Many Blood Tests May Soon Be Replaced By Spit Tests

One day soon patients may spit in a cup, instead of bracing for a needle prick, when being tested for cancer, heart disease or diabetes. A major step in that direction is the cataloguing of the "complete" salivary proteome, a set of proteins in human ductal saliva, identified by a consortium of three research teams, according to an article published in the Journal of Proteome Research. Replacing blood draws with saliva tests promises to make disease diagnosis, as well as the tracking of treatment efficacy, less invasive and costly.



Saliva proteomics and diagnostics is part of a nationwide effort to create the first map of every human protein and every protein interaction, as they contribute to health and disease and as they act as markers for disease states. Following instructions encoded by genes, protein "machines" make up the body's organs and regulate its cellular processes. Defining exact protein pathways on a comprehensive scale enables the development of early diagnostic testing and precise drug design. In the current study, researchers sought to determine the "complete" set of proteins secreted by the major salivary glands (parotid, submandibular (SM) and sublingual (SL)). Recent, parallel efforts that mapped the blood (plasma) and tear proteomes allows for useful comparisons of how proteins and potential disease markers are common or unique to different body fluids.



"Past studies established that salivary proteins heal the mouth, amplify the voice, develop the taste buds and kill bacteria and viruses," said James E. Melvin, D.D.S., Ph.D., director of the Center for Oral Biology at the University of Rochester Medical Center, and an author on the paper. "Our work, and the work of our partners, has shown that salivary proteins may represent new tools for tracking disease throughout the body - tools that are potentially easier to monitor in saliva than in blood," said Melvin, who conducts his research at the Eastman Dental Center, in collaboration with the research labs of Mark Sullivan, Ph.D., and Fred K. Hagen, Ph.D.



The National Institute of Dental and Craniofacial Research (NIDCR), part of the National Institutes of Health, funded the current study. The saliva proteome study represents a consortium effort with research teams at The Scripps Research Institute (John R. Yates III), University of Rochester, University of Southern California (Paul Denny), The University of California at San Francisco (Susan J. Fisher) and UC Los Angeles (David T. Wong, Joseph A. Loo).



Not Your Parent's Saliva



To describe the results of the current study, it is important to note that the definition of saliva is evolving. Saliva once referred to everything in oral fluid, including: bacterial waste products, dead cells that had shed from mucous membranes and substances oozing from gum crevices. Among researchers today, however, the term saliva is increasingly reserved for just the salivary gland secretions (ductal saliva). The new definition is significant because of the emerging theory that the mix of proteins in ductal saliva tracks closely with that of blood, making saliva a potential diagnostic stand-in for blood.
















To construct a credible protein list for saliva, the teams used competing techniques both to capture the greatest number of protein candidates for the list and to lend extra credibility to those found using different methodologies. Each team subjected saliva collected from patients to some form of mass spectrometry, which determines the identity of proteins based on measurements of their mass and charge. Saliva was collected from 23 adults of several races and both sexes. Although small, the set of study subjects was large enough to serve as a baseline list for near-future comparisons between healthy people and individuals with major diseases, researchers said.



Using mass spectrometry techniques, three teams at five institutions identified 1,166 proteins in parotid and submandibular/sublingual saliva. The results indicated that more than a third of saliva proteins were found in the blood proteome, as well. Comparison of these proteins against known protein pathways and other proteomes provided a first glimpse of the function of the core proteins. In addition, a number of the salivary proteins were found to match proteins with known roles in Alzheimer's, Huntington's and Parkinson's diseases; breast, colorectal and pancreatic cancer; and type I and II diabetes. Specifically, a majority of the proteins were found to be part of signaling pathways, which is central to the body's response to (and thus diagnosic of) system-wide diseases, researchers said.



Determining the salivary proteome is only the first step toward salivary-based diagnosis and treatment. These findings provide crucial protein information that is already being incorporated into microarray technology, a high-speed test that can determine the levels of multiple proteins, during disease progression. Related work is underway under within the NIH-funded Bioengineering Nanotechnology Initiative to design biochips, nano-scale computer chips packed with salivary protein chains. Protein probes on the chip react with proteins in a saliva sample, say from the mouth of someone with oral cancer, and inform a computer about which proteins are present.



"We believe these projects will dramatically accelerate diagnosis and improve prognosis by treating diseases at the earliest stages," said Mireya GonzГЎlez BegnГ©, D.D.S., Ph.D., research assistant professor of Dentistry in the Center for Oral Biology at the Medical Center. "Researchers have already shown that saliva proteins can be used to detect oral cancer and HIV infection. We think this list will soon expand to include leading causes of death like cancer and heart disease, which, if caught early, are much more likely to be successfully treated."







Source: Greg Williams


University of Rochester Medical Center

Unselfish Molecules May Have Helped Give Birth To The Genetic Material Of Life

One of the biggest questions facing scientists today is how life began. How did non-living molecules come together in that primordial ooze to form the polymers of life? Scientists at the Georgia Institute of Technology have discovered that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix. The research appears in the online early edition of the Proceedings of the National Academy of Sciences beginning March 8, 2010.



"Our hypothesis is that before there were protein enzymes to make DNA and RNA, there were small molecules present on the pre-biotic Earth that helped make these polymers by promoting molecular self-assembly," said Nicholas V. Hud, professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology. "We've found that the molecule ethidium can assist short oligonucleotides in forming long polymers and can also select the structure of the base pairs that hold together two strands of DNA."



One of the biggest problems in getting a polymer to form is that, as it grows, its two ends often react with each other instead of forming longer chains. The problem is known as strand cyclization, but Hud and his team discovered that using a molecule that binds between neighboring base pairs of DNA, known as an intercalator, can bring short pieces of DNA and RNA together in a manner that helps them create much longer molecules.



"If you have the intercalator present, you can get polymers. With no intercalator, it doesn't work, it's that simple," said Hud.



Hud and his team also tested how much influence a midwife molecule might have had on creating DNA's Watson-Crick base pairs (A pairs with T, and G pairs with C). They found that the midwife used could determine the base pairing structure of the polymers that formed. Ethidium was most helpful for forming polymers with Watson-Crick base pairs. Another molecule that they call aza3 made polymers in which each A base is paired with another A.



"In our experiment, we found that the midwife molecules present had a direct effect on the kind of base pairs that formed. We're not saying that ethidium was the original midwife, but we've shown that the principle of a small molecule working as a midwife is sound. In our lab, we're now searching for the identity of a molecule that could have helped make the first genetic polymers, a sort of 'unselfish' molecule that was not part of the first genetic polymers, but was critical to their formation," said Hud.



The work was supported by the National Aeronautics and Space Administration and the National Science Foundation.



Source:

David Terraso

Georgia Institute of Technology

Entire Yeast Genome Mapped By University Of Toronto Scientists

University of Toronto scientists have devised a tool to help understand and predict the state of a cell by successfully mapping all 70,000 nucleosomes in yeast. Nucleosomes wrap DNA before it is transformed into proteins and are critical indicators and regulators of a cell's state.



Led by Corey Nislow, a U of T Assistant Professor with the Banting and Best Department of Medical Research and Department of Molecular Genetics, the team created a complete, three-dimensional map of the yeast genome. This information was fed into a computer to build a software program that can predict where nucleosomes should be. The program worked remarkably well, and its accuracy will only improve with more data.



"When control is lost, cells make inappropriate proteins or divide inappropriately, which is what happens in diseases like cancer," says Nislow, whose team worked closely with U of T Professor Timothy Hughes on the project. "Knowing where nucleosomes are is the first step in identifying what is going on in a cell and what the cell plans to do next, so this initial research could have big implications down the road for early detection of certain diseases."



Scientists can tell by the presence of nucleosomes which genes are actively being converted into protein, and this information can function as an important first clue to disease detection.







The research appeared in the scientific journal Nature Genetics.



Corey Nislow, Lead Author



Source: April Kemick


University of Toronto

While Infecting Humans Tiny Fungi May Reproduce Sexually

A fungus called microsporidia that causes chronic diarrhea in AIDS patients, organ transplant recipients and travelers has been identified as a member of the family of fungi that have been discovered to reproduce sexually. A team at Duke University Medical Center has proven that microsporidia are true fungi and that this species most likely undergoes a form of sexual reproduction during infection of humans and other host animals.



