Would you gaze into a genetic crystal ball?

..At 6 foot 4 and with hands the size of oven mitts, Mr. Zentil doesn't scare easily. So with a swab of his inner cheek, a nurse collected cells for an emerging brand of crystal-ball medicine -- a DNA test that promised to reveal his potential health risks and the illnesses that could one day befall the fit father of three... genetic testing

Pacific Symposium on Biocomputing

The eleventh Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2006 at the Grand Wailea Resort on Maui. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. PSB will provide a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. PSB intends to attract a balanced combination of computer scientists and biologists, presenting significant original research, demonstrating computer systems, and facilitating formal and informal discussions on topics of importance to computational biology... more about the event

Genes essential for the proper muscle development identified

Researchers at the University of North Carolina have found two genes that are essential for the proper muscle development, according to a study published in the online edition of the journal Nature Genetics.

The genes are among a recently discovered group of genes known as microRNAs (miRNAs), which were first discovered in worms 12 years ago. Only in the past few years have they become recognized as essential gene regulators in many multicellular organisms, including humans... muscle genes

Researchers Discover Mechanistic Link Between High-Fat Diet and Type 2 Diabetes

Researchers have discovered a molecular link between a high-fat, Western-style diet, and the onset of type 2 diabetes. In studies in mice, the scientists showed that a high-fat diet interferes with a genetic mechanism they discovered that promotes insulin production, resulting in the classic signs of type 2 diabetes.

In an article published in the December 29, 2005, issue of the journal Cell, the researchers report that knocking out a single gene encoding the enzyme GnT-4a glycosyltransferase (GnT-4a ) disrupts insulin production. Importantly, the scientists showed that a high-fat diet suppresses the activity of GnT-4a and leads to type 2 diabetes due to failure of the pancreatic beta cells... Howard Hughes Medical Institute

Molecule from the Sea Kills Cancer Cells

--"PatA" is believed to be the first molecule found to do so in human cells

A natural chemical made by a New Zealand sea sponge exerts its deadly effects on cancer cells by preventing the cells' protein-building machinery from turning on, Johns Hopkins scientists report in the Dec. 9 issue of Molecular Cell.

The chemical's anti-cancer effects have been known since 1991, but this is the first comprehensive report to show how the molecule, known as pateamine A (PatA), stalls the growth of so-called eukaryotic cells -- cells that have membranes and a nucleus... PatA kills cancer

Scientists lift malaria's cloak of invisibility

The world's deadliest malaria parasite, Plasmodium falciparum, sneaks past the human immune system with the help of a wardrobe of invisibility cloaks. If a person's immune cells learn to recognize one of the parasite's many camouflage proteins, the surviving invaders can swap disguises and slip away again to cause more damage. Malaria kills an estimated 2.7 million people annually worldwide, 75 percent of them children in Africa.

Howard Hughes Medical Institute (HHMI) international research scholars in Australia have determined how P. falciparum can turn on one cloaking gene and keep dozens of others silent until each is needed in turn. Their findings, published in the December 28, 2005, issue of Nature, reveal the mechanism of action of the genetic machinery thought to be the key to the parasite's survival.

A DNA sequence near the start of a cloaking gene, known as the gene's promoter, not only turns up production of its protein, but also keeps all other cloaking genes under wraps, according to Alan Cowman and Brendan Crabb, HHMI international research scholars at the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia, and their co-authors. "The promoter is all you need for activation and silencing," Cowman said. "It's the main site of action where everything is happening." malaria genes

Study suggests way to re-energize immune response to chronic viral infection

Findings provide potential strategy to improve therapeutic vaccines, T cell immunotherapy
Like boxers wearied by a 15-round bout, the immune system's CD8 T cells eventually become "exhausted" in their battle against persistent viral infection, and less effective in fighting the disease.

In a study to be published Dec. 28 on the journal Nature's website, researchers at Dana-Farber Cancer Institute and Emory University have traced the problem to a gene that turns off the infection-fighting drive of CD8 T cells in mice. The discovery raises the possibility that CD8 cell exhaustion can be reversed in human patients, reinvigorating the immune system's defenses against chronic viral infections ranging from hepatitis to HIV, the virus that causes AIDS.

"CD8 T cells that have fought viral infections retain a 'memory' of the viruses they've encountered, so they can rapidly respond to new infections from those viruses," says the study's author, Gordon Freeman, PhD, of Dana-Farber. In the case of chronic infection, however, senior author Rafi Ahmed, PhD, of Emory, has shown that memory cells become exhausted and lose the capacity to respond to the virus. Why this occurs, on a molecular level, has been unclear... immune response

India to file case against Monsanto

HYDERABAD: The State Government has decided to file a case against Monsanto Biotech Limited before the Monopolies and Restrictive Trade Practices Commission for collecting an "abnormally high price" from farmers for Bt cottonseed on which it enjoys a monopoly.

M/s Mahyco, Pro-Agro, Raasi and Nuzvid, all seed companies, will be named as respondents in the petition, which will be filed on January 2. Announcing this at a press conference here on Wednesday, Agriculture Minister N. Raghuveera Reddy said Monsanto was paying a procurement price of only Rs 200-250 for 750 gm of Bt cottonseed to its seed-growers but sold the same to cotton-growers at Rs 1,850 per packet of 450 gm. Of this, the company held back Rs. 1,250 against the "trait value" it had assigned to the seeds... Monsanto seeds

Sickle Cell Disease Corrected in Human Models Using Stem Cell-Based Gene Therapy

In a study to be published in the January 2006 issue of Nature Biotechnology, researchers led by a team of scientists at Memorial Sloan-Kettering Cancer Center have devised a novel strategy that uses stem cell-based gene therapy and RNA interference to genetically reverse sickle cell disease (SCD) in human cells. This research is the first to demonstrate a way to genetically correct this debilitating blood disease using RNA interference technology.

