the Human Genome

2006-03-07T08:38:00.000-07:00

Within the past 100,000 years, Homo sapiens left Africa in search of new opportunities, likely crossing paths with H. erectus in Asia and H. neanderthalensis in Europe. These early pioneers encountered unfamiliar climates, habitats, and food sources (not to mention alien human species). Then, after adjusting to a major climate change following the last ice age, they underwent a dramatic lifestyle switch, from hunting and gathering to agriculture—a change that brought crowded living conditions and new infections. All these radical changes likely precipitated significant genetic adaptations, with selection favoring genotypes most suited to the novel conditions. Indeed, recent studies have found evidence of strong selection on new gene variants reflecting adaptations to disease (conferring resistance to malaria) and dietary changes (lactose tolerance).

In a new study, Benjamin Voight, Sridhar Kudaravalli, Jonathan Pritchard, and their colleagues take a global approach to search for such signals across the genome and characterize the types of gene variants, or alleles, targeted by selection. Analyzing variants called single nucleotide polymorphisms (SNPs) in three populations—one sampled from Africa; one, a combined sample of Japanese and Chinese individuals from Asia; and one from Europe—they found widespread signals of recent positive selection in all three populations. These signals highlight the types of biological processes that have been targeted by selection during the evolution of modern humans.

Voight et al. based their analysis on data recently collected by the HapMap Project, a repository of the SNPs that researchers use to identify genetic variants involved in human health and disease risk. Humans differ by just 0.1% at the nucleotide level, but these polymorphisms and the linked loci they are inherited with (called haplotypes) contain a wealth of clues to our evolutionary history.

The authors analyzed about 800,000 SNPs from 309 individuals, looking for genomic regions where strong selection has pushed new alleles to intermediate frequency. While these polymorphisms could become fixed (widespread in the population) or remain as SNPs, they likely reflect recent adaptations. To systematically detect this type of signal across the genome, they developed a new statistical scoring method (called integrated haplotype score, or iHS) that builds on an existing test for positive selection... recent positive selection in humans

Newly discovered killer cell fights cancer

2006-03-06T08:10:00.000-07:00

A mouse immune cell that plays dual roles as both assassin and messenger, normally the job of two separate cells, has been discovered by an international team of researchers from the United States and France. The discovery has triggered a race among scientists to find a human equivalent of the multitasking cell, which could one day be a target for therapies that seek out and destroy cancer.

"In the same way that intelligence and law enforcement agencies can face deadly threats together instead of separately, this one cell combines the ability to kill foreign pathogens and distribute information about that experience," says Drew Pardoll, M.D., Ph.D., the Seraph Professor of Oncology at the Johns Hopkins Kimmel Cancer Center.

"We think this hybrid cell speeds up immune reactions and makes the system more efficient," adds Pardoll, whose findings are reported in the February issue of Nature Medicine.

The Hopkins investigators speculate that the hybrid, dubbed "IKDC" for interferon-producing killer dendritic cell, has been missed by cancer biologists because it is rare, making up one-tenth of cells in the spleen with similar features, such as other dendritic cells, according to Frank Housseau, Ph.D., research associate at Hopkins' Kimmel Cancer Center and member of Pardoll's immunology laboratory... cell fight cancer

Eye genes identified as blindness risk

2006-03-06T08:07:00.000-07:00

Just two genes are responsible for almost three-quarters of the world's most common causes of blindness, a new study has suggested.

The research, conducted by scientists at the Columbia University Medical Center, has identified Factor H and Factor B as the two genes which play a role in the development of almost three out of four cases of age-related macular degeneration (AMD).

AMD causes blindness in millions of elderly people around the world and is marked by a progressive loss of central vision due to the deterioration of the macula – a part of the retina responsible for fine vision.

The Factor H gene is responsible for controlling the levels of a protein which helps to shut down an immune response to infection in the eye after its elimination.

People with a variant of Factor H are less able to control the inflammation, which could lead to AMD in their later years... eye genes causing blindness

Genetic background to ravages of obesity

2006-03-06T07:58:00.000-07:00

Why do some overweight people stay healthy (apart from possible musculo-skeletal disorders) while obesity in other individuals leads to complications like diabetes and cardiovascular disease?

The explanation lies in the genes. Scientists at the Department of Clinical Sciences at Lund University in Malmo, Sweden , have identified a gene that exists in a special variant in most overweight people, a variant that makes fatty acids "leak" into the blood stream, where they don't belong.

Fat is constantly being metabolized by the body-being produced, broken down, and rebuilt. Adiponutrin is a protein that takes part in this process. But overweight people often have a variant of the adiponutrin gene that causes the amounts of this protein to be lower than normal.