The findings could help develop effective treatments against these common global pathogens and may help explain their most virulent attacks.



"Microsporidian infections are hard to treat because until now we haven't known a lot about this common pathogen," says Soo Chan Lee, Ph.D., lead author and a postdoctoral researcher in the Duke Department of Molecular Genetics and Microbiology. "Up to 50 percent of AIDS patients have microsporidial infections and develop chronic diarrhea. These infections are also detected in patients with traveler's diarrhea, and also in children, organ transplant recipients and the elderly."



Of the 1200 species of microsporidia, more than a dozen infect humans. Their identity had been obscured because these tiny fungi cannot live outside of an infected host cell and they have a small number of genes which are rapidly evolving.



The Duke scientists used two genetic studies to show that microsporidia apparently evolved from sexual fungi and are closely related to the zygomycete fungus in particular.



They found that microsporidia share 33 genes out of 2,000 with zygomycetes. which the microsporidia did not share with other fungi. This genomic signature also shows that microsporidia and zygomycetes likely shared a common ancestor and are more distantly related to other known fungal lineages.



In addition, these two types of fungi have the same sex-locus genes - and in the same order - in their DNA. Other genes involved in sexual reproduction are also present. The findings suggest that microsporidia may have a genetically controlled sexual cycle, and may be undergoing sexual reproduction while they infect the host, Lee said.



Lee said the next step is to explore the sexual reproduction of these species, which may cause more severe (more virulent) infections because they use the host's cellular environment and machinery as a safe haven in which to reproduce.



"These studies resolve the enigma of the evolutionary origins and proper placement of this highly successful group of pathogens, and provide better approaches to their experimental study," said senior author Joseph Heitman, M.D., Ph.D., director of the Center for Microbial Pathogenesis and director of the Duke University Program in Genetics and Genomics.



The team will pursue further studies with Duke genetic researchers Raphael Valdivia, Ph.D., and Alejandro Aballay, Ph.D., using cultured cells and C. elegans, a worm that researchers recently found is a natural host for microsporidia. "Using this roundworm may prove to be a useful way to study microsporidia genetics in a living creature," Heitman said.







This work was published online in the Oct. 30 edition of Current Biology, and was supported by grants from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, and by the Canadian Institutes for Health Research.



Other authors on this study include Nicolas Corradi and Patrick J. Keeling of the Canadian Institute for Advanced Research, Department of Botany, University of British Columbia - Vancouver; Edmond J. Byrnes III of the Duke Department of Molecular Genetics and Microbiology; Santiago Torres-Martinez of the Departamento de Genetica y Microbiologia, Facultad de Biologia, Universidad de Murcia, Spain; and Fred S. Dietrich of Duke Molecular Genetics and Microbiology and the Duke Institute for Genome Sciences and Policy.



Source: Mary Jane Gore


Duke University Medical Center

Models Begin To Unravel How Single DNA Strands Combine

Using computer simulations, a team of University of
Wisconsin-Madison researchers has identified some of the pathways through
which single complementary strands of DNA interact and combine to form the
double helix.



Present in the cells of all living organisms, DNA is composed of two
intertwined strands and contains the genetic "blueprint" through which all
living organisms develop and function. Individual strands consist of
nucleotides, which include a base, a sugar and a phosphate moiety.



Understanding hybridization, the process through which single DNA strands
combine to form a double helix is fundamental to biology and central to
technologies such as DNA microchips or DNA-based nanoscale assembly. The
research by the Wisconsin group begins to unravel how DNA strands come
together and bind to each other, says Juan J. de Pablo, UW-Madison Howard
Curler Distinguished Professor of Chemical and Biological Engineering.



The team published its findings in the Proceedings of the
National Academy of Sciences. In addition to senior author de Pablo, the
group included David C. Schwartz, a UW-Madison professor of chemistry and
genetics, and former postdoctoral research fellow Edward J. Sambriski, now
an assistant professor of chemistry at Delaware Valley College in
Pennsylvania.



The three drew on detailed molecular DNA models developed by de Pablo's
research group to study the reaction pathways through which
double-stranded DNA undergo denaturation, where the molecule uncoils and
separates into single strands, and hybridization, through which
complementary DNA strands bind, or "hybridize." In Watson-Crick base
pairing, A (adenine) pairs with T (thymine), while G (guanine) pairs with
C (cytosine). Reaction pathways are the trajectories single DNA strands
follow to find each other and connect via such complementary pairs.



The researchers studied both random and repetitive base sequences. Random
sequences of the four bases - A, T, G and C - contained little or no
regular repetition. To the researchers' surprise, a couple of bases
located toward the center of the strand associate early in the
hybridization process. The moment they find each other, they bind and the
entire molecule hybridizes rapidly and in a highly organized manner.


Conversely, in repetitive sequences, the bases alternated regularly, and
the group found that these sequences bind through a so-called diffusive
process. "The two strands of DNA somehow find each other, they connect to
each other in no particular order, and then they slide past each other for
a long time until the exact complements find one another in the right
order, and then they hybridize," says de Pablo.



Results of the team's study show that DNA hybridization is very sensitive
to DNA composition, or sequence. "Contrary to what was thought previously,
we found that the actual process by which complementary DNA strands
hybridize is very sensitive to the sequence of the molecules," he says.



Knowledge of how the process occurs could enable researchers to more
strategically design technologies such as gene chips. For example, says de
Pablo, if a researcher wanted to design sequences that bind very rapidly
or with high efficiency, he or she could place certain bases in specific
locations, so that the hybridization reaction could occur faster or more
reliably.



Ultimately, the research could help biologists understand why some
hybridization reactions are faster or more robust than others. "One of the
really exciting things about this work is that the hybridization reaction
between two strands of DNA is really fundamental to life itself," says de
Pablo. "It is the basis for much of biology. And it is amazing to me that,
until now, we knew little of how this reaction actually proceeds."



The National Science Foundation-funded Nanoscale Science and Engineering
Center on Templated Synthesis and Assembly at the Nanoscale at UW-Madison
sponsored the research.




Source
University of Wisconsin-Madison

Newly Discovered Epidermal Growth Factor Receptor Active In Human Pancreatic Cancers

Finally some promising news about pancreatic cancer, one of the most fatal cancers, due to the difficulties of early detection and the lack of effective therapies: Johns Hopkins University pathologist Akhilesh Pandey has identified an epidermal growth factor receptor aberrantly active in approximately a third of the 250 human pancreatic cancers studied.



In a presentation April 18, at Experimental Biology 2009 in New Orleans, Dr. Pandey explained why this finding and related work in his Hopkins laboratory is promising in terms of both a new treatment for a large subset of pancreatic cancers and a potential blood or urine screening tool that might eventually do for pancreatic cancer detection what biomarkers like prostate-specific antigen levels have done for prostate cancer. His presentation was part of the scientific program of the American Society for Investigative Pathology.



Personalized treatment. Phosophorylated epidermal growth factor receptor (pEGFR), the receptor identified by Dr. Pandey, is closely related to HER-2, a growth factor receptor found and used as a drug target in a subset of breast cancers. After he found and profiled the pEGFR activated in the pancreatic cancers, Dr. Pandey realized the same receptor had been found by other researchers to be activated in a subset of lung cancers. And, most promising, an EGFR inhibitor named erlotinib already has been through the long and complex Food and Drug Administration approval process and is in use for treatment of these specific lung cancers.



But would the drug work in pancreatic cancers? Dr. Pandey's group moved from studies of human cell lines to studies in mice in which human pancreatic tumor cells with activated EGFT had been placed. The tumors began growing. But when treated with erlotinib, they began to shrink. Other tumors without activated pECFR showed no response.



The promise - and the challenge - of using pEGFR is that of personalized medicine, says Dr. Pandey. Obviously a growth factor receptor that is activated only in a subset of all pancreatic cancers cannot be a one-size-fits-all target for treatment. Earlier studies in other laboratories and clinical trials already had tried EGF inhibitors as a treatment for pancreatic cancer and concluded that they did not work. When Dr. Pandey's collaborators allowed them to re-examine their samples, they found that the only case in 12 cases that had responded to the EGF inhibitor was the only case with an activated EGF receptor. Dr. Pandey would like to see other researchers go back and re-analyze their data, separating patients with and without the activated receptor, and then determining the success rate. He believes it would tell a different, more hopeful story.



