Artificial Liver For Drug Tests.

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ScienceDaily (June 25, 2009) — If you have hay fever, headaches or a cold, it’s only a short way to the nearest chemist. The drugs, on the other hand, can take eight to ten years to develop. Until now animal experiments have been an essential step, yet they continue to raise ethical issues. “Our artificial organ systems are aimed at offering an alternative to animal experiments,” says Professor Heike Mertsching of the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB in Stuttgart.

“Particularly as humans and animals have different metabolisms. 30 per cent of all side effects come to light in clinical trials.” The test system, which Professor Mertsching has developed jointly with Dr. Johanna Schanz, should in future give pharmaceutical companies greater security and shorten the path to new drugs. Both researchers received the “Human-centered Technology” prize for their work.
“The special feature, in our liver model for example, is a functioning system of blood vessels,” says Dr. Schanz. “This creates a natural environment for cells.” Traditional models do not have this, and the cells become inactive. “We don’t build artificial blood vessels for this, but use existing ones – from a piece of pig’s intestine.” All of the pig cells are removed, but the blood vessels are preserved. Human cells are then seeded onto this structure – hepatocytes, which, as in the body, are responsible for transforming and breaking down drugs, and endothelial cells, which act as a barrier between blood and tissue cells.
In order to simulate blood and circulation, the researchers put the model into a computer-controlled bioreactor with flexible tube pump, developed by the IGB. This enables the nutrient solution to be fed in and carried away in the same way as in veins and arteries in humans. “The cells were active for up to three weeks,” says Dr. Schanz. “This time was sufficient to analyze and evaluate the functions. A longer period of activity is possible, however.”
The researchers established that the cells work in a similar way to those in the body. They detoxify, break down drugs and build up proteins. These are important pre-conditions for drug tests or transplants, as the effect of a substance can change when transformed or broken down – many drugs are only metabolized into their therapeutic active form in the liver, while others can develop poisonous substances. The researchers have demonstrated the basic possibilities for use of the tissue models – liver, skin, intestine and windpipe. At the moment, the test system is being examined. Within two years it could provide a safer alternative to animal experiments.
Adapted from materials provided by Fraunhofer-Gesellschaft.

TRAPping Proteins That Work Together Inside Living Cells

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ScienceDaily (June 18, 2009) — DNA might be the blueprint for living things, but proteins are the builders. Researchers trying to understand how and which proteins work together have developed a new crosslinking tool that is small and unobtrusive enough to use in live cells. Using the new tool, the scientists have discovered new details about a well-studied complex of proteins known as RNA polymerase. The results suggest the method might uncover collaborations between proteins that are too brief for other techniques to pinpoint.

"Conventional methods used to find interacting proteins have limitations that we are trying to circumvent," said biochemist Uljana Mayer of the Department of Energy's Pacific Northwest National Laboratory. "They also create conditions that are different from those inside cells, so you can't find all the interactions that proteins would normally engage in."
Proteins are the workhorses in an organism's cells. Whole fields of research are dedicated to teasing out which proteins work together to make cells function. For example, drug researchers seek chemicals that disrupt or otherwise change how proteins interact to combat diseases; environmental scientists need to understand how proteins collaborate in ecosystems to make them thrive or fail.
To learn about protein networks, scientists start with a familiar one and use it as bait to find others that work alongside it. To pin down the collaborators, researchers make physical connections between old and new proteins with chemicals called crosslinkers. The sticky crosslinkers will only connect proteins close enough to work together, the thinking goes. But most crosslinkers are too large to squeeze into living cells, are harmful to cells, or link proteins that are neighbors but not coworkers.
To address these issues, Mayer and her PNNL colleagues developed a crosslinking method that uses small crosslinkers whose stickiness can be carefully controlled. To find coworkers of a protein of interest, Mayer and her colleagues build a tiny molecule called a tag into the initial protein. They then add a small molecule called TRAP to the living cell, which finds and fits into the tag like two pieces in a puzzle. TRAP waves around, bumping into nearby proteins. The scientists control TRAP with a flash of light, causing it to stick to coworkers it bumps into. The researchers then identify the new "TRAPped" proteins in subsequent analyses.
To demonstrate how well this method works, Mayer and colleagues tested it out on RNA polymerase, a well-studied machine in cells. The polymerase is made up of many proteins that cooperate to translate DNA. One of the polymerase proteins has a tail that is known to touch the DNA and some helper proteins just before the polymerase starts translating. No one knew if this tail -- also known as the C-terminus of the alpha subunit -- touches anything else in the core of the RNA polymerase complex.
The team engineered a tag in the C-terminus and cultured bacteria with the tagged RNA polymerase. After adding TRAP to the cells and giving it time to find the C-terminus tag, the team shined a light on the cultures.
The team then identified the proteins marked with TRAP using instruments in EMSL, DOE's Environmental Molecular Sciences Laboratory on the PNNL campus. They found that the tagged protein, as expected, interacts with many other proteins, for example previously identified helper proteins, so-called transcription factors. But they also found it on another core protein called the beta subunit, suggesting the tail of the alpha subunit makes contact with the beta subunit as it plugs along. This interaction had never been seen before.
"No one knows what the polymerase looks like when it is running," said Uljana Mayer. "Here we see the C-terminus swings back to grab the beta subunit once the polymerase starts working."
The team report their results June 15 in the journal ChemBioChem. The tag in their unique method is made up of a "tetracysteine motif" -- two pairs of the amino acid cysteine separated by two other amino acids that doesn't interfere with the normal function of the protein of interest. TRAP includes a small "biarsenical" probe, which fluoresces so the team can find the proteins to which it has become attached. TRAP can also be easily unlinked from the tag with a simple biochemical treatment, allowing researchers to piece out the coworker from their original protein of interest.
The team also tested the method on other proteins, such as those found in young muscle cells. Mayer said they will use the method in the future to understand how environmental conditions affect how proteins work together in large networks.
Journal reference:
P. Yan, T. Wang, G.J. Newton, T.V. Knyushko, Y. Xiong, D. J. Bigelow, T.C. Squier, and M.U. Mayer. A Targeted Releasable Affinity Probe (TRAP) for In Vivo Photocrosslinking. ChemBioChem, 2009; 10: 1507-1518 DOI: 10.1002/cbic.200900029
Adapted from materials provided by DOE/Pacific Northwest National Laboratory.