"Adiponutrin is supposed to constitute a kind of 'corset' that keeps fat in its place in fatty tissue. If the protein doesn't do its job after a sugar-rich meal, fatty acids leak into the blood instead. The high content of fat in the blood then affects the cardiovascular system, the liver, muscles, and pancreas," explains Associate Professor Martin Ridderstrale... genetic background to obesity

Variations in Genes Can Influence the Risk of Developing Age-Related Macular Degeneration and Other Disease Such as Cancer

2006-03-06T07:55:00.000-07:00

A team of researchers has determined that variations in certain genes involved in fighting infection can successfully predict the risk of developing age-related macular degeneration (AMD), the leading cause of blindness in white Americans over the age of 60. The team*, led by Bert Gold, Ph.D., and Michael Dean, Ph.D., of the National Cancer Institute (NCI), part of the National Institutes of Health (NIH), identified a genetic variant that is associated with an increased risk of developing AMD. They also found two genetic variants that protect against developing this disease. Study results appear online March 5, 2006 in Nature Genetics**.

The genes analyzed in this study — Complement Factor B (BF) and Complement Component 2 (C2) — contain the instructions to make proteins that activate the body’s immune defense against microbial infections. These defense responses are part of a system called the complement pathways. These pathways involve numerous proteins in the blood that work in association with the body’s immune cells and antibodies to destroy bacteria, viruses or fungi invading the body. Some complement proteins can stimulate inflammation, the redness and swelling that result in tissues when they are infected. ... gene variation macular degeneration

Why We Have Sex: It's Cleansing

2006-03-04T10:29:00.000-07:00

Scientists have long wondered why organisms bother with sexual reproduction. It makes a whole lot more sense to just have a bunch of females that can clone themselves, which is how asexual reproduction works.

Turns out sex might have evolved as a way to concentrate lots of harmful mutations into individual organisms so they could be easily weeded out by natural selection, a new computer model suggests.

The classic explanation for the onset of whoopee, about 1 billion years ago, is that it provides a way for organisms to swap and shuffle genes and to create offspring with new gene combinations that might survive if the environment suddenly changes.

But some scientists think this isn't enough of a justification to outweigh the many costs of getting together to make little ones. Just ask any single person—sexual organisms have to spend valuable time and resources finding and attracting mates.

If all organisms were like starfishes and cacti, which just drop pieces of themselves when they want to multiply, reproduction would be a whole lot simpler. There would be no need for elaborate peacock feathers or bird songs; stags wouldn't need antlers; elephant bulls wouldn't have to produce stinky cologne and guys probably wouldn't spend so much money on dates.

Natural cleansing

The new work could help test a hypothesis first proposed nearly 20 years ago, stating that sex evolved as a way to purge harmful mutations from a population. According to this view, the random shuffling of genes through sex will sometimes have the effect of concentrating many harmful mutations into single individuals.

These individuals will be less healthy than their peers, and therefore more likely to be weeded out by natural selection, the thinking goes.

This hypothesis, called the "mutational deterministic hypothesis," is controversial though, because it assumes that single mutations by themselves are only slightly harmful, while a combination of many mutations together is much more damaging. Scientists call this phenomenon "negative epistasis." why we have sex

A new tree of life allows a closer look at the origin of species

2006-03-03T07:47:00.000-07:00

A global evolutionary map reveals new insights into our last common ancestor

In 1870 the German scientist Ernst Haeckel mapped the evolutionary relationships of plants and animals in the first 'tree of life'. Since then scientists have continuously redrawn and expanded the tree adding microorganisms and using modern molecular data, yet, many parts of the tree have remained unclear. Now a group at the European Molecular Biology Laboratory [EMBL] in Heidelberg has developed a computational method that resolves many of the open questions and produced what is likely the most accurate tree ever. The study, which appears in the current issue of the journal Science, gives some intriguing insights into the origins of bacteria and the last common universal ancestor of all life on earth today.

"DNA sequences of complete genomes provide us with a direct record of evolution", says Peer Bork, Associate Coordinator for Structural and Computational Biology at EMBL, whose group carried out the project. "For a long time the overwhelming amount of data [the human genome alone contains enough information to fill 200 telephone books] has made it very difficult to pinpoint the information needed for a high-resolution map of evolution. But our study shows how this challenge can be tackled by combining different computational methods in an automated process."

Bork's lab specialises in the computational analysis of genomes, and recently they applied this expertise to the tree of life. Since all organisms descend from the same ancestor, they share some common genes. Francesca Ciccarelli and Tobias Doerks of Bork's group managed to identify 31 genes with clear relatives in 191 organisms, ranging from bacteria to humans, to reconstruct their relationships... tree of life. also see university of arizona tree of life

Nature, nurture and the risk of depression

2006-03-03T07:43:00.000-07:00

Some people are more than twice as likely to become depressed as others, given similar circumstances, according to landmark research from Brain Sciences UNSW.

The paper, which has just been published in the British Journal of Psychiatry, has found more than a fifth of the population has a genetic predisposition to depression, in response to a series of stressful life events.