To prevent the production of the abnormal hemoglobin that causes sickle cell disease, a viral vector was introduced in cell cultures of patients who have the disease. The vector carried a therapeutic globin gene harboring an embedded small interfering RNA precursor designed to suppress abnormal hemoglobin formation. Tested in adult stem cells from SCD patients, researchers found that the newly formed red blood cells made normal hemoglobin and suppressed production of the sickle shaped hemoglobin typical of the disease... sickle cell gene therapy

Gene Therapy May Help Muscular Dystrophy

STANFORD, Calif., A gene therapy that has shown promise in skin disease and hemophilia might one day be useful for treating muscular dystrophy, says a U.S. study.

Researchers at Stanford University School of Medicine used gene therapy to introduce a healthy copy of the gene dystrophin into mice with a condition that mimics muscular dystrophy.

The dystrophin gene is mutated and as a result produces a defective protein in the roughly 20,000 people in the United States with the most common form of the disease... continue

Genome Trees from Conservation Profiles

The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes... genome trees

Playing a key role at TGen

...Guerra has emerged as a key player in Arizona's ambitious move to become a biomedical hub. Civic leaders are looking to her to excite and rally the community behind their biotech mission. TGen backers are relying on her to bring accountability and sound business practices to the organization, as well as increase its international stature and philanthropic support... TGen

Arizona State and Penn State Scientists Narrow the Time Limits for the Human and Chimpanzee Split

A team of researchers has proposed new limits on the time when the most recent common ancestor of humans and their closest ape relatives - the chimpanzees - lived. Scientists at Arizona State and Penn State Universities have placed the time of this split between 5 and 7 million years ago - a sharper focus than that given by the previous collection of molecular and fossil studies, which have placed the divergence anywhere from 3 to 13 million years ago...

..."No study before has taken into account all of the error involved in estimating time with the molecular-clock method," said Sudhir Kumar, lead author on the report, which was published early online in the journal, Proceedings of the National Academy of Sciences. The team describes its new statistical technique as a "multifactor bootstrap-resampling approach."

"There is considerable interest in knowing when we diverged from our closest relative among animal species," said Kumar, who is director of the Center for Evolutionary Functional Genomics in the Biodesign Institute at Arizona State University . "This divergence time also has considerable importance because it is used to establish how fast genes mutate in humans and to date the historical spread of our species around the globe." Kumar was assisted at Arizona State by research associate Alan Filipski and graduate student Vinod Swarna... continue

New Tamiflu-resistant bird flu cases stir fears

Fears have been raised over more evidence suggesting that the deadly H5N1 avian influenza can mutate into strains resistant to the frontline flu drug Tamiflu.

Two more patients with drug-resistant bird flu have been documented by researchers in Vietnam. The two patients, of eight studied, died from H5N1 influenza A, despite treatment with Tamiflu (oseltamivir) having been started early in one of them. The first case of Tamiflu-resistant bird flu was reported in October 2005 .

Although the case raised alarm, some scientists noted at the time that in becoming resistant to Tamiflu, the H5N1 virus also seemed to become less virulent. In addition, ordinary human flu with such a mutation rarely goes on to cause a new infection in another person.

“Becoming resistant to this class of drugs seems to impose a fitness penalty on the virus,” Frederick Hayden of the University of Virginia, US, an expert in antiviral drugs, told New Scientist at the time.... Tamiflu resistance

A finger in the eye for biometrics

Researchers at Clarkson University appear to have confirmed what a number of recent experiments into the reliability of biometrics have strongly hinted at – in its current form it can be easily, almost routinely, fooled.

With funding from the National Science Funding Foundation (NSF) behind them, as team at the University investigated the “legal and privacy issues raised from broader applications of biometric system technology in airport security, computer access, or immigration.”

The major area of enquiry was fingerprint technology. Casts were made of live fingers using kiddie Play-Doh, and the team even went to the extreme of taking fingers from cadavers, all to test how easily the systems could be spoofed. From 60 samples, a shocking false verification rate of 90 percent was achieved.

This rate was reversed when the experiments were conducted again with the addition of a new system developed by the University for detecting real fingerprints using patterns of sweat found on live or real fingers. That still left a false verification rate of 10 percent, however... biometrics

Volunteers sought for biotech research in Phoenix

...Companies that conduct clinical trials are focusing on the growing Valley population as potential subjects for their studies. An estimated 2,000 clinical trials currently are being conducted in the Valley and those numbers are expected to grow within the next decade as research sites continue to expand.

"There are 80,000 clinical trials going on worldwide on any given day," says Linda Mottle, director of a clinical research program at GateWay Community College that debuted in February 2003. "It is expected to increase four- or five-fold in the number of clinical trials within this coming decade. It's a very exciting field, because clinical research is what helps plan how health care is delivered in the future." biotech clinical trials

2006 Arizona Bio Expo

The 2006 Arizona Bio Expo will be on April 4 at the Double Tree in Tucson and organized by the BioIndustry Organization of Southern Arizona (BIO-SA), a
nonprofit trade organization committed to promoting bioindustry in the region through business enablement and community building. For more Info contact David Thorpe, BIO-SA Chairperson, at: David.Thorpe@sanofi-aventis.com

New view of cancer: 'Epigenetic' changes come before mutations

...Cells affected by epigenetic changes look normal under a microscope at low levels of resolution, Feinberg says, "but if you look carefully at the genome, you find there are subtle changes." By tracking these changes, he suggests, doctors potentially could treat people before tumors develop in much the same way as cardiologists prescribe cholesterol-lowering drugs to help prevent heart disease.

