суббота, 29 октября 2011 г.

DNA Conclusive Yet Still Controversial, Carnegie Mellon Professor Says

Although the odds that DNA evidence found at a crime scene will match by chance the DNA of a person who was not there are infinitesimal, controversy continues about DNA identification and its use in criminal investigations, says Carnegie Mellon University Statistics Professor Kathryn Roeder. Roeder will present a historical overview of the use of DNA identification on Tuesday, April 25, during the Annual Symposia of the National Academy of Sciences in Washington, D.C.



Almost 28,000 cases nationwide have been prosecuted with help from the FBI's data bank of DNA profiles, while at least 170 people have seen their convictions overturned on appeal thanks to DNA evidence. Nonetheless, the use of DNA evidence in appeals has been impeded by political considerations and legal uncertainties, according to Roeder. "After all other legal avenues have been tried, the hope of any innocent person is that biological evidence from their cases still exists and can be subjected to DNA testing. But DNA's value to free the wrongfully convicted can be attained only if political leaders allow its full application," Roeder said. "Thousands currently await the evaluation of their cases."



In the early phases, technical disputes among scientists impeded the use of DNA evidence, Roeder said. One of the earliest controversies to erupt over DNA testing was the magnitude of genetic diversity among people of different ancestry.



Some controversy remains concerning the so-called "cold hit" technique, in which investigators search a DNA database to find a match of DNA found at a crime scene and then collect other evidence to build their case -- as opposed to first identifying a suspect through other evidence and then using DNA to confirm their case. Some critics claimed that this practice could snag an innocent person, but Roeder has demonstrated through her own research that the likelihood of a false hit are miniscule -- in one case, for example, it was about 1 in 26 quintillion, a probability so slight it needn't be shared with juries, Roeder said.



"The jury can't handle such small numbers. We would do them a service to simply tell them it matches or it doesn't match," Roeder said.



Roeder began her career as a biologist, and much of her current research is focused on using statistical tools to understand the workings of the human genome and the nature of inherited diseases. She is a member of the Bioinformatics and Statistics Genetics Group, which includes researchers in the departments of Statistics and Biological Sciences at Carnegie Mellon, and the departments of Psychiatry and Human Genetics at the University of Pittsburgh. The group's primary research goal is to develop statistical tools for finding associations between patterns of genetic variation and complex disease.







Contact: Jonathan Potts

Carnegie Mellon University

среда, 26 октября 2011 г.

Genome Connects The Dots Between Amphimedon, Animal Descendants

The simple sponge can reveal much about life on Earth. Researchers who have sequenced the genome of one Down Under inhabitant are learning just how common those roots are.



In a paper published online this week in the journal Nature, Rice University's Nicholas Putnam is among a group of scientists who have established a draft genome sequence for Amphimedon queenslandica, a sponge found off the coast of Australia. The genome is helping evolutionary biologists connect the dots as they look for DNA sequences shared by metazoans, or multicelled animals.



Sponges are an ancient group, with fossils dating back at least 650 million years. They are thought to have been the first group of animals to branch from all the others. Therefore, genes shared by sponges and other animals must have been present in the common ancestor of all metazoans. This ancestor would have evolved mechanisms to coordinate cell division, growth, specialization, adhesion and death; this suggests that early sponges already had a developmental set of tools similar to those in metazoans today, said Putnam, an assistant professor of ecology and evolutionary biology.



"What's exciting is the new things we're learning about animal evolution," said Putnam, who got involved with the project while working at the Department of Energy's Joint Genome Institute in 2006. "For example, sponges have embryos, and having the genome helps us look at how they develop and make specific connections to developmental pathways in other animals.



"It's the kind of thing that will lead to a much clearer understanding of what the very first metazoans looked like," he said.



That distant ancestor may well have looked like a sponge. For the paper, Putnam helped compare Amphimedon's draft genome with 13 other complete animal genomes, including a selection of invertebrates, as well as a choanoflagellate. The researchers wrote of a "striking conservation of gene structure and genome organization" that is common to all. "We can now say that the large-scale patterns of genome organization we've seen conserved in other animal groups come from the very root of the animal tree," Putnam said.