Scientists Show Bacteria Can 'Learn' And Plan Ahead

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ScienceDaily (June 18, 2009) — Bacteria can anticipate a future event and prepare for it, according to new research at the Weizmann Institute of Science. In a paper that appeared June 17 in Nature, Prof. Yitzhak Pilpel, doctoral student Amir Mitchell and research associate Dr. Orna Dahan of the Institute's Molecular Genetics Department, together with Prof. Martin Kupiec and Gal Romano of Tel Aviv University, examined microorganisms living in environments that change in predictable ways.

Their findings show that these microorganisms' genetic networks are hard-wired to 'foresee' what comes next in the sequence of events and begin responding to the new state of affairs before its onset.
E. coli bacteria, for instance, which normally cruise harmlessly down the digestive tract, encounter a number of different environments on their way. In particular, they find that one type of sugar – lactose – is invariably followed by a second sugar – maltose – soon afterward. Pilpel and his team of the Molecular Genetics Department, checked the bacterium's genetic response to lactose, and found that, in addition to the genes that enable it to digest lactose, the gene network for utilizing maltose was partially activated. When they switched the order of the sugars, giving the bacteria maltose first, there was no corresponding activation of lactose genes, implying that bacteria have naturally 'learned' to get ready for a serving of maltose after a lactose appetizer.
Another microorganism that experiences consistent changes is wine yeast. As fermentation progresses, sugar and acidity levels change, alcohol levels rise, and the yeast's environment heats up. Although the system was somewhat more complicated that that of E. coli, the scientists found that when the wine yeast feel the heat, they begin activating genes for dealing with the stresses of the next stage. Further analysis showed that this anticipation and early response is an evolutionary adaptation that increases the organism's chances of survival.
Ivan Pavlov first demonstrated this type of adaptive anticipation, known as a conditioned response, in dogs in the 1890s. He trained the dogs to salivate in response to a stimulus by repeatedly ringing a bell before giving them food. In the microorganisms, says Pilpel, 'evolution over many generations replaces conditioned learning, but the end result is similar.' 'In both evolution and learning,' says Mitchell, 'the organism adapts its responses to environmental cues, improving its ability to survive.' Romano: 'This is not a generalized stress response, but one that is precisely geared to an anticipated event.'
To see whether the microorganisms were truly exhibiting a conditioned response, Pilpel and Mitchell devised a further test for the E. coli based on another of Pavlov's experiments. When Pavlov stopped giving the dogs food after ringing the bell, the conditioned response faded until they eventually ceased salivating at its sound. The scientists did something similar, using bacteria grown by Dr. Erez Dekel, in the lab of Prof. Uri Alon of the Molecular Cell Biology Department, in an environment containing the first sugar, lactose, but not following it up with maltose. After several months, the bacteria had evolved to stop activating their maltose genes at the taste of lactose, only turning them on when maltose was actually available.
'This showed us that there is a cost to advanced preparation, but that the benefits to the organism outweigh the costs in the right circumstances,' says Pilpel. What are those circumstances? Based on the experimental evidence, the research team created a sort of cost/benefit model to predict the types of situations in which an organism could increase its chances of survival by evolving to anticipate future events. They are already planning a number of new tests for their model, as well as different avenues of experimentation based on the insights they have gained.
Pilpel and his team believe that genetic conditioned response may be a widespread means of evolutionary adaptation that enhances survival in many organisms – one that may also take place in the cells of higher organisms, including humans. These findings could have practical implications, as well. Genetically engineered microorganisms for fermenting plant materials to produce biofuels, for example, might work more efficiently if they gained the genetic ability to prepare themselves for the next step in the process.
Prof. Yitzhak Pilpel's research is supported by the Ben May Charitable Trust and Madame Huguette Nazez, Paris, France.
Adapted from materials provided by Weizmann Institute of Science, via EurekAlert!, a service of AAAS.