Epigenetic changes -- those that don't affect the gene's sequence of DNA but change the gene in other ways -- influence a wide variety of human diseases, including cancer, birth defects and psychiatric conditions. Epigenetic alterations include the turning off or quieting of genes that normally suppress cancer and the turning on of oncogenes to produce proteins that set off malignant behavior...epigenetic changes

Phoenix company Zila shares could double if OraTest is approved, analysts say

...Zila, Inc., an Arizona biotech, began late-stage testing on OraTest, its detection drug for oral cancer, earlier this month. If clinical trials for the drug are successful and if it's approved by the Food and Drug Administration, the company's stock could jump dramatically, analysts say. Zila has a similar product on the market ViziLite, that is considered a precursor to OraTest... Zila Oratest

Fertility Genes Discovered At Rugters - Genetics May Guide New Infertility Therapies

Rutgers geneticists have reported groundbreaking research on the genetics of fertility. They have discovered two genes, aptly named egg-1 and egg-2, required for fertilization to take place. The proteins encoded by these genes are similar to low density lipoprotein (LDL) receptors, known from cholesterol and fat metabolism but never before specifically implicated in fertilization.

One in six couples is experiencing fertility problems worldwide, and people are asking why. This is a question of great medical, social and economic importance - one that cannot be answered until the process of fertilization is more fully understood... fertility genes

Genetic study may help Indian elephants' conservation

The genetic analysis of about 300 Asian elephants by researchers in India and from the US may help to conserve Indian tuskers, scientists say.

Prithiviraj Fernando and Don Melnick of the Center for Environmental Research and Conservation (CERC) of Columbia University and colleagues from the Indian Institute of Science in Bangalore collected dung samples from nearly 300 wild and 30 captive Asian elephants.

The DNA findings showed that the elephants that inhabit the forests in India's northeast are composed of two genetically distinct populations separated by the Brahmaputra river, said a Columbia University release. indian elephant genetics

Biotech progress report for Arizona

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 fourth quarter of 2005.
Strategy 1: Build research infrastructure

* The city of Phoenix offers a $25 million loan to help pay for renovation of the three historic buildings that will house the Phoenix campus of the University of Arizona medical school in partnership with Arizona State University. The funds come from the New Market Tax Program to assist underdeveloped areas.

The city also approved a bond package requiring voter approval that would include $3 million for campus construction costs.... biotech progress of Arizona

Can Most Types Of Cancers Be Prevented?

...For example, her research has revealed a possible hereditary component to nicotine addiction and an inability to quit, showing some smokers receive more pleasure from nicotine than others because of genetic differences in the brain's dopamine reward pathway.

Another process under genetic control that could explain susceptibility is DNA repair capacity. These systems help maintain the integrity of genes by continually fixing the damage that occurs to DNA from exposure to harmful chemicals as well as to the daily assault of cosmic X-rays and UV light. If errors in this repair system occur, DNA damage can result in unstable genes and an increased cancer risk... cancer prevention

Scientists Rebuild Part of Woolly Mammoth's Genome

In a world first, German scientists say they have reconstructed a key sequence in the genome of the woolly mammoth, enabling them to show that the extinct beast's closest modern relative is the Asian elephant.

Reporting online Sunday in Nature, the British science journal, the researchers say they devised a new technique for the feat, teasing out DNA from just 200 milligrams (0.007 of an ounce) of bone found at a mammoths' graveyard in the Siberian permafrost.

Their technique, called multiplex polymerase chain reaction, copied 46 chunks of sequence, which were rearranged to give a picture of the creature's mitochondrial DNA.

The mitochondria are an internal part of a cell that is the cell's power supply. Mitochondrial DNA is handed down through the maternal line, and is a relatively stable genetic sequence -- it changes little from generation to generation, and at a measurable rhythm. This makes mitochondrial DNA a useful "molecular clock" that can be wound backwards into time, to see how a species evolved. By comparing the sequence with that of modern animals, scientists can spot when and where species diverged from their common ancestor... mammoth genome

Valley becoming hotbed of clinical research

More than 2,000 medical studies are under way in Arizona, making the state a breeding ground for new prescription drugs and medical devices.

"You could just about bet any of your major drugs have had clinical trials here," said Linda Mottle, director of the clinical research program at GateWay Community College, which trains technicians to work at research sites.

"Most of the major pharmaceutical companies do multisite national and international clinical trials to assess the safety and efficacy, looking at different populations, ethnicities, culture, and genomic differences," she said.

And Arizona is becoming a more popular state in which to conduct these clinical trials, evidenced by New Jersey-based Covance Inc.'s recent announcement to build a research facility in Chandler and hire 400 employees.

"The key is that Arizona is moving forward in the biosciences in a number of areas," said Jon McGarity, president of the Arizona BioIndustry Association. "Clinical research is one of those key areas." arizona biotech research

NIH uses live viruses for bird flu vaccine

WASHINGTON (AP) — In an isolation ward of a Baltimore hospital, up to 30 volunteers will participate in a bold experiment: A vaccine made with a live version of the most notorious bird flu will be sprayed into their noses.