The challenge ahead is learning what they do. "The focus of my research is to understand whether patterns that have been around for a billion years have some particular functions -- or if they're hanging around because not enough time has gone by to erase them."



What's missing is also interesting, he said. The ancestral patterns of genome organization common to other creatures is absent from certain arthropods -- invertebrates that include the likes of centipedes and lobsters -- and nematodes. "If the missing pattern is neutral, you'd say that somewhere along the history of those groups, the rate of (evolutionary) change sped up enough to break the connection," Putnam said. "If it's functional, then somehow those groups overcame whatever constraint is on it in other lineages."



Also puzzling is that while Amphimedon shares key developmental genes with a diverse set of metazoans, its basic structure hasn't changed in 600 million years. Given the same roots, researchers wonder why it didn't evolve more radically, and they are working to identify the differences that gave rise to, say, nerve cells in other creatures but not sponges.



Unlocking the basic mechanisms of multicellularity may also help researchers understand what happens when those mechanisms go wrong and lead to cancer and autoimmune disorders.



Notes:

The paper's senior authors are Daniel Rokhsar of the University of California, Berkeley, and Bernard Degnan of the University of Queensland in Australia.

The work was funded by the Australian Research Council, the Department of Energy Joint Genome Institute, Harvey Karp, the National Science Foundation, the National Institutes of Health/National Human Genome Research Institute, the University of Queensland Postdoctoral Fellowship, the Sars International Center for Marine Molecular Biology, Deutsche Forschungsgemeinschaft, Agricultural and Natural Resources/University of California, the French National Center for Scientific Research, the Gordon and Betty Moore Foundation and Richard Melmon.



Source:

David Ruth

Rice University

воскресенье, 23 октября 2011 г.

Innovative Research Grant From Stand Up To Cancer Goes To UNC Lineberger Scientist

Angelique Whitehurst, PhD, assistant professor of pharmacology and a member of UNC Lineberger Comprehensive Cancer Center, has been awarded one of 13 Innovative Research Grants from Stand Up to Cancer, the scientific partner of the American Association of Cancer Research.



The grants were announced during an event at the American Association for Cancer Research (AACR) 102nd Annual Meeting 2011.



SU2C's Innovative Research Grants Program, which made its first round of 13 grants in December 2009, was designed specifically to support work that incorporates new ideas and new approaches to solve critical problems in cancer research.



These innovative projects are characterized as "high-risk" because they challenge existing paradigms, and because in order to receive a grant, the applicants were not required - as they would be by most conventional funding mechanisms - to have already conducted a portion of the research resulting in an established base of evidence. If successful, the projects have the potential for "high-reward" in terms of saving lives.



Whitehurst will use the grant to study how genes, otherwise required only for human reproduction, contribute to tumor cell survival. She will evaluate these genes to determine which are most critical for tumor survival and how they support growth of tumor cells. Ultimately her work will present new therapeutic targets that will selectively destroy tumor cells and leave normal tissue unharmed.



Whitehurst earned her bachelor's degree in biochemistry and chemistry from Virginia Polytechnic Institute and he doctorate in cell and molecular biology from the UT Southwestern Medical Center where she also completed her postdoctoral fellowship in cell biology before joining the UNC faculty in 2009.



Source:

Dianne Shaw

University of North Carolina School of Medicine

четверг, 20 октября 2011 г.

Einstein Researchers Take The Pulse Of A Gene In Living Cells

Scientists at the Albert Einstein College of Medicine of Yeshiva University have observed for the first time that gene expression can occur in the form of discrete "pulses" of gene activity. The researchers used pioneering microscopy techniques, developed by Dr. Robert Singer and colleagues at Einstein, that for the first time allow scientists to directly watch the behavior of a single gene in real time. Their findings appeared in the current issue of Current Biology.



When a gene is expressed or "turned on," genetic information is transferred from DNA into RNA. This process, known as transcription, is crucial for translating the gene's message into a functional protein. Diseases such as cancer can result when genes turn on at the improper time or in the wrong part of the body.