Brain Sciences UNSW represents researchers from the University of New South Wales (UNSW) and its affiliated research institutes and teaching hospitals including the Prince of Wales Medical Research Institute, Black Dog Institute, Garvan Institute of Medical Research, St Vincent's Hospital and Prince of Wales Hospital.

The researchers based their findings on DNA samples of a group of 127 people who have been monitored for over 25 years for depression onset and major life events. Forty-two percent met criteria for lifetime major depression.

"We have been following a group of school teachers who graduated in 1978," said the lead author of the paper, UNSW Associate Professor of Psychiatry Kay Wilhelm, who is based at St Vincent's Hospital in Sydney. "We've been catching up with them every five years since, to see if there has been any onset of depression and if there have been any major life events."

"There is an 80 percent chance that those with the genetic predisposition will become depressed, if there are three or more negative life events in a year," said the geneticist on the paper, Professor Peter Schofield, who is Director of the Prince of Wales Medical Research Institute (POWMRI).

"This contrasts with some people who have genetic resilience against depression," said Professor Schofield. "Even in similar situations, there's only a 30 percent chance of them becoming depressed."

There are three different genetic types in the population.

* 21 percent of people have the genotype that predisposes them to depression
* 26 percent of people have the genotype with resilience to depression
* 53 percent of people have a mix of the two genotypes

The research also showed there was a 'tipping point' in regards to environmental factors... continue

Combined, Genes and Environment Affect Health More Than They Do Alone

2006-03-03T07:36:00.000-07:00

Both nature and nurture -- genetic makeup and the environment experienced through life -- combine to influence health and well-being, Duke University Medical Center researchers and their colleagues have determined in four new studies. The researchers showed that people's genes play a key role in how they respond both biologically and psychologically to stress in their environment.

The researchers presented four studies that examine genetics and the environment on Thursday, March 2, 2006, as part of a symposium organized by Duke researchers at the American Psychosomatic Society annual meeting in Denver. The studies were conducted at Vrije Universiteit in Holland, the Medical College of Georgia and Duke. The studies were funded by the National Institute on Aging and the National Heart Lung and Blood Institute.

Two studies from Duke evaluated effects of a particular mutation in the gene that makes monoamine oxidase-A (MAOA-uVNTR), an enzyme responsible for breaking down serotonin as well as other neurotransmitters in the brain. One form of this mutation causes the gene to make more of the enzyme, while the other form results in less production of enzyme.

Neurotransmitters are chemical signals by which one neuron triggers a nerve impulse in a neighbor. Thus, neurotransmitters are fundamentally responsible for all brain function, and subtle changes in their level or activity can profoundly affect not only brain function but physiological function influenced by the brain... read

UCR researchers design chip that can improve citrus varieties

2006-03-02T08:13:00.000-07:00

UC Riverside researchers, in partnership with Affymetrix, Inc., have designed a chip – the GeneChip® Citrus Genome Array – that can improve citrus varieties and suggest ways to better manage them. By helping determine which genes are turned on in a tissue of citrus – genes that are associated with taste, acidic content and disease, for example – the chip provides information useful to researchers for rectifying existing problems and making improvements to the fruit.

The citrus array will be used to develop new diagnostic tools for the improvement of citrus agriculture and post-harvest fruit handling, as well as to understand mechanisms underlying citrus diseases. Researchers will study traits pertinent to the citrus industry such as easy peeling, seedlessness, flavor components, pest and disease control, nutritional characteristics, and reproductive development.

"The citrus array helps us quickly examine a certain trait in citrus," said Mikeal Roose, a professor of genetics in the Department of Botany and Plant Sciences at UCR and a leader of the three-year research project. "For a trait posing a problem for the consumer, such as an undesirable flavor, we can identify genes associated with the trait and target these for correction to improve the flavor. The chip also helps us address citrus diseases by helping us see what happens in cells when a citrus plant is under attack from a virus. And with this chip we can better understand what happens at the cellular level when oranges are put in cold storage after they are harvested, leading eventually to better methods of storage that improve fruit flavor."

Manufactured by Affymetrix, Inc., the GeneChip® Citrus Genome Array is made up of a glass wafer on to which nearly one million different pieces of citrus DNA are deposited on a grid or microarray using methods similar to those used to produce computer chips. The glass wafer is encased in a plastic container somewhat smaller than the size of a credit card.

To use the chip, researchers purify total RNA (which reflects the genes expressed in the tissue) from plant tissue, make a copy of these molecules with a chemical tag added, and then "wash" the chip with the RNA sample. If a gene is being expressed in the tissue, its corresponding RNA will be present and bind to the complementary DNA sequences on the chip. The locations of the bound RNA have a visible signal because of the tag, rather like bright and dim pixels on a computer screen. Analysis of which pieces of DNA on the chip have signals indicates which genes are expressed in the tissue... citrus gene chip