First, scientists are dripping that vaccine into the tiny nostrils of mice. It doesn't appear harmful — researchers have weakened and genetically altered the virus so that no one should get sick or spread germs — and it protects the animals enough to try in people.

This is essentially FluMist for bird flu, and the hope is that, in the event of a flu pandemic, immunizing people through their noses could provide faster, more effective protection than the troublesome shots — made with a killed virus — the nation now is struggling to produce... bird flu virus vaccine

New Methods Offer Insight into Regulatory DNA

Through the Human Genome Project, the HapMap Project and other efforts, we are beginning to identify genes that are modified in some diseases. More difficult to measure and identify are the regulatory regions in DNA – the ‘managers’ of genes – that control gene activity and might be important in causing disease.

Today, a team led by the Wellcome Trust Sanger Institute, together with colleagues in the USA and Switzerland, provide a measure of just how important regulatory region variation might be in a pilot study based on some 2% of the human genome. As many as 40 of 374 genes showed alteration in genetic activity that could be related to changes in DNA sequence called SNPs.

“We were amazed at the power of this study to detect associations between SNP variations and gene activity,” commented Dr Manolis Dermitzakis, Investigator, Division of Informatics at the Wellcome Trust Sanger Institute. “We were even more amazed at the number of genes affected: more than 10% of our sample – or perhaps 3000 genes across the genome – could be subject to modification of activity in human populations due to common genetic variations...” continue this article here and view the publication here.

Phoenix based Zila starts Phase III OraTest(R) clinical trial

PHOENIX--Dec. 13, 2005--Zila, Inc., (Nasdaq: ZILA), announced that it has begun its Phase III clinical trial for OraTest, its oral cancer detection drug, with the completion of a meeting of the investigators in Phoenix, Arizona. Last week Zila reached an agreement with the United States Food and Drug Administration (FDA), under their Special Protocol Assessment (SPA) process, on the design and size of its new Phase III clinical trial for OraTest.

The investigators received two days of intensive technical training specific to the protocol that will be followed in the clinical trial. The meeting offered an opportunity to review Investigator and Zila responsibilities under Good Clinical Practices (GCPs) and provided training in an electronic data capturing system that will provide a more timely review of enrollment progress. Zila Inc

NIH Funds Two New Biomedical Technology Resource Centers

More Than $18 Million Will Support Development of Image Guided Therapies and Biochemistry Studies

The National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), announced today that $18.2 million will be awarded to create two new biomedical technology resource centers to develop new image guided therapies and to further biochemistry studies of diseases such as alcoholism and cancer.

Brigham and Women’s Hospital of Boston will receive $15 million over five years in a cooperative agreement to establish a national Image Guided Therapy (IGT) Center. The new resource will provide a unique, “one-stop-shopping” research, training, and service center that will develop and make available to scientists and clinicians image processing and display tools; dynamic and adaptive Magnetic Resonance Imaging methods; novel therapy techniques; and image-guided robotics. The funding will allow the IGT Center to expand its range of research areas to include cardiovascular interventions and targeted drug delivery. NIH News

Key gene 'controls skin colour'

A team at Penn State University has found just one tiny change in a key gene plays a major role in determining skin pigmentation.

The finding, published in Science, may help explain why people of European descent have lighter skin than those from Africa.

It is hoped the research may lead to new ways to treat skin cancer.

Potentially, it may also lead to the development of new ways to modify skin colour without damaging it by tanning or using harsh chemical lighteners.

The genetic determination of human skin colour is one of biology's enduring mysteries.

Alterations in some of these genes are associated with disorders such as albinism, which causes very light skin, but also vision problems... skin color gene

Couple tries pre-implantation genetic diagnosis to prevent having haemophiliac baby

...But a new testing method in New Zealand, called pre-implantation genetic diagnosis, or PGD, could mean they will not have to face aborting another haemophiliac fetus.

Instead, the test, used with in vitro fertilisation, IVF, allows embryos to be checked for genetic disorders, including haemophilia. Only those deemed normal are implanted in the woman's uterus.

The Government said yesterday that it would within six months start paying for couples at high risk of having children with serious genetic disorders to have PGD and the associated IVF, which together cost around $12,000... PGD test

Kellogg teams up with Monsanto to reduce trans fats

Cereal giant Kellogg is to reformulate some of its products with a low linolenic soybean oil in an effort to reduce or eliminate trans fatty acids while also minimizing the saturated fat content of the products, the company announced last week.

Kellogg is the first major food manufacturer to announce its use of Monsanto's Vistive low-lin soybeans, though Monsanto said “several other companies are currently also working with Vistive,” but could not reveal which ones.

The move is part of an industry drive to reduce trans fats in food formulations ahead of new legislation in the US that will require food manufacturers to label the trans fat content of their products as from January 1 2006. The new labeling is designed to give consumers the choice to avoid trans fatty acids (TFAs) after a body of scientific evidence has linked these to increased risk of heart disease because they lower HDL (good) cholesterol while raising LDL (bad) cholesterol. Kellogg and Monsanto

Tempe, Arizona Getting Complete Wireless Internet

Tempe, Ariz. — Call it a municipal status symbol in the digital age: a city blanketed by a wireless Internet network, accessible at competitive prices throughout the town's homes, cafes, offices and parks.

Tempe, the Phoenix suburb that is home to Arizona State University, is due to have wireless Internet available for all of its 160,000 residents in February, becoming the first city of its size in the United States to have Wi-Fi throughout.