Researchers customarily use microarrays (also known as "gene chips") to assess gene expression in tumors and other tissues. But with millions of cells involved, microarrays reflect only "average" gene expression. Just how a gene is transcribed in a single cell--continuously, intermittently or some other way--has largely been a mystery.



Now, in observing a gene that plays a major role in how an organism develops, the Einstein researchers observed a phenomenon that until now has been indirectly observed and only in bacteria: pulses of transcription that turn on and off at irregular intervals. Dr. Singer and his co-workers used a fluorescent marker that sticks to the gene only when it is active. Under a microscope, this fluorescent marker appears when the gene turns on, then disappears (gene "off") and then appears again (gene "on").



The focus of the study was a gene important in the life cycle of the social amoeba Dictyostelium, thousands of which sometimes aggregate into a single slug-like mass. This developmental gene plays a major role in transforming the "slug" into a stalk-like structure called a fruiting body, which releases new amoebae.



"The pulsing we observed in this gene would allow it to very precisely regulate development," says Dr. Singer, the study's senior author and professor and co-chair of the Department of Anatomy & Structural Biology at Einstein. He likens a gene to a thermostat:



"Heating a home all the time would be wasteful and would overheat the house," he says. "The solution is a thermostat, which injects a little bit of heat when needed and then turns off. Similarly, a cell needs the gene to be turned on--but too much activity at the wrong time can be a problem, so the solution is to have small bursts of activity."



Still to be discovered, says Dr. Singer, is how the pulsing mechanism itself is controlled. In addition, these findings pertain to developmental genes, which are turned on selectively and only in certain tissues. "Other genes--so-called constitutive genes--are regularly expressed by all the cells of an organism," Dr. Singer notes. "We'd like to find out whether these genes pulse as well."



Also involved in this study were Jonathan R. Chubb (now at University of Dundee in the U.K.), Tatjana Trcek and Shailesh M. Shenoy.







Contact: Karen Gardner

Albert Einstein College of Medicine

понедельник, 17 октября 2011 г.

Detection Of DNA On Nanotubes Offers New Sensing, Sequencing Technologies

Researchers at the University of Illinois at Urbana-Champaign who recently reported that DNA-wrapped carbon nanotubes could serve as sensors in living cells now say the tiny tubes can be used to target specific DNA sequences. Potential applications for the new sensors range from rapid detection of hazardous biological agents to simpler and more efficient forensic identification.



In the Jan. 27 issue of the journal Science, chemical and biomolecular engineering professor Michael Strano and his students reported that single-walled carbon nanotubes coated with DNA could be placed in living cells and detect trace amounts of harmful contaminants. In a paper accepted for publication in the journal Nano Letters, and posted on its Web site, the researchers report they have taken the technique a significant step further.



"We have successfully demonstrated the optical detection of selective DNA hybridization on the surface of a nanotube," said Strano, who is also a researcher at the Beckman Institute for Advanced Science and Technology and at the university's Micro and Nanotechnology Laboratory. "This work opens possibilities for new types of nanotube-based sensing and sequencing technologies."



In its natural state, DNA is in the double stranded form, consisting of two complementary strands, each resembling the side of a ladder and having a specific sequence of nucleotide bases as rungs. Hybridization refers to the spontaneous binding of two complementary strands through base pair matching.



By wrapping one strand of DNA around the surface of a carbon nanotube, the researchers can create a sensor that is targeted for a particular piece of complementary DNA. When the complementary DNA then binds to the DNA probe, the nanotube's natural near-infrared fluorescence is shifted slightly, and can readily be detected.



"The optical detection of specific DNA sequences through hybridization with a complementary DNA probe has many potential applications in medicine, microbiology and environmental science," said Esther Jeng, a graduate student at Illinois and the paper's lead author. "For example, this system could be used in genomic screening to detect sequences that encode for genetic disorders, and that are precursors to diseases such as breast cancer."



"Optical detection allows for passive sensing of hybridization, meaning there is no need to pass voltage or current through the system," Jeng said. "Furthermore, optics yield high-resolution signals and require a relatively simple setup. And, because our detection setup is in solution, we can sense in a natural biological environment."







Co-authors of the paper with Strano and Jeng are undergraduate students Joseph Gastala, Anthonie Moll and Amanda Roy. The work was funded by the National Science Foundation.