Screening for pancreatic cancer. Dr. Pandey's other goal in his research is to use mass spectrometry to find additional markers of pancreatic cancer in the tumors themselves but also in blood and urine, which would avoid the problems of invasive biopsies. As a first step, his team has gone through the scientific literature to create a compendium of several hundred proteins and genes reported to be overexpressed in pancreatic cancers, making them excellent candidates for further study. The compendium already is being used by a consortium of investigators who are developing antibodies against the 60 most promising targets.



Co-authors of the Experimental Biology study are Hopkins faculty Dr. Antonio Jimeno, Dr. Henrik Molina, Dr. Ralph Hruban, Dr. Anirban Maitra, and Dr. Manuel Hidalgo; and H. C. Harsha, a graduate student in Dr. Pandey's laboratory who is also a member of the Institute of Bioinformatics in Bangalore, India. The research was supported by the Sol Goldman Trust for Pancreatic Cancer Research.



Source:
Sylvia Wrobel


Federation of American Societies for Experimental Biology

Microbial Analysis, Micropatterning Methods Featured In Cold Spring Harbor Protocols

Microbial populations have traditionally been studied in carefully controlled, laboratory-grown cultures. New metagenomic approaches are being developed to study these organisms in environmental or medical samples. The July issue of Cold Spring Harbor Protocols presents a method developed by Holger Daims from the University of Vienna for quantifying populations of microorganisms in a variety of naturally occurring conditions such as plankton samples or biofilms. Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples combines fluorescent in situ hybridization using rRNA-targeted probes with digital image analysis. The results show an organism's "biovolume fraction" in a given sample; this indicates the share of biochemical reaction space occupied by the quantified population and can be more relevant ecologically than absolute cell numbers. The article is freely available on the website for Cold Spring Harbor Protocols.



Micropatterning methods are rapidly becoming standard approaches for investigating cellular behaviors such as growth and migration. Adhesive Micropatterns for Cells: A Microcontact Printing Protocol from Matthieu Piel and colleagues at the Institut Curie offers a simple, fast, and efficient method for generating micropatterns for cellular studies. Employing an elastomeric stamp to print proteins on the substrate of choice, this technique does not require much of the expensive equipment and technical expertise needed for most micropatterning methods, making it easier to implement in biology laboratories. The authors have provided a movie that illustrates the technique step-by-step as part of the protocol. The article is freely accessible on the website for Cold Spring Harbor Protocols.


Source

Cold Spring Harbor Protocols

Team Explores PARIS; Finds A Key To Parkinson's

Johns Hopkins scientists have discovered that PARIS the protein facilitates the most common form of Parkinson's disease (PD), which affects about 1 million older Americans. The findings of their study, published March 4 in Cell, could lead to important new targets for treatment.


Previous research has shown that a protein dubbed parkin protects brain cells by "tagging" certain toxic elements for natural destruction. Mutations in the parkin gene cause rare forms of PD that run in families, but its role remained unclear in sporadic late-onset PD, the prevalence of which is increasing as the population ages.


Using genetically altered mice as well as human brain tissue, the Hopkins team showed that another protein, PARIS, accumulates when the parkin gene is mutated and its protein degrading ability is blocked. Too much toxic PARIS tamps down the manufacture of a protective protein named PGC-1alpha. The less protection afforded to brain cells by this protein, the more they die and the greater the progression of PD.


"Of all the important changes that lead to the death of brain cells as a result of parkin inactivation, our studies show that PARIS is, without a doubt, a key player," says Ted Dawson, M.D., Ph.D., Leonard and Madlyn Abramson Professor in Neurodegenerative Diseases and scientific director of the Johns Hopkins Institute for Cell Engineering.


To pin down the role of the PARIS protein, the researchers first knocked out the parkin gene in embryonic mice. These animals, despite a 20-percent buildup of PARIS compared with wild-type mice, showed no significant change in the levels of the protective PGC-1alpha, and none of the neurodegeneration that is characteristic of PD, which the researchers measured by counting brain cells. In order to bypass the compensation that they suspected was at play in these young mice (which typically live about 2 years), the team next disabled the parkin gene in 8-week-old (adult) mice. By 10 months of age, these animals with the temporal loss of parkin showed three times the amount of PARIS accumulation in brain cells similar to the amount in brain tissue from human patients who had mutations in the parkin gene or sporadic PD. Also, PGC-1alpha levels had decreased and a significant loss of neurons known as neurodegeneration -- had occurred.


"Some might wonder why this same kind of compensation isn't occurring in humans," Dawson says. "Well, it is, but the difference is time. It usually takes us 60 or more years to get the most common form of PD. A body can compensate for only so long and so much. By disabling the gene in the brain cells of adult mice, we accelerated that process and thwarted compensation."


In a further experiment with PARIS, the team created a so-called double knock-out by disabling the gene for PARIS in those same mice in which the gene for parkin already was knocked out. The protective PGC-1alpha levels of these animals which had no parkin or PARIS were rescued, and no neurodegeneration occurred. The team then demonstrated that genetically altered mice with an abundance of PGC-1alpha were protected against the same significant loss of neurons.


When the scientists looked at human brain tissue, they also found evidence that PARIS is dependent on parkin function and a chief regulator of the protective PGC-1alpha. By comparing tissue of patients who died with Parkinson's disease with those who died of other causes, they established that when parkin is shut down and PARIS, the "garbage" protein, accumulates, PGC-1alpha levels drop precipitously and neurons die en masse.


"No one has shown that neurons can be rescued by knocking out any of the other elements that parkin tags for destruction," Dawson says. "The fact that we can prevent parkin-associated brain cell death by blocking PARIS gives a promising new drug target that could someday enable us to slow or stop the progression of PD."


With people living longer, more people are developing this common, debilitating neurological disorder, according to Dawson, noting that one in 100 people are afflicted at the age of 60, and four times that many by the age of 80.


The study was funded by the National Institutes of Health and the Bachmann Strauss Dystonia and Parkinson Foundation.


Authors of the study, in addition to Ted Dawson, are Joo-Ho Shin, Han Seok Ko, Hochul Kang, Yunjong Lee, Yun-Il Lee, Olga Pletinkova, Juan C. Troconso, and Valina L. Dawson, all of Johns Hopkins.


Source: Johns Hopkins Medicine

Enhancer Of Prostate Cancer Risk Located In Gene Desert

A genetic variant implicated in several cancers by genome-wide association studies (GWAS) has been found to drive increased expression of a known oncogene in the prostate.


The study, published July 13th in Genome Research, showcases a new protocol for studying the activity of cancer-risk variants suggested by GWAS studies. The results also underscore the dramatic consequences of small genetic changes even in the vast stretches of DNA, known as "gene deserts," that do not code for proteins.


"This paper shows a way to follow-up on GWAS leads that pointed to these barren areas of the genome," said senior author Marcelo Nobrega, MD, PhD, assistant professor of human genetics and member of the University of Chicago Comprehensive Cancer Center at the University of Chicago Medical Center.


Since the completion of the Human Genome Project in 2000, GWAS projects seeking genetic risk factors for disease have become a popular scientific tool. A population of people with a particular disease is compared to controls without the disease, uncovering genetic variants correlated with increased disease risk.


But the hope that such genetic variants would provide easy targets for novel therapies was initially deflated by an unexpected result. Most of the variants, called single nucleotide polymorphisms or SNPs, associated with disease risk were found not in the sequences encoding proteins, but in the other 98 percent of the genome where the biological role is less clear.


Attention has since turned to short regulatory sequences lying undiscovered as of yet in the "gene deserts." With the power to control expression of faraway genes including when and where they are expressed these regulators could exert dramatic effects.


"There are all kinds of functional DNA sequences that have important biological roles that are not protein-encoding sequences," Nobrega said. "There's every reason to believe that mutations in these non-coding sequences may lead to disease or increase the risk of disease."


But finding those non-coding sequences, much less determining their function, is a challenge. Regulatory sequences are typically around 500 base pairs in length, Nobrega said, dispersed in regions that are millions of base pairs long.