Tempe officials hope that by making high-speed Internet as accessible as water or electricity across its 65 square kilometres, it will attract more technology and biotech companies — and the young, upwardly mobile employees they bring. tempe wireless internet

Biotechnology and Pharmaceuticals R&D Spending

According to an article in the latest issue of IEEE's Spectrum magazine pharmaceutical and biotechnology sector cut back in R&D spending by 1.1% to $51.7 billion, but it did gain more spots in the top 25 R&D spenders, from four in 2000 to seven this year:

Phizer Inc ----------$6.6 billion
Johnson & Johnson ---$5.2 billion
Novartis AG ---------$4.2 billion
Roche Holding -------$4.2 billion
Merck & Co ----------$3.9 billion
Astrazeneca PLC -----$3.8 billion

...You would expect the life sciences sector to have a high R&D profile. First, drugmakers and biomedical companies are busily creating products for a rapidly growing market spurred on by an aging population. Second, they spend billions to attract still more customers—you can't watch TV for half an hour without seeing two or three drug commercials, with branding ads touting research prowess side by side with those aimed at erectile dysfunction. Third, the merger fever that has gripped Big Pharma over the last few years—Pfizer's acquisitions of Pharmacia and Warner Lambert, Astra's merger with Zeneca, and most recently Sanofi-Synthelabo's hostile takeover of Aventis—has reduced overhead, presumably leaving more money for R&D...

...It could come down to a question of timing. On average, it takes more than a decade to bring a drug to market from the discovery phase, and the NIH puts money into basic research, not commercialization. Given that the NIH funding increases began almost eight years ago, it stands to reason that pharmaceutical and biotechnology firms should be increasing R&D spending to exploit new discoveries and technologies generated by NIH-funded projects. And with the exception of 2004, these firms have increased spending, albeit at a more moderate pace than you might expect... biotech R&D spenders

ASU spin-out company acquired by Agilent Technologies

In a celebratory event held at the Biodesign Institute, Agilent Technologies, Inc., announced it has acquired ASU spin-out company Molecular Imaging Corporation.

The company, which is a leading developer of atomic force microscopes and scanning probe microscope systems, was founded in 1993 by ASU professors Stuart Lindsay and Tianwei Jing. Lindsay now directs the Center for Single Molecule Biophysics at the Biodesign Institute. Jing leads the R&D team at Molecular Imaging.

The company has had a continuous relationship with ASU and Lindsay’s laboratory since then. Because of the strong ties between Molecular Imaging and ASU, Agilent leaders said they have no plans to move Molecular Imaging operations from the Tempe area. Molecular Imaging employees have joined Agilent.

“This is an example of how the research growth strategies put in place by President Michael Crow benefit the Valley’s biotech sector development as well as ASU,” said Lindsay... asu biotech company

Mathematics Used for Discerning Imune Response to Infectious Diseases, Vaccine Development

The National Institutes of Health (NIH) has awarded the University of Pittsburgh School of Medicine a five-year, $9.1 million contract to develop sophisticated mathematical models for investigating how the immune system responds to the pathogens that cause flu, tuberculosis (TB) and tularemia, an especially dangerous infection that some authorities believe could be used as a biological weapon. Such models should help expedite the development of vaccines and therapies against these and other infectious agents and help researchers and public health officials in their efforts to predict or prevent disease outbreaks as well as determine the best courses of treatment... mathematics in immune response

Researchers Publish Dog Genome Sequence; Analysis Sheds Light On Human Disease; Differences Among Canine Breeds

An international team, led by researchers at the Broad Institute of MIT and Harvard, today announced the publication of the genome sequence of the dog. In the Dec. 8 issue of the journal Nature, the researchers present a detailed analysis of the dog genome and describe how the data offer the potential for improving the health of man and man's best friend.

"When compared with the genomes of human and other important organisms, the dog genome provides a powerful tool for identifying genetic factors that contribute to human health and disease," said Francis S. Collins, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), which supported the research. "This milestone is especially gratifying because it will also directly benefit veterinary researchers' efforts to better understand and treat diseases afflicting our loyal canine companions."... dog genome

A perfect virus 'is a weak virus'

Viruses need to make some mistakes when they reproduce in order to infect a person effectively, according to research carried out by a group of US researchers.

They suggest that their findings, published online by Nature this week (5 December), could lead to the development of a new class of antiviral drugs and vaccines to combat infections caused by a type of viruses known as RNA viruses. perfect virus

ASU researchers 'wire' DNA to identify mutations

A team of ASU researchers led by Nongjian Tao and Peiming Zhang has developed a new, breakthrough technique for the detection of DNA mutations.

Their results, published in the journal Proceedings of the National Academy of Sciences, demonstrate for the first time, the possibility of directly identifying these mutations, or single nucleotide polymorphisms (SNPs), by means of measuring the electrical conductance of a single DNA molecule.

SNPs are buried in the 3 billion DNA bases of the human genome. On average, SNPs occur about once in every 1,000 DNA bases, though not every SNP found will necessarily cause a disease mutation. Cataloging these subtle DNA differences among the populace will aid the ongoing quest to understand and prevent disease.

"There is a high demand to track mutations for cancer research or future applications in personalized medicine," said Zhang, an associate research professor of the Center for Single Molecule Biophysics in the Biodesign Institute at ASU. "Currently, the main issue in doing this type of detection is that it is still costly and time consuming." ASU Biodesign

Computer Simulation Shows Buckyballs (C60) Deform DNA

A new study published in December 2005 in Biophysical Journal raises a red flag regarding the safety of buckyballs when dissolved in water. It reports the results of a detailed computer simulation that finds buckyballs bind to the spirals in DNA molecules in an aqueous environment, causing the DNA to deform, potentially interfering with its biological functions and possibly causing long-term negative side effects in people and other living organisms...