Geography And History Shape Genetic Differences In Humans

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ScienceDaily (June 5, 2009) — New research indicates that natural selection may shape the human genome much more slowly than previously thought. Other factors -- the movements of humans within and among continents, the expansions and contractions of populations, and the vagaries of genetic chance – have heavily influenced the distribution of genetic variations in populations around the world.

The study, conducted by a team from the Howard Hughes Medical Institute, the University of Chicago, the University of California and Stanford University, is published June 5 in the open-access journal PLoS Genetics.
In recent years, geneticists have identified a handful of genes that have helped human populations adapt to new environments within just a few thousand years—a strikingly short timescale in evolutionary terms. However, the team found that for most genes, it can take at least 50,000-100,000 years for natural selection to spread favorable traits through a human population. According to their analysis, gene variants tend to be distributed throughout the world in patterns that reflect ancient population movements and other aspects of population history.
"We don't think that selection has been strong enough to completely fine-tune the adaptation of individual human populations to their local environments," says co-author Jonathan Pritchard. "In addition to selection, demographic history -- how populations have moved around -- has exerted a strong effect on the distribution of variants."
To determine whether the frequency of a particular variant resulted from natural selection, Pritchard and his colleagues compared the distribution of variants in parts of the genome that affect the structure and regulation of proteins to the distribution of variants in parts of the genome that do not affect proteins. Since these neutral parts of the genome are less likely to be affected by natural selection, they reasoned that studying variants in these regions should reflect the demographic history of populations.
The researchers found that many previously identified genetic signals of selection may have been created by historical and demographic factors rather than by selection. When the team compared closely related populations they found few large genetic differences. If the individual populations' environments were exerting strong selective pressure, such differences should have been apparent.
Selection may still be occurring in many regions of the genome, says Pritchard. But if so, it is exerting a moderate effect on many genes that together influence a biological characteristic. "We don't know enough yet about the genetics of most human traits to be able to pick out all of the relevant variation," says Pritchard. "As functional studies go forward, people will start figuring out the phenotypes that are associated with selective signals," says lead author Graham Coop. "That will be very important, because then we can figure out what selection pressures underlie these episodes of natural selection."
But even with further research, much will remain unknown about the processes that have resulted in human traits. In particular, Pritchard and Coop urge great caution in trying to link selection with complex characteristics like intelligence. "We're in the infancy of trying to understand what signals of selection are telling us," says Coop, "so it's a very long jump to attribute cultural features and group characteristics to selection."
Journal reference:
Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, et al. The Role of Geography in Human Adaptation. PLoS Genetics, 2009; 5 (6): e1000500 DOI: 10.1371/journal.pgen.1000500
Adapted from materials provided by Public Library of Science, via EurekAlert!, a service of AAAS.

Breakthrough in the treatment of bacterial meningitis

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It can take just hours after the symptoms appear for someone to die from bacterial meningitis. Now, after years of research, experts at The University of Nottingham have finally discovered how the deadly meningococcal bacteria is able to break through the body's natural defence mechanism and attack the brain.