With colleagues Nora Wasserman and Ivy Aneas, Nobrega devised a method of quickly testing gene deserts to find biologically relevant sequences. A gene desert upstream of a known oncogene called MYC was chosen because of several GWAS results implicating the region in different cancers, including prostate. "This is one of strongest genetic signals to prostate cancer that has been identified so far," Nobrega said.


Three artificial chromosomes were created that reproduced partial, overlapping segments of that gene desert, plus a gene called lacZ that produces a blue color in the cell when expressed. After introducing the chromosomes into a strain of mouse, the researchers measured where blue dye appeared reflecting organs where MYC expression was under the control of regulatory sequences present in each of the artificial chromosomes. Because two of the three chromosomes promoted expression in the prostate, the team was able to narrow down the relevant sequence to a 5,000 base pair segment.















That segment included a SNP called rs6983267, which had previously been associated through GWAS studies with increased risk of prostate and colorectal cancer. A second phase of experiments tested the "risk allele" version of that SNP against the non-risk allele different by only a single nucleotide.


Such a small difference produced dramatically different expression patterns, the study found. Transgenic mice carrying the risk allele exhibited robust blue staining in their prostate, while mice given the non-risk allele showed little to no detectable gene expression in the organ.


"Perhaps what this is telling us is that by inheriting the risk allele here, you may drive the overexpression of MYC," Nobrega said. "It's not going to cause prostate cancer, but it could increase the risk for prostate cancer."


The differences in prostate expression between risk allele and non-risk allele are also apparent as early as embryonic stages, suggesting that the predisposition toward prostate cancer is set long before the disease actually appears.


"The mechanistic link between MYC expression levels and prostate may be much earlier than the cancer itself," Nobrega said. "It could potentially prime the system for cancer and then, depending on either secondary mutations or environmental injuries, it might or might not develop."


A next step would be to determine why the risk allele is capable of enhancing prostate expression with only a single nucleotide change. Nobrega suggested that an intermediary protein that binds to the enhancer sequence may be a promising target for preventive therapy in those carrying the risk allele.


But most importantly, the results confirm that the small genetic variants turned up by GWAS analyses are not artifacts, but highly relevant biological differences.


"This is a convincing demonstration in vivo that these noncoding SNPs that have been associated with complex diseases do lead to phenotypic differences," Nobrega said. "It strongly suggests that this is a way to follow up on these associations for all kinds of disease; not only for cancer but for diabetes, obesity, and other conditions."


The paper, "An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer," appears in the July 13, 2010 issue of Genome Research. The research was funded by the National Human Genome Research Institute and the Department of Defense.


Source: University of Chicago Medical Center

Chemists Explain The Switchboards In Our Cells

Our cells are controlled by billions of molecular "switches" and chemists at UC Santa Barbara have developed a theory that explains how these molecules work. Their findings may significantly help efforts to build biologically based sensors for the detection of chemicals ranging from drugs to explosives to disease markers.



Their research is described in an article published this week in the Proceedings of the National Academy of Sciences (PNAS).



Biosensors are artificial molecular switches that mimic the natural ones, which direct chemical responses throughout the cell. "These switching molecules control the behavior of our cells," said Alexis VallГ©e-BГ©lisle, a postdoctoral scholar who spearheaded the project and is first author of the paper. "By studying these switches, we can better understand how living organisms are able to monitor their environment and use this knowledge to build better sensors to detect, for example, disease markers."



All creatures, from bacteria to humans, must monitor their environments in order to survive, explained the authors. They do so with biomolecular switches, made from RNA or proteins. For example, in our sinuses, there are receptor proteins that can detect different odors. Some of those scents warn us of danger; others tell us that food is nearby.



In addition to deriving the mathematical relationships underlying switching, VallГ©e-BГ©lisle spent months performing a hands-on study of an artificial biomolecular switch to demonstrate that the theory holds up quantitatively.



Like a light switch, biomolecular switches often exist in two states - on or off. When a biomolecule switches from on to off, or vice versa, its shape changes. This change in structure is often triggered by the physical binding of a signaling molecule (for example, the odorant molecule responsible for a given smell) to the switch. However, unlike the single light switch that controls any one light in a house, cells use hundreds to millions of copies of each switch. Because there is more than one copy involved, the switching process is not a binary, "all-or-none" process. Instead, the output signal is determined by the fraction of switches that move from the off state to the on state.



In their PNAS paper, the authors describe a simple mathematical model that will allow biotech researchers to fine-tune the ease with which artificial biomolecular switches can be "flipped." They also shed light on how natural biomolecular switches evolved.



Additional co-authors are Francesco Ricci of the University of Rome Tor Vergata, and senior author Kevin Plaxco, professor in the Department of Chemistry and Biochemistry at UCSB.



Source:

Gail Gallessich

University of California - Santa Barbara

Francis Crick: Hunter Of Life's Secrets - New Biography

Cold Spring Harbor Laboratory Press has just released a new biography, Francis Crick: Hunter of Life's Secrets. It is the first full-length intellectual biography of Francis Crick, a greatly admired and influential scientist who co-discovered the structure of DNA and then followed up this discovery with important contributions that shaped the foundations of molecular biology. He later worked in the field of neuroscience, studying vision and the biological basis of consciousness. This book is an in-depth exploration of Crick's passion for the discovery and understanding of the molecules that orchestrate the essential processes of life.



Francis Crick: Hunter of Life's Secrets is written by Robert Olby, a Research Professor in the History and Philosophy of Science Department at the University of Pittsburgh and one of molecular biology's foremost scholars. Before his death in 2004, Crick invited Olby to write about his life and gave Olby full access to his archives, family, and friends.



"I have immersed myself in Crick's personal papers, spoken with many of his friends, and sought to weave together the insights and vignettes thus won with my account of his life as scientist," wrote Olby in the book's preface. "This, then, is an attempt to shape a dynamic picture of the remarkable evolution of Dr. Crick's career and his role in the shaping of the new foundations for biology."



In 21 chapters, this engrossing biography reveals how, from somewhat unpromising beginnings, Crick became a vital contributor to a remarkably creative period in science. Olby chronicles Crick's life from his early studies in biophysics, to the discovery of the structure of DNA in 1953 and his critical role in deciphering the genetic code, to his later work in neuroscience. In particular, Olby's detailed exploration of Crick's scientific life to the point of the famous 1953 discovery provides a clear demonstration of how chance does indeed favor the prepared mind.



The book contains quotes from personal papers and a gallery of family photographs. It also includes a timeline to help readers track significant events during the course of the 88-year span covered in the book, as well as a biographical index and a full subject index. This fascinating biography will be of interest to readers with a general interest in science, as well as to professional scientists, science historians, and students.



Olby's work on the book was supported by the National Science Foundation and an Archives Fellowship award from Churchill College, Cambridge. His previous works include The Origins of Mendelism (1966) and The Path to the Double Helix: The Discovery of DNA (1994).



Francis Crick: Hunter of Life Secrets (© 2009; ISBN 978-087969798-3) is published by Cold Spring Harbor Laboratory Press. For more information and a complete table of contents, see cshlpress/link/crick.htm.



Source:
Ingrid Benirschke


Cold Spring Harbor Laboratory

Cells Lost In Parkinson Disease Replaced By Cultured Cells

Parkinson disease (PD) is caused by the progressive degeneration of brain cells known as dopamine (DA) cells. Replacing these cells is considered a promising therapeutic strategy. Although DA cell-replacement therapy by transplantation of human fetal mesencephalic tissue has shown promise in clinical trials, limited tissue availability means that other sources of these cells are needed. Now, Ernest Arenas and colleagues at the Karolinska Institue, Sweden, have identified a new source for DA cells that provided marked benefit when transplanted into mice with a PD-like disease.



In the study, DA cells were derived from ventral midbrain (VM) neural stem cells/progenitors by culturing them in the presence of a number of factors - FGF2, sonic hedgehog, and FGF8 - and engineering them to express Wnt5a. This protocol generated 10-fold more DA cells than did conventional FGF2 treatment. Further analysis revealed that these cells initiated substantial cellular and functional recovery when transplanted into mice with PD-like disease. Importantly, the mice did not develop tumors, a potential risk that has precluded the clinical development of embryonic stem cells as a source of DA cells. These data led the authors to suggest that Wnt5a-treated neural stem cells might be an efficient and safe source of DA cells for the treatment of individuals with PD.