...Cummings’ team found that, depending on the form the DNA takes, the 60-carbon-atom (C60) buckyball molecule can lodge in the end of a DNA molecule and break apart important hydrogen bonds within the double helix. They can also stick to the minor grooves on the outside of DNA, causing the DNA molecule to bend significantly to one side. Damage to the DNA molecule is even more pronounced when the molecule is split into two helices, as it does when cells are dividing or when the genes are being accessed to produce proteins needed by the cell... 60-carbon-atom damage DNA

Carnegie Mellon U. transforms DNA microarrays with standard Internet communications tool

A standard Internet protocol that checks errors made during email transmissions has now inspired a revolutionary method to transform DNA microarray analysis, a common technology used to understand gene activation. The new method, which blends experiment and computation, strengthens DNA microarray analysis, according to its Carnegie Mellon University inventor, who is publishing his findings in the December issue of Nature Biotechnology with collaborators at the Hebrew University in Israel.

The innovative method combines a new experimental procedure and a new algorithm to identify gene activation captured by DNA microarray analysis with greater sensitivity and specificity. The work holds great promise for vastly improving research on health and disease, according to Ziv Bar-Joseph, assistant professor of computer science and biological sciences at Carnegie Mellon... DNA microarrays

Humans have ancient genes

The result, according to a new study by scientists at the European Molecular Biology Laboratory (EMBL), is that our species has retained characteristics of a very ancient ancestor that have been lost in more quickly-evolving animals. This overturns a commonly-held view of the nature of genes in the first animals. The work appears in the current issue of the journal Science.

Genes hold the recipes for proteins. The genes of animals usually contain extra bits of DNA sequence, called introns - information which has to be removed as cells create new molecules. The number of introns in genes, however, varies greatly among animals. While humans have many introns in their genes, common animal models such as flies have fewer. From an evolutionary perspective, it was long assumed that the simpler fly genes would be more ancient. The current study reveals the opposite: early animals already had a lot of introns, and quickly-evolving species like insects have lost most of them... ancient genes

Bright path of bioscience for Arizona

Among the many paths our state can follow, one stands out for its ability to attract the brightest minds to work for the benefit of Arizona: biosciences.

This path to a vibrant future became tantalizingly clear in the recently presented "Meds and Eds" report commissioned by the Arizona Board of Regents. The report recognizes Arizona's impressive bioscience strengths in its universities and health care providers, then calls for a collaboration by these entities. In little more than a decade this collaboration, anchored by a medical school brimming with cutting edge research, new cures and treatments, and excellent patient care, can fuel an economic powerhouse of innovation and culture, attracting highly skilled health care professionals and bioscience researchers... bioscience for Arizona

New Nanosensor Uses Quantum Dots to Detect DNA

Using tiny semiconductor crystals, biological probes and a laser, Johns Hopkins University engineers have developed a new method of finding specific sequences of DNA by making them light up beneath a microscope. The researchers, who say the technique will have important uses in medical research, demonstrated its potential in their lab by detecting a sample of DNA containing a mutation linked to ovarian cancer.

The Johns Hopkins team described the new DNA nanosensor in a paper published in the November 2005 issue of the journal Nature Materials.

"Conventional methods of finding and identifying samples of DNA are cumbersome and time-consuming," said Jeff Tza-Huei Wang, senior author of the paper and supervisor of the research team. "This new technique is ultrasensitive, quick and relatively simple. It can be used to look for a particular part of a DNA sequence, as well as for genetic defects and mutations. nanosensor detect DNA

UCLA scientists discover immune response to HIV differs, even in identical twins

In findings illustrating the difficulty of developing an AIDS vaccine, UCLA AIDS Institute researchers report the immune systems in two HIV-positive identical twins responded to the infection in different ways.

Detailed in the Dec. 5 issue of the peer-reviewed Journal of Virology (http://jvi.asm.org), the findings show that the body's defenses against the virus are random rather than genetically determined.

The researchers followed the cases of male twins who were infected shortly after their 1983 births in Los Angeles by blood transfusions administered from the same donor at the same time. Infected with the same strain of the virus, the twins continue to live in the Los Angeles area and grew up exposed to the same environmental forces... continue

Poste Named ASU Regents’ Professor

George Poste, director of the Biodesign Institute and the Del E. Webb Distinguished Professor of Biology, has been named an ASU Regents’ Professor, joining the university’s most prestigious ranks. His selection, along with five other exceptional ASU professors, was ratified Dec. 2 by the Arizona Board of Regents.

Regents’ Professors stand out for their accomplishments in many areas: excellence in teaching, exceptional achievements in research or other creative activities, and national and international distinction in their fields. They serve as advisers to the university president and take on a broader role as consultants and teachers throughout the university.

Poste, who joined ASU in May of 2003, is internationally prominent in several fields, having made contributions to the research, legislative policy and private enterprise. In 2004, he was named "Scientist of the Year" by R&D Magazine in tribute to his incredible past accomplishments and recognition of his leadership in establishing the Biodesign Institute as a confluence of leading edge technologies... george poste

A Salty Tale: New Bacterial Genome Sequenced From Ancient Salterns

...The bacterium is Salinibacter ruber , a bright red, rod-shaped organism. Several years ago, scientists first isolated S. ruber from saltern crystallizer ponds in Alicante and Mallorca , Spain . Although extreme-loving microbes called archaea were known to eke out life in the ponds, scientists were surprised to discover ordinary bacteria also thriving in such a physically demanding environment, at salt concentrations up to 30 percent. How could these microbes—which normally prefer milder environments—thrive in such high salt?