The discovery could lead to better treatment and vaccines for meningitis and could save the lives of hundreds of children.
Bacterial meningitis in childhood is almost exclusively caused by the respiratory tract pathogens Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. The mechanism used by these lethal germs to break through the blood brain barrier (BBB) has, until now, been unknown.
The team led by Dlawer Ala'Aldeen, Professor of Clinical Microbiology and Head of the Molecular Bacteriology and Immunology Group at the Centre for Biomolecular Sciences, recently discovered that all three pathogens target the same receptor on human cerebrovascular endothelial cells — the specialised filtering system that protects our brain from disease — enabling the organisms to cross the blood-brain barrier.
Their findings, published today in The Journal of Clinical Investigation, suggest that disruption or modulation of this interaction of bacterial adhesins with the receptor might offer unexpectedly broad protection against bacterial meningitis and may provide a therapeutic target for the prevention and treatment of disease.
Professor Ala'Aldeen, who has been studying meningitis and its causes for over 20 years, said: "This is a significant breakthrough which will help us design novel strategies for the prevention and treatment of bacterial meningitis. Identification of the human receptor and bacterial ligands is like identifying a mysterious key and its lock, which will open new doors and pave the way for new discoveries."
The research, carried out in collaboration with the Department of Infectious Diseases at St. Jude Children's Research Hospital in Memphis Tennessee, also involved students from the University who have been regular and willing volunteers in the research programme.
Professor Ala'Aldeen said: "The ultimate aim is to save lives by protecting the healthy and curing the sick. We are one step closer to new breakthroughs that would prevent disease or its complications. There still is a long way to go before we have the ultimate vaccine and the ultimate treatment of bacterial meningitis."
Source: University of Nottingham (news : web)

Developed a human monoclonal antibody that neutralizes the Hepatitis C virus (HCV).

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ScienceDaily (May 11, 2009) — aking aim at a leading cause of liver failure in the United States, a team of scientists at the Massachusetts Biologic Laboratories (MBL) of the University of Massachusetts Medical School (UMMS) has developed a human monoclonal antibody that neutralizes the Hepatitis C virus (HCV). The new antibody effectively neutralized the virus in culture, and then prevented infection by the virus in a pre-clinical animal model of the disease.

Details of the research were presented April 23 in Copenhagen, Denmark at the 44th Annual Meeting of the European Association for the Study of the Liver (EASL). "We are pleased with the progress of this program," said Donna Ambrosino, MD, executive director of the MBL and a professor of pediatrics at the Medical School. "This antibody shows significant efficacy against the virus."
In the current study, MBL scientists injected transgenic mice (HuMAb Mouse® technology, Medarex, Inc.) with elements of HCV and then painstakingly searched for individual human antibodies produced in the mice that would recognize and bind to the HCV's outer coat, known as the glycoprotein. Once they found human antibodies that looked promising, they evaluated in vitro the ability of those antibodies to neutralize the virus and selected a lead candidate antibody for further characterization. Collaborative work with clinical researchers from the Department of Medicine at the Medical School's Worcester campus demonstrated that this antibody, now known as MBL-HCV1, was able to bind tightly with all genotypes of HCV tested from infected patient samples.
MBL-HCV1 was then tested off-site on three non-human primates. In that study, one animal received no antibody, one a low dose of the new antibody, and one a higher dose. Then all three animals were exposed to HCV. The animals with low or no antibody dosages developed HCV infections, but the animal with the higher dose was protected. Subsequently, researchers gave the high-dose of the antibody to the animal that originally received no antibody, and in that case the HCV was cleared from that animal's system. "These results are encouraging as a possible treatment for HCV infected patients, but more work needs to be done before we know how effective it will be in people," Dr. Ambrosino noted.
HCV attacks the liver and can eventually lead to liver failure. According to the U.S. Centers for Disease Control and Prevention, 3.2 million Americans are chronically infected with HCV and some 10,000 die annually of the disease. Globally, as many as 170 million people are estimated to suffer from HCV infection. For the most serious cases of HCV that do not respond to antiviral drugs, liver transplantation is the only option.
Typically 2,000 to 4,000 liver transplants are done each year in the United States (far less than the number of people on the waiting list for available organs). Transplantation can be a life saving treatment; however, in nearly all cases the patient's new liver is eventually infected by HCV because the virus remains in the patient's bloodstream during surgery. The powerful antiviral drugs now used to attack HCV prior to end-stage liver failure are not routinely used during surgery due to the patients' weakened condition and because of the strong medication used to avoid rejection of the new liver. After re-infection with HCV, nearly 40 percent of patients suffer rapid liver failure.
To close that clinical gap, the new antibody developed at MBL is designed to be a therapy shortly before and after transplant surgery. By giving a patient the new antibody before and during the time when the donor liver is implanted, researchers hope the HCV virus left in the bloodstream will be neutralized and rendered unable to infect the new liver. Then, because monoclonal antibodies are highly specific and typically have little or no side-effects, additional dosages of the new antibody could, theoretically, be given immediately after transplant surgery to continue neutralizing any remaining virus.
It is also possible, researchers theorize, that the antibody could be used in combination with new antiviral drugs for treatment in patients with newly diagnosed HCV infection. Use of the new antibody for both liver transplant patients and in newly diagnosed HCV patients will now be further evaluated. A Phase 1 human clinical trial of MBL-HCV1 in healthy subjects is expected to begin later this year.
Adapted from materials provided by University of Massachusetts Medical School, via EurekAlert!, a service of AAAS.