Title: Wnt5a-treated midbrain neural stem cells improve dopamine cell replacement therapy in parkinsonian mice



Author Contact:

Ernest Arenas

Karolinska Institute, Stockholm, Sweden.



Source: Karen Honey


Journal of Clinical Investigation

DeCODE Launches Phase II Clinical Testing Of DG051 For The Prevention Of Heart Attack

deCODE genetics
(Nasdaq: DCGN) announced that it has begun enrolling patients for its
Phase IIa clinical trial for DG051, the company's leukotriene A4 hydrolase
inhibitor being developed for the prevention of heart attack.



In Phase I studies completed earlier this year, DG051 significantly
reduced the production of leukotriene B4 (LTB4) in a dose dependent manner.
LTB4 is a pro-inflammatory molecule that deCODE's gene discovery and
functional biology work identified as a key factor in modulating risk of
heart attack. The Phase I studies showed DG051 to be safe and
well-tolerated at all dose levels tested, with a favourable pharmacokinetic
profile. DG051 was also recently evaluated in a 28-day Phase I study that
further demonstrated that the drug can deliver significant, sustained
reductions in LTB4 levels with once-daily dosing.



The design of the Phase IIa study is based upon these findings by
studying the effect of DG051 in patients with a history of heart attack or
coronary artery disease. The Phase IIa is a randomized, double-blind,
placebo- controlled trial that will examine the impact of DG051 on the
production of LTB4 as well as the compound's pharmacokinetic and safety and
tolerability profiles in heart patients. The company will use the results
from this study to inform dose selection for a larger Phase IIb trial
planned to commence early next year.



"We are advancing DG051 as a novel means of preventing heart attack,
the leading cause of death in the industrialized world. Our clinical
studies thus far have shown that it effectively reins in the activity of a
branch of the leukotriene pathway that has been linked to risk of heart
attack, and it has demonstrated a solid safety and pharmacokinetic profile.
The 28-day study we just completed shows that DG051 can achieve good
reductions in leukotriene B4 levels with once-daily dosing. We are excited
to have begun testing its potential in patients," said Kari Stefansson, CEO
of deCODE.



About DG051



DG051 is a first-in-class, small-molecule inhibitor of leukotriene A4
hydrolase (LTA4H) discovered by deCODE's chemistry unit and is being
developed for the prevention of heart attack. LTA4H is encoded by one of
the genes deCODE has linked to increased risk of heart attack. The at-risk
versions of these genes confer increased risk of heart attack by increasing
the production of the pro-inflammatory molecule LTB4. DG051 is designed to
decrease risk of heart attack by decreasing the production of LTB4.



About deCODE



deCODE genetics (Nasdaq: DCGN) is a global leader in applying human
genetics to develop drugs and diagnostics for common diseases. Our
population approach has enabled us to discover and target key biological
pathways involved in conditions ranging from heart attack to cancer. We are
turning these discoveries into new medicine to better treat and prevent
many of the biggest challenges to public health. deCODE is delivering on
the promise of the new genetics.(SM) Visit us on the web at decode,
and on our diagnostics site at decodediagnostics.



Any statements contained in this presentation that relate to future
plans, events or performance are forward-looking statements within the
meaning of the Private Securities Litigation Reform Act of 1995. These
forward-looking statements are subject to a number of risks and
uncertainties that could cause actual results to differ materially from
those described in the forward- looking statements. These risks and
uncertainties include, among others, those relating to technology and
product development, integration of acquired businesses, market acceptance,
government regulation and regulatory approval processes, intellectual
property rights and litigation, dependence on collaborative relationships,
ability to obtain financing, competitive products, industry trends and
other risks identified in deCODE's filings with the Securities and Exchange
Commission. deCODE undertakes no obligation to update or alter these
forward-looking statements as a result of new information, future events or
otherwise.


deCODE genetics

decode

Scientists In UK See Clearer Picture Of Fetal Development With The Help Of Chicks

Scientists hope to gain a greater understanding of disease and birth defects with a new imaging database that will map the expression of genes that control development.



The research coordinated by The Roslin Institute at the University of Edinburgh, in collaboration with the MRC Human Genetics Unit (Edinburgh), University College London, University of Bath and Trinity College Dublin, will log thousands of three dimensional images of chicks taken during the first 10 days of their development.



The so-called chick atlas will exploit the information and resources recently made available from the sequencing of the mouse and chicken genomes. In particular, it will build on the pioneering Edinburgh Mouse Atlas at the MRC Human Genetics Unit in Edinburgh (e-MouseAtlas).



Images from the chick atlas will show not only where genes key to our biological make-up are switched on but also when they are turned on and off to ensure healthy development.



The ВЈ2.6 million initiative, which is funded by the Biotechnology and Biological Science Research Council (BBSRC) through its new LOLA ("longer and larger") scheme will help researchers understand why problems occur in the development of limbs and of the nervous system, which can cause conditions such as spina bifida.



In the long term it could also have implications for the treatment of diseases such as cancer as it will provide insight into the role genes play when cells divide and proliferate.



The images will be stored in an online database, which can be accessed and added to by scientists from across the world. As an online database or encyclopaedia it is also available to the public and educators, to be used as a tool to teach development.



Professor Dave Burt, of the Roslin Institute, University of Edinburgh, said: "The chick atlas has the benefit of looking at how genes relate to development in both time and space; letting us know when and where genes make an impact."



"These early stages of a chick embryo are essential in the development of the nervous system, heart and limbs and by understanding what happens we can also understand why things may go wrong."



In the initial stages the chick atlas will look at mapping 1,000 of around 18,000 chick genes predicted from the chicken genome sequence. By cross referencing similarities with the mouse atlas, scientists can identify the most relevant genes in human development.



Professor Richard Baldock, of the MRC's Human Genetics Unit in Edinburgh said: "The mouse atlas team will contribute their expertise in atlas databases to deliver this important resource. The ability to capture and compare data between species will provide critical clues to how embryogenesis is controlled by gene activity. As a physicist and computer scientist this is an exciting time to be in biomedical research".







Notes:



The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Supported by Government, BBSRC annually invests around ВЈ420 million in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agricultural, food, chemical, healthcare and pharmaceutical sectors. bbsrc.ac.uk. Information on the BBSRC's LOLA - "longer and larger" scheme can be found at bbsrc.ac.uk/funding/grants/lola.html.



The Roslin Institute, which became part of the University of Edinburgh in April 2008, aims to enhance the lives of animals and humans through world class research in animal biology. The Roslin Institute's mission is to gain fundamental understanding of genetic, cellular, organ and systems bioscience underpinning common mechanisms of animal development and pathology, and to drive this into prevention and treatment of important veterinary diseases and develop sustainable farm animal production systems. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336



The University of Bath is one of the UK's leading universities, with an international reputation for quality research and teaching.



Source: Tara Womersley


University of Edinburgh

Like Little Golden Assassins, 'Smart' Nanoparticles Identify, Target And Kill Cancer Cells

Another weapon in the arsenal against cancer: Nanoparticles that identify, target and kill specific cancer cells while leaving healthy cells alone.


Led by Carl Batt, the Liberty Hyde Bailey Professor of Food Science, the researchers synthesized nanoparticles shaped something like a dumbbell made of gold sandwiched between two pieces of iron oxide. They then attached antibodies, which target a molecule found only in colorectal cancer cells, to the particles. Once bound, the nanoparticles are engulfed by the cancer cells.


To kill the cells, the researchers use a near-infrared laser, which is a wavelength that doesn't harm normal tissue at the levels used, but the radiation is absorbed by the gold in the nanoparticles. This causes the cancer cells to heat up and die.


"This is a so-called 'smart' therapy," Batt said. "To be a smart therapy, it should be targeted, and it should have some ability to be activated only when it's there and then kills just the cancer cells."


The goal, said lead author and biomedical graduate student Dickson Kirui, is to improve the technology and make it suitable for testing in a human clinical trial. The researchers are now working on a similar experiment targeting prostate cancer cells.