To find out, TIGR researchers Emmanuel Mongodin and Karen Nelson, working with Canadian and Spanish colleagues, set out to sequence S. ruber 's genome. In doing so, the scientists discovered evidence that the resourceful bacterium independently evolved some salt-surviving biochemistry. More surprising, S. ruber apparently also borrowed some genes from neighboring archaeal species, in an unusual example of cross-domain lateral gene transfer... Salinibacter ruber

TGen Interns Take First Place in Prestigious Science Competition

New York, NY, December 5, 2005-The Translational Genomics Research Institute (TGen) today announced that two graduates of the Institute's summer internship program took the top prize at the nation's premier high school science competition, the Siemens Westinghouse Competition in Math, Science and Technology.

Anne Lee, a senior at Phoenix Country Day School in Paradise Valley, and Albert Shieh, a junior at Chaparral High School in Scottsdale, won the $100,000 prize in the team category, which they will share equally, for developing new software that more accurately analyzes genetic data. In addition to the prize, the winners will ring the closing bell at the New York Stock Exchange today.

Grandparents buy babies' stem cells

Parents and grandparents are buying Christmas gift certificates to store babies' stem cells for decades to come.

Growing hype about the future potential of stem cell technology to treat a range of medical problems is driving demand for storage, with a number of companies offering to collect and keep stem cells in umbilical cord blood.

One such company - Smart Cells International - says it has had more than 1,000 inquiries and 50 purchases of "Christmas gift certificates" for stem cell collection from UK customers... continue

Biotech popular in Arizona's high schools

Twenty-seven miles from the Translational Genomics Research Institute sits the new home of Mesa High School's Biotechnology Academy, the state's first intensive high school biotech program.

At Mesa High this year there are more than 100 students in introductory biotechnology and 28 students in the two-year Biotech Academy. Based on this success, Mesa's biotech program could be Arizona's most prominent model, but it is not the only one.

In Chandler, Hamilton High School started a biotech course this year.

In the West Valley, 29 students conduct biotechnology experiments in Peoria High School's state-of-the-art research facility. In Tucson, former pharmacologist Andrew Lettes teaches his first year-long class of Pueblo High School biotech students. arizona biotech

Earliest Bird Had Feet Like Dinosaur, Fossil Shows

A 150-million-year-old fossil of Archaeopteryx, long considered the oldest bird, may put to rest any scientific doubt that dinosaurs—specifically the group of two-legged meat-eaters known as theropods—gave rise to modern birds.

Until recently, the crow-size specimen was housed in a private collection. It is now owned by the Wyoming Dinosaur Center in Thermopolis.

The fossil is the ninth example of Archaeopteryx known to science. (A tenth specimen of a winged dinosaur from a closely related genus also exists.) All ten fossils were found in a limestone deposit near Solnhofen, Germany.

The latest specimen is among the best preserved. It is a slightly broken skeleton in a single slab of pure limestone, showing clear wing- and tail-feather impressions... Archaeopteryx

Poison + Water = Hydrogen

...In a paper published in the November 27 th issue of PLoS Genetics, a research team led by scientists at The Institute for Genomic Research (TIGR) report the determination and analysis of the complete genome sequence of this organism. Isolated from a hot spring on the Russian volcanic island of Kunashir , this microbe lives almost entirely on carbon monoxide. While consuming this normally poisonous gas, the microbe mixes it with water, producing hydrogen gas as waste.

As the world increasingly considers hydrogen as a potential biofuel, technology could benefit from having the genomes of such microbes. “ C. hydrogenoformans is one of the fastest-growing microbes that can convert water and carbon monoxide to hydrogen,” remarks TIGR evolutionary biologist Jonathan Eisen, senior author of the PLoS Genetics study. “So if you're interested in making clean fuels, this microbe makes an excellent starting point.” sequencing hydrogen breathing organism

Scientists unlock solid tumor treatment genetic secrets

A biochemical mechanism that cells use to cope with hypoxia (lack of oxygen) actually cooperates with a less well-known mechanism that helps increase the expression of those hypoxia-sensitive genes, according to investigators at St. Jude Children’s Research Hospital.

The two mechanisms each enable a transcription factor called hypoxia-inducible factor (HIF) to increase expression of genes that the cell uses to respond to the stress of hypoxia. Transcription factors bind to a site on the gene called the promoter and trigger the process that decodes the gene and makes the protein for which that gene codes. HIF binds to and activates many genes that contribute to the survival response of tumors; for example, genes that control biochemical reactions that don’t require oxygen to extract energy from glucose or genes needed to build new blood vessels that bring additional oxygen to hypoxic cells... tumor treatment

Molecular Basis of Human Aging

There are a handful of biological questions that affect all of us directly in everyday life. How are emotions formed, what is the basis for consciousness, and why do we look the way we do? One that strikes particularly close to home is the question of how we age. The sheer complexity of this problem has had many scientists throw up their hands in frustration and most of the postulated theories have been vague and generally have involved ill-defined wear-and-tear mechanisms. But the pursuit of the biological basis of aging has been revitalized within the last decade by studies in yeast, worms, flies, and mice that have firmly established that there indeed exist specific molecular mechanisms that contribute to the aging process. These efforts point to several distinct, likely interrelated, mechanisms, ranging from improper protein metabolism, to alterations of specific signaling pathways, progressive damage due to generation of oxidative free radicals, and increased genome instability.