Contact: James E. Kloeppel, Physical Sciences Editor

kloeppeluiuc.edu

University of Illinois at Urbana-Champaign

пятница, 14 октября 2011 г.

Deciphering The Metabolism Of Sexual Assault Drug

It's a naturally occurring brain chemical with an unwieldy name: 4-hydroxybutyrate (4-HB). Taken by mouth, it can be abused or used as a date-rape drug.



Now, a team of Ohio and Michigan scientists have determined new routes by which 4-HB is metabolized by the body. "This is new and important information," said K. Michael Gibson, professor and chair of biological sciences at Michigan Technological University and a member of the research team. "It may provide new clues on how to counteract the drug's effects, or to enhance its metabolism and decrease toxicity for chronic abusers or victims of sexual assault."



Gibson is co-author with Guo-Fang Zhang and others in the laboratory of Prof. Henri Brunengraber from the Department of Nutrition at Case Western Reserve University School of Medicine of a paper published online by the Journal of Biological Chemistry. Their findings will appear in as "paper of the week" in the the print edition of the weekly journal on Nov. 27, 2009.



4-HB is a derivative of a major brain neurotransmitter in humans and other species. . It occurs naturally in small amounts in the brains of most animals and humans. In a rare genetic metabolic disorder, 4-HB accumulates in extremely high levels, causing significant developmental delays and seizures.



But 4-HB - also called gamma hydroxybutyrate or GHB - is best known and most feared when it is taken orally, because it is a drug that impairs the capacity to exercise judgment, like rohypnol and ketamine hydrochloride. For that reason, it can be used to facilitate acquaintance sexual assault, commonly called date rape.



Analyzing the chemicals produced by the breakdown of 4-HB in mice and rats, Zhang, Gibson and colleagues used very sophisticated mass spectrometry approaches to identify previously unknown enzymes and pathways that appear to act on 4-HB and other similarly structured compounds. They discovered that 4-HB is metabolized by two different chemical mechanisms or pathways. Their discovery of those pathways should open the door for future studies that can identify the enzymes involved in the following steps of the breakdown of 4-HB.



"This work may help to develop new antidotes and treatments for people who have ingested 4-HB, as well as treatment for children with the rare genetic disorder that causes the compound to accumulate in high levels," Gibson said. (For more information on genetic disorders of 4-HB, see pndassoc)



Source: Jennifer Donovan


Michigan Technological University

вторник, 11 октября 2011 г.

Research To Examine Connection Between Cancer, Genetics Among American Indians

The Montana Cancer Institute Foundation and the Confederated Salish and Kootenai Tribal Health Department are collaborating on a new program to determine whether American Indians possess certain genetic traits that could fight cancer or make them respond less effectively to cancer treatments, the Lake County Leader & Advertiser reports.

American Indians coming to Tribal Health for regular appointments will be able to donate blood to the research. Participants each will be given $10 for donating. MCIF President Pat Beatty said that the goal is to collect blood from 1,000 local American Indians. Researchers at the University of Rochester will examine the blood samples to look for nine specific genetic markers. Beatty said similar testing has been conducted among other populations. According to Beatty, "Nobody has ever studied this systematically in Native Americans."

Research among American Indians has been difficult because of a lack of research institutions in areas with large American Indian populations. In addition, American Indians are often resistant to "outsiders performing research experiments," the Leader & Advertiser reports. Beatty said, "Many Native Americans, for good reason, don't have a lot of trust in the medical system. So that means that it's almost impossible for some unknown research project to come out and do something like this." The research project is being run through Tribal Health to help gain participants' trust, the Leader & Advertiser reports (McBride, Lake County Leader & Advertiser, 2/7).


Reprinted with kind permission from kaisernetwork. You can view the entire Kaiser Daily Health Policy Report, search the archives, or sign up for email delivery at kaisernetwork/dailyreports/healthpolicy. The Kaiser Daily Health Policy Report is published for kaisernetwork, a free service of The Henry J. Kaiser Family Foundation© 2005 Advisory Board Company and Kaiser Family Foundation. All rights reserved.