"If, down the line, you could clinically just target the cancer cells, you could then spare the health surrounding cells from being harmed that is the critical thing," Kirui said.


Gold has potential as a material key to fighting cancer in future smart therapies. It is biocompatible, inert and relatively easy to tweak chemically. By changing the size and shape of the gold particle, Kirui and colleagues can tune them to respond to different wavelengths of energy.


Once taken up by the researchers' gold particles, the cancer cells are destroyed by heat just a few degrees above normal body temperature while the surrounding tissue is left unharmed. Such a low-power laser does not have any effect on surrounding cells because that particular wavelength does not heat up cells if they are not loaded up with nanoparticles, the researchers explained.


Using iron oxide which is basically rust as the other parts of the particles might one day allow scientists to also track the progress of cancer treatments using magnetic resonance imaging, Kirui said, by taking advantage of the particles' magnetic properties.


The research was funded by the Sloan Foundation and the Ludwig Institute for Cancer Research, which has been a partner with Cornell since 1999 to bring laboratory work to clinical testing. The research is reported in the Feb. 15 online edition of the journal Nanotechnology.


Source: Cornell University

Quark Pharmaceuticals Extends Research Agreement With State University Of New York For Proprietary SiRNA Compounds For Acute Hearing Loss

Quark Pharmaceuticals, Inc., a
clinical-stage biopharmaceutical company focused on discovering and
developing novel RNA interference-based therapeutics, announced that
it has expanded its relationship with the State University of New York at
Buffalo, Center for Hearing & Deafness, which is the Company's primary site
for the pre-clinical studies of its product candidate, AHLi-11, for the
treatment of acute hearing loss. Quark initiated its collaboration with the
State University of New York in 2005.



The current studies, led by Professor Richard Salvi, focus on the
in-depth analysis of the effect of AHLi-11 and other molecules in
preventing chemotherapy induced hearing loss. Based on these studies, Quark
Pharmaceuticals expects to file an IND within 2007 for AHLi-11 for the
prevention chemotherapy-induced hearing loss.



AHLi-11 is a siRNA-based drug that temporarily inhibits the expression
of human gene p53. Cochlear hair cell apoptosis (cell death), a key factor
in several of the more common causes of acute hearing loss, is believed to
be induced by molecular mechanisms most likely associated with
p53-dependent stress response. Inhibition of p53, therefore, is suggested
as a potential modality for the prevention of ototoxic hearing loss, a
common side effect of certain drugs including aminoglycoside antibiotics
and cancer therapeutics such as cisplatin, as well as acoustic trauma.



Quark has demonstrated delivery of siRNA into target cells in rats and
monkeys along with its persistence in the cochlear hair cells for at least
15 days. In preclinical animal studies, AHLi-11 appears to protect cochlear
hair cells from apoptotic cell death induced by the chemotherapeutic
agents, cisplatin and carboplatin, and by acoustic trauma.



Daniel Zurr, CEO of Quark Pharmaceuticals, said, "We are encouraged by
the advancement of AHLi-11 for acute hearing loss and look forward to
filing an IND by year-end for the prevention of chemotherapy-induced
hearing loss. Up to a million people per year are treated with cisplatin in
the US and Europe, and the risk of serious hearing impairment is
particularly devastating in children. With this in mind, Quark will
continue its efforts to advance AHLi- 11 in response to this major unmet
medical need.



"We are also thrilled to expand our relationship with Professor Salvi
and his colleagues at the State University of New York as it will enable us
to deepen our understanding of the molecular processes underlying acute
hearing loss and to examine several variables related to the impact of
AHLi-11 as a curative measure. Our collaborations with leading academic
institutions mark the ongoing development of our pipeline and reinforce
Quark's expertise in the development of siRNA-based therapeutics that offer
the potential to treat a wide range of disease targets."
















About AHLi-11



AHLi-11 is a synthetic siRNA that is a temporary and reversible
suppressor of p53, and contains the same active compound as AKIi-5, Quark's
drug candidate for the prevention of acute renal failure. AHLi-11 is in
development for the prevention of acute hearing loss, initially induced by
the ototoxic cancer therapeutic agent cisplatin. AHLi-11 is based on
Quark's proprietary, patented concept of temporary and reversible
inhibition, for therapeutic purposes, of the expression of the
transcription factor human p53, which is associated with DNA repair and
apoptosis. In response to certain chemotherapeutic agents, such as
cisplatin and carboplatin, molecular mechanisms, most likely associated
with p53-dependent stress response, are suspected of triggering cochlear
hair cell apoptosis. Temporary inhibition of p53 prevents apoptosis,
allowing restoration of normal DNA and cellular integrity. The AHLi-11
active molecule was designed and patented by Quark. The Company has
licenses for certain RNAi intellectual property from Alnylam and Silence
Therapeutics



About Quark Pharmaceuticals, Inc.



Quark Pharmaceuticals, Inc. is a clinical-stage biopharmaceutical
company focused on discovering and developing novel therapeutics based on
its proprietary gene discovery science and technology, with an initial
focus on drug candidates that work through the natural mechanism in the
cell known as RNA interference, or RNAi, for the treatment of diseases
associated with oxidative stress. Quark believes that its proprietary
target gene discovery platform, BiFAR(TM), combined with its ability to
design and successfully deliver synthetic molecules of the new class of
RNAi therapeutics known as small-interfering RNA, or siRNA, to specific
organs in the body, enables the Company to rapidly develop drug candidates.
Quark has two internally discovered and developed lead product candidates:
RTP801i-14 in phase 1 clinical trial for the treatment of wet age-related
macular degeneration, and AKIi-5 for the prevention of acute renal failure.
The Company has licensed RTP801i-14 to Pfizer on an exclusive worldwide
basis. Quark has, in addition, a product candidate portfolio of RNAi
therapeutics based on novel targets and therapeutic concepts discovered
using BiFAR(TM) and designed for the treatment of oxidative stress
associated diseases of the inner ear, lungs and additional organs of the
body.



Quark is headquartered in Fremont, California and operates research and
development facilities in Boulder, Colorado and Ness-Ziona, Israel.
Additional information is available at quarkpharma



Forward-looking statement



Various statements in this release concerning the Company's future
expectations, plans and prospects, including its intention to publicly
offer shares of its common stock, constitute forward-looking statements for
the purposes of the safe harbor provisions under The Private Securities
Litigation Reform Act of 1995. Actual results may differ materially from
those indicated by these forward-looking statements as a result of various
important factors, including risks related to fluctuations in our stock
price, as well as those risks more fully discussed in the "Certain Factors
That May Affect Future Results" section of the Company's most recent
Quarterly Report on Form 10-Q on file with the Securities and Exchange
Commission. In addition, any forward- looking statements represent the
Company's views only as of today and should not be relied upon as
representing its views as of any subsequent date. The Company does not
assume any obligation to update any forward-looking statements.


Quark Pharmaceuticals, Inc.

quarkpharma

Research Of Cell Movements In Developing Frogs Reveals New Twists In Human Genetic Disease

Mutations in a gene known as "Fritz" may be responsible for causing human genetic disorders such as Bardet-Biedl syndrome, University of Texas at Austin developmental biologist John Wallingford and Duke University human geneticist and cell biologist Nicholas Katsanis have found.



Their results are published online in Science.



Bardet-Biedl syndrome, and its related Meckel-Gruber syndrome, are two rare but well-studied disorders that result in conditions such as mental retardation, obesity, blindness and kidney failure. This is the first study implicating Fritz's role in human disorders, and the first study of the gene in vertebrates.



Wallingford found that the gene plays a role in two processes in developing embryos - first, the collective movement of cells as they mold the shape of developing embryos, and second, the creation of cilia, which are projections from cells that serve as sensory antennae.



The Fritz gene regulates these processes by controlling molecules called septins. Septins provide structural support to cell membranes much like metal struts support an umbrella.



Wallingford and his team were pointed toward the role of Fritz in controlling septins by watching time-lapse videos of developing frog embryos with and without the gene.



"Normally, movement of the cell membrane is smooth in developing embryos," said Wallingford, associate professor of biology, "but those embryos without Fritz had cell membranes that were waving and jostling around. Septins basically make a coat across the plasma membrane and stabilize it. Because the membranes looked floppy, the septins are one of the things we looked at."