Although much has been learned about the aging process from simple model organisms, one intuitively suspects that things might be somewhat different when it comes to human aging. So how does one best study the molecular basis of human aging? The answer might be premature aging diseases, or progeroid syndromes. The advantage of these often rare diseases is that they are mostly monogenic and thus experimentally tractable. On the other hand, one should keep in mind that such disorders usually only mimic some of the features of normal aging and it can be difficult to distinguish true aging symptoms from unrelated developmental defects. Regardless, it appears that progeroid syndromes may be legitimately used as model systems to investigate the physiological processes contributing to aging. In fact, the study of some of these diseases has recently brought tantalizing clues as to how we age. One of the most intriguing ones is a possible involvement of structural components of the cell nucleus. Aging and the Cell Nucleus

Know your dog's ancestors, Canine Genomics and Genetics: Running with the Pack

The domestication of the dog from its wolf ancestors is perhaps the most complex genetic experiment in history, and certainly the most extensive. Beginning with the wolf, man has created dog breeds that are hunters or herders, big or small, lean or squat, and independent or loyal. Most breeds were established in the 1800s by dog fanciers, using a small number of founders that featured traits of particular interest. Popular sire effects, population bottlenecks, and strict breeding programs designed to expand populations with desirable traits led to the development of what are now closed breeding populations, with limited phenotypic and genetic heterogeneity, but which are ideal for genetic dissection of complex traits. In this review, we first discuss the advances in mapping and sequencing that accelerated the field in recent years. We then highlight findings of interest related to disease gene mapping and population structure. Finally, we summarize novel results on the genetics of morphologic variation. canine genomics

Darwin's Other Books: “Red” and “Transmutation” Notebooks, “Sketch,” “Essay,” and Natural Selection

Depending on how you count them up, Charles Darwin published just over twenty books in his lifetime. His first—the Journal of Researches, also known as The Voyage of the Beagle was his most famous—until Darwin, pressured by the arrival in 1858 of A. R. Wallace's manuscript on evolution through natural selection, stopped working on his “Big Species Book,” and wrote instead his epochal On the Origin of Species by Means of Natural Selection. Or the Preservation of Favoured Races in the Struggle for Life . In between, and thereafter, Darwin published monographs and specialized narratives on topics as disparate as barnacle taxonomy, coral reef development, and insectivorous plants. Yet it is, of course, the Origin of Species that changed the world, establishing Darwin as one of the great thinkers in Western cultural history.

So much is well-known. Far less appreciated is the fact that Darwin wrote several other books, all on evolution, none of which were published in his lifetime. Together, they form a series that preserves the “evolutionary” history of Darwin's ideas from their very inception to their most mature form—while also revealing the more prosaic development of Darwin's written rhetoric of the Origin of Species. All have been subsequently published, and are now freely available online, constituting the initial components of the Darwin manuscript project page of the American Museum of Natural History Digital Library of Evolution. The Darwin manuscript project complements the museum's exhibition, Darwin, opening 19 November 2005; further analysis of these works can be found in my companion volume to the exhibition. continue this article or buy Darwin's books.

How to Choose What to Sequence Next

After humans, mice, chickens and others what genomes should scientists sequence next? In a paper published today in PLoS Genetics, Fabio Pardi and Nick Goldman of the EMBL-European Bioinformatics Institute present a way to decide. Surprisingly, they show that always choosing the next best single species is just as effective as planning to sequence several genomes in advance.

DNA sequencing has revealed a vast amount of information about biology. But genome sequencing remains expensive and time consuming, so scientists need a strategy to help them select the organisms that will give them the most new information. decide what to sequence

Genetic Key To Growth Of New Arteries Is Identified

Researchers at the San Francisco VA Medical Center have uncovered part of the genetic mechanism that causes new arteries to grow in response to blocked arteries.

A team led by SFVAMC vascular surgeon Rajabrata Sarkar, MD, PhD, has demonstrated in mice that the MMP2 gene is essential for the growth of new arteries when the femoral (leg) artery is blocked.

The team also identified and described, for the first time, the specific DNA sequences of the MMP2 gene that are expressed when new arteries are grown... continue

Monkey Gene Chip May Help Researchers

Researchers studying infectious diseases, such as AIDS, may be able to find answers more quickly thanks to a new tool that lets them see how a Rhesus monkey's 20,000 genes respond.

That tool, called a gene chip or microarray, was developed with the help of researchers at the University of Nebraska Medical Center in roughly half the time and cost of previous gene chips of humans and mice, said John Harding, with the National Center for Research Resources at the National Institutes of Health.

The gene chip for the Rhesus macaque monkey will be especially useful because the genetic code of the monkey is similar to humans, and many experiments cannot be performed on humans because of ethical concerns. monkey gene chip

Designing Chemical Compound Libraries for Drug Discovery

by Dr. Richard M. Casey

Published: December 1, 2005

The design of chemical compound libraries is a highly relevant skill for bioinformaticians involved in drug discovery.

Well-designed chemical compound libraries truly jump-start the search for new drugs. Today, many biopharmaceutical companies search large compound libraries to identify promising leads for potentially marketable drugs. High-throughput screening (HTS) is a technique widely used in the industry to rapidly scan and analyze these libraries. However, a key feature for a successful library search is the strategy used to design the library itself, and whether the design increases the probability of retrieving promising “hits” and potential leads. Consequently, there is now an intense focus on research in compound library design strategies. drug discovery