Lack of the Fritz gene manifested in several ways in the developing embryo. In early stages, embryos had problems associated with collective cell movement and growing longer. That resulted in a number of morphological problems such as defects in the neural tube.



Later stage embryos showed cranio-facial malformations similar to those seen in Meckel-Gruber patients. Those deformities were likely caused by malfunctions in cilia.



"This suggests that septins are being deployed in different ways in these different cell types," said Wallingford.



Armed with the information from the Wallingford lab, Katsanis and his group then discovered that patients with Bardet-Biedl and Meckel-Gruber syndromes have mutations in the Fritz gene.



"This result obviously furthers our understanding of these syndromes," said Katsanis. "Perhaps more important, however, we now have both hard evidence for previous suspicions and a brand new set of mechanistic underpinning for ciliary dysfunction in people".



Ultimately, these findings shed light on the mechanisms by which fundamental cellular machinery is regulated during embryonic development and is related to human disease.



"This is a good example of studying basic cellular biology that leads to insights in human diseases," said Wallingford. "If we just think about the way basic biology links in with humans, there's the ability to make that leap. We will discover things about human diseases even when we are trying to study frog development."



Katsanis concurs: "This work is such an elegant example of the progress that can be achieved, and quickly, when scientific disciplines intermesh."



Wallingford is a Howard Hughes Medical Institute Early Career Scientist. Katsanis is the Distinguished George W. Brumley Professor and director of the Center for Human Disease Modeling at Duke. First authorship on the Science paper is shared by Su Kyoung Kim and Asako Shindo, a graduate student and a postdoctoral fellow, respectively, in The University of Texas at Austin cell and molecular biology program.



Source:

John Wallingford

University of Texas at Austin

Populations Of Nerve Cells Adapt To Changing Images Demonstrated By First Empirical Study

Neuroscientists studying the mind's ability to process images have completed the first empirical study to demonstrate, using animal models, how populations of nerve cells in visual cortex adapt to changing images. Their findings could lead to sight-improving therapies for people following trauma or stroke. The study at The University of Texas Health Science Center at Houston appears in the March 13 issue of the journal Nature.



"Our perception of the environment relies on the capacity of neural networks to adapt rapidly to changes in incoming stimuli," wrote senior author Valentin Dragoi, Ph.D., assistant professor of neurobiology and anatomy at The University of Texas Medical School at Houston. "It is increasingly being realized that the neural code is adaptive, that is, sensory neurons change their responses and selectivity in a dynamic manner to match the changes in input stimuli." The neural code is the set of rules that transforms electrical impulses in the brain into thoughts, memories and decisions.



In the study, Dragoi and co-author Diego Gutnisky, a graduate research assistant at The University of Texas Graduate School of Biomedical Sciences at Houston, measured the effects of visual stimulation on the responses of multiple neurons whose electrical activity was measured simultaneously in animals. They carefully examined the responses of a population of cells in visual cortex to dynamic stimuli, which consisted of movie sequences displayed on a video monitor.



"We provide empirical evidence that brief exposure, or adaptation, to a fixed stimulus causes pronounced changes in the degree of cooperation between individual neurons and an improvement in the efficiency with which the population of cells encodes information," Dragoi and Gutnisky report. "These results are consistent with the 'efficient coding hypothesis' - that is, sensory neurons are adapted to the statistical properties of the stimuli that they are exposed to and with changes in human discrimination performance after adaptation."



This information may be helpful in the fight against brain illness. "Right now, we don't know the causes of brain illnesses such as Alzheimer's disease or disorders caused by trauma," Dragoi said. "However, it is our belief that understanding not only how individual neurons work, but how they cooperate with their neighbors to impact the functions of the brain involved in diseases may help develop better diagnostic tools and therapies to improve visual function following trauma, stroke or disease, or even prevent brain disorder."



While their study focused on how neuronal populations adapt to visual stimulation, the same could hold true for other senses - hearing, smell, taste and touch, Dragoi said. "We're trying to understand how a network of sensory neurons changes its encoding properties to properly represent the environment," he said. "Our results may have general implications for sensory and motor coding in a variety of brain areas."



The brain is the control center of the central nervous system and is responsible for behavior. It contains more than 100 billion neurons or nerve cells, each linked to as many as 10,000 other neurons or nerve cells. "One dream of neuroscientists is to crack the neural code and through our study we have made steps in understanding how populations of neurons encode information," Dragoi said.







Dragoi heads the five-person Cortical Mechanisms of Visual Behavior Laboratory at the UT Medical School at Houston. Its research goal is to understand how individual neurons and populations encode and process information in real time.



The study in Nature is titled "Adaptive coding of visual information in neural populations" and was supported by the Pew Scholars Program, the James S. McDonnell Foundation and the National Eye Institute.



Source: Robert Cahill


University of Texas Health Science Center at Houston

Methane-Producing Molecule Can Also Repair DNA

The Archaea are single-celled organisms and a domain unto themselves, quite apart from the so called eukaryotes, being bacteria and higher organisms. Many species live under extreme conditions, and carry out unique biochemical processes shared neither with bacteria nor with eukaryotes. Methanogenic archaeans, for example, can produce methane gas out of carbon dioxide and hydrogen. The underlying chemical reaction, a reduction, involves the cofactor known as F0 or F420 which is the tiny molecule deazaflavin. It has previously been found only in methanogenic bacteria, and has accordingly been considered the signature molecule for those species. A research group working with Professor Thomas Carell, however, has now shown that this cofactor is also common in eukaryotes, where it performs an entirely different function: deazaflavin is involved in DNA repair processes. (PNAS Early Edition online, 1 July 2009)



Catalysts assist in chemical reactions without undergoing any alteration of their own. In the cells of living organisms, proteins perform this important function. They carry out the metabolism fundamental to all living processes. Proteins are instrumental in cellular respiration, they for instance reduce oxygen to water and oxidize food into carbon dioxide. This releases the energy that makes life possible at all. Proteins cannot perform these functions on their own. They depend on small helper molecules. Such molecules are stored inside special pockets in the proteins and carry out essential metabolic functions. The living organism itself produces many of these helpers. Others - like vitamins - must be obtained from food. Severe vitamin deficiencies are a harsh reminder of how essential these molecules are.



Methanogenic bacteria have quite an exceptional task to accomplish: They have to produce methane. In terms of chemistry, this is no mean feat. Methane production is currently one of the most hotly pursued goals for the purposes of renewable energy. It is also a serious greenhouse gas.



Enzymatic methane production involves the tiny molecule deazaflavin, known as cofactor F0 or cofactor F420. This cofactor is stored inside special proteins of methanogenic bacteria, and is essential for methane biosynthesis. Cofactor F0/F420 is a small molecule that, until now, has only been found in methanogenic bacteria. It is regarded as the signature molecule for such species.



"We have now shown that this picture is not entirely true," Carell says. "This cofactor is significantly more widespread in the biosphere than previously assumed. Most importantly, it also occurs in higher organisms, the so-called eukaryotes. But in these, it performs a completely different task." As the researchers were able to demonstrate, the cofactor is involved in DNA repair processes. Specifically, repair of UV damage to the DNA molecule.



Plants and many other organisms that are exposed to intense sunlight must cope with an enormous degree of damage to their genes. To repair those mutations, they need the help of complex enzymes. These photolyases in turn require cofactor FAD - aka vitamin B2 - to accomplish this function. It has long been suspected that these crucial enzymes require yet another cofactor to provide the energy that DNA repair requires.



"We have now shown that, in many organisms, this cofactor is F0/F420," Carell reports. "This molecule has been conclusively detected in DNA repair enzymes of Drosophila melanogaster, the fruit fly. Not long ago, another research group even postulated that F0/F420 is co-responsible for DNA repair in plants. Our view of cofactor F420 as a signature molecule for methanogenic species has therefore radically changed: this cofactor is widespread and it is essential for both methane synthesis and for DNA repair."



Notes:

Professor Thomas Carell is speaker of the "Center for Integrated Protein Science Munich (CiPSM)" center of excellence which supported this research.


Publication: "The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes", Andreas F. Glas, Melanie J. Maul, Max Cryle, Thomas R. M. Barends, Sabine Schneider, Emine Kaya, Ilme Schlichting, and Thomas Carell



Source:
Professor Thomas Carell


Ludwig-Maximilians-Universität München

Bio-engineered Proteins: Trial Confirms New Way To Tackle Cancer

Re-engineering a protein that helps prevent tumours spreading and growing has created a potentially powerful therapy for people with many different types of cancer. In a study published in the first issue of EMBO Molecular Medicine, Canadian researchers modified the tumour inhibiting protein, von Hippel-Lindau (VHL), and demonstrated that it could suppress tumour growth in mice.


When solid tumours grow they often have relatively poor and disorganised blood supplies. As a result, various regions including the centre of the tumour have low levels of oxygen and are said to be hypoxic. Cells in these hypoxic areas produce hypoxia-inducible factor (HIF) that helps them carry on growing. Consequently HIF is associated with aggressiveness in some of the most common types of cancer, including prostate, breast, colon and lung cancer. Under normal conditions VHL degrades HIF, but VHL is deactivated when oxygen levels are low. So, in hypoxic regions of a tumour, just where VHL is needed to inhibit cancer, it is ineffective.


The researchers, therefore, created a new version of VHL that does not stop working when oxygen is scarce. Introducing this newly engineered version of VHL into mice that had kidney tumours dramatically reduced levels of HIF, caused tumours to regress and limited the formation of new blood vessels within the tumours.



"We have genetically removed the Achilles' heel of VHL to permit unrestricted destruction of HIF," says lead researcher Professor Michael Ohh, who works in the Faculty of Medicine at the University of Toronto. "The level of HIF is usually very high under conditions of low oxygen, but when we put in our bioengineered VHL its levels go right down to a level that would be comparable to that in normal oxygen levels."


Their findings could have implications for any type of cancer in which HIF plays a role. "We used kidney cancer as a model because it is one of the most resistant tumours to conventional radiation and chemotherapy, but our findings provide a novel concept that could potentially serve as a foundation for smarter anti-cancer strategy for a wide variety of cancers," says Ohh.


Full citation:

Oxygen-Independent Degradation Of Hif Via Bioengineered Vhl Tumour Suppressor Complex;

Sufan R.I., Moriyama E.H., Mariampillai A., Roche O., Evans A.J., Alajez N.M., Vitkin I.A., Yang V.X.D., Liu F., Wilson B.C., Ohh M.;

EMBO Mol Med 2009 1(1); DOI: emmm.200900004


About the Journal


Molecular Medicine is a rapidly-growing area of research at the interface between clinical research and basic biology. Powerful new analytical tools provided by molecular biology allow unprecedented insights into human physiology and the molecular basis of diseases. These insights are being translated into better diagnosis, prevention and patient care. EMBO Molecular Medicine is a peer-reviewed journal dedicated to the publication of original, cutting-edge research in the field of Molecular Medicine of interest to medical and basic scientists. The Journal publishes research articles and reviews highly relevant to all fields of clinical medicine and their related research areas in basic biology. Studies based on model organisms also fall within the scope of the journal, provided that the results presented are evidently relevant to human disease.
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EMBO Molecular Medicine will be made freely available for the first two years of publication. Institutional customers can opt to receive complimentary online access for this journal. Institutions may also request one complimentary print subscription when registering for online access to EMBO Molecular Medicine. Register your institution here.



About EMBO


The European Molecular Biology Organization (EMBO) promotes excellence in molecular life sciences by recognizing and fostering talented scientists, empowering them to advance the life sciences to understand how life works and share knowledge to help address the challenges of a changing world. For details about EMBO and its activities please visit embo.


Wiley-Blackwell was formed in February 2007 as a result of the acquisition of Blackwell Publishing Ltd. by John Wiley & Sons, Inc., and its merger with Wiley's Scientific, Technical, and Medical business. Together, the companies have created a global publishing business with deep strength in every major academic and professional field. Wiley-Blackwell publishes approximately 1,400 scholarly peer-reviewed journals and an extensive collection of books with global appeal. For more information on Wiley-Blackwell, please visit wiley-blackwell or interscience.wiley.


Source
Wiley-Blackwell

Current Approach To Drug Discovery For Lou Gehrig's Disease Should Be Re-examined

Most research on Lou Gehrig's disease therapeutics has been based on the assumption that its two forms (sporadic and hereditary) are similar in their underlying cause. Now, researchers at the University of Pennsylvania School of Medicine have found an absolute biochemical distinction between these two disease variants, suggesting that current approaches to drug discovery should be re-examined.



About 5 percent of all cases of Lou Gehrig's disease, or amyothrophic lateral sclerosis (ALS), are passed from generation to generation. The most common genetic variant in this familial form is caused by a mutation in the SOD-1 gene. The researchers looked at a large set of ALS patients, including hereditary cases, both with and without the SOD-1 mutation.



The present study - published in the May issue of the Annals of Neurology - was conducted by Penn; a group led by Ian Mackenzie from the University of British Columbia; the University of Munich; and others across the U.S. and Canada.



"Most ALS research has focused on how mutant SOD-1 proteins are toxic to nerve cells," says senior author John Trojanowski, MD, PhD, who directs the Penn Institute on Aging. Last year, Penn investigators led by co-author Virginia Lee, PhD, who directs the Penn Center for Neurodegenerative Disease Research, identified TDP-43 as the major disease protein in sporadic (non-hereditary) forms of ALS, which are not those caused by SOD-1 gene mutations.



By examining the various forms of ALS in post-mortem tissue, the researchers found that TDP-43 was the disease protein in sporadic ALS cases, but not in patients with SOD-1 mutations, all of whom have the familial form of ALS. Patients with the SOD-1 mutation account for about 1 percent of all ALS cases.



"We argue that SOD-1 ALS does not equal sporadic ALS," says Trojanowski. "If you pursue drug discovery focusing on SOD-1-mediated pathways of brain and spinal cord degeneration you may benefit SOD-1-bearing patients, but not the vast majority of ALS patients who have the sporadic form of this disorder with TDP-43 pathologies underlying the disease."



"Motor neuron degeneration in TDP-43 cases may result from a different mechanism than cases with SOD-1 mutations, so this form of ALS may not be the familial counterpart of sporadic ALS," surmises Lee.



"This may also partially account for why therapeutic strategies, shown to be effective in SOD-1 mouse models, have generally not been effective in clinical trials of sporadic ALS patients," explains Trojanowski. "This also sounds a cautionary note in all other diseases in which you have familial and sporadic versions of the disease because it will prompt researchers to ask if mouse models for drug discovery are based on the correct mutations or disease protein."






This research was funded by the Canadian Institutes of Health Research, the National Institute on Aging, the German Federal Ministry of Education and Research, the Wellcome Trust (United Kingdom) and the UK Medical Research Council.



Co-authors in addition to Trojanowski, Lee, and Mackenzie are Eileen H. Bigio, Paul G. Ince, Felix Geser, Manuela Neumann, Nigel J. Cairns, Linda K. Kwong, Mark S. Forman, John Ravits, Heather Stewart, Andrew Eisen, Leo McClusky, Hans A. Kretzschmar, Camelia M. Monoranu, J. Robin Highley, Janine Kirby, Teepu Siddique, and Pamela J. Shaw.



PENN Medicine is a $2.9 billion enterprise dedicated to the related missions of medical education, biomedical research, and high-quality patient care. PENN Medicine consists of the University of Pennsylvania School of Medicine (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System.



Penn's School of Medicine is ranked #2 in the nation for receipt of NIH research funds; and ranked #3 in the nation in U.S. News & World Report's most recent ranking of top research-oriented medical schools. Supporting 1,400 fulltime faculty and 700 students, the School of Medicine is recognized worldwide for its superior education and training of the next generation of physician-scientists and leaders of academic medicine.



The University of Pennsylvania Health System includes three hospitals, all of which have received numerous national patient-care honors [Hospital of the University of Pennsylvania; Pennsylvania Hospital, the nation's first hospital; and Penn Presbyterian Medical Center]; a faculty practice; a primary-care provider network; two multispecialty satellite facilities; and home care and hospice.



Contact: Karen Kreeger


University of Pennsylvania School of Medicine