New Telomere Discovery Could Help Explain Why Cancer Cells Never Stop Dividing

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http://www.sciencedaily.com/releases/2007/10/071004143131.htm

Science Daily — A group working at the Swiss Institute for Experimental Cancer Research (ISREC) in collaboration with the University of Pavia has discovered that telomeres, the repeated DNA-protein complexes at the end of chromosomes that progressively shorten every time a cell divides, also contain RNA.

This discovery, published in Science Express, calls into question our understanding of how telomeres function, and may provide a new avenue of attack for stopping telomere renewal in cancer cells.
Inside the cell nucleus, all our genetic information is located on twisted, double stranded molecules of DNA which are packaged into chromosomes. At the end of these chromosomes are telomeres, zones of repeated chains of DNA that are often compared to the plastic tips on shoelaces because they prevent chromosomes from fraying, and thus genetic information from getting scrambled when cells divide.
The telomere is like a cellular clock, because every time a cell divides, the telomere shortens. After a cell has grown and divided a few dozen times, the telomeres turn on an alarm system that prevents further division. If this clock doesn't function right, cells either end up with damaged chromosomes or they become "immortal" and continue dividing endlessly -- either way it's bad news and leads to cancer or disease. Understanding how telomeres function, and how this function can potentially be manipulated, is thus extremely important.
The DNA in the chromosome acts like a sort of instruction manual for the cell. Genetic information is transcribed into segments of RNA that then go out into the cell and carry out a variety of tasks such as making proteins, catalyzing chemical reactions, or fulfilling structural roles. It was thought that telomeres were "silent" -- that their DNA was not transcribed into strands of RNA. The researchers have turned this theory on its head by discovering telomeric RNA and showing that this RNA is transcribed from DNA on the telomere.
Why is this important" In embryonic cells (and some stem cells), an enzyme called telomerase rebuilds the telomere so that the cells can keep dividing. Over time, this telomerase dwindles and eventually the telomere shortens and the cell becomes inactive. In cancer cells, the telomerase enzyme keeps rebuilding telomeres long past the cell's normal lifetime. The cells become "immortal", endlessly dividing, resulting in a tumor. Researchers estimate that telomere maintenance activity occurs in about 90% of human cancers. But the mechanism by which this maintenance takes place is not well understood. The researchers discovered that the RNA in the telomere is regulated by a protein in the telomerase enzyme. Their discovery may thus uncover key elements of telomere function.
"It's too early to give yet a definitive answer," to whether this could lead to new cancer therapies, notes Joachim Lingner, senior author on the paper. "But the experiments published in the paper suggest that telomeric RNA may provide a new target to attack telomere function in cancer cells to stop their growth."
Joachim Lingner is an Associate Professor at the EPFL (Ecole Polytechnique Fédérale de Lausanne). Funding for this research was provided in part by the Swiss National Science Foundation NCCR "Frontiers in Genetics".
Article: "Telomeric Repeat Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends"
Note: This story has been adapted from material provided by Ecole Polytechnique Fédérale de Lausanne.

Fausto Intilla

www.oloscience.com

Individual Differences Caused By Shuffled Chunks Of DNA In The Human Genome

Source:

http://www.sciencedaily.com/releases/2007/09/070927154931.htm

Science Daily — A study by Yale researchers offers a new view of what causes the greatest genetic variability among individuals -- suggesting that it is due less to single point mutations than to the presence of structural changes that cause extended segments of the human genome to be missing, rearranged, or present in extra copies.

"The focus for identifying genetic differences has traditionally been on point mutations or SNPs -- changes in single bases in individual genes," said Michael Snyder, the Cullman Professor of Molecular, Cellular & Developmental Biology and senior author of the study, which was published in Science Express. "Our study shows that a considerably greater amount of variation between individuals is due to rearrangement of big chunks of DNA."
Although the original human genome sequencing effort was comprehensive, it left regions that were poorly analyzed. Recently, investigators found that even in healthy individuals, many regions in the genome show structural variation. This study was designed to fill in the gaps in the genome sequence and to create a technology to rapidly identify structural variations between genomes at very high resolution over extended regions.
"We were surprised to find that structural variation is much more prevalent than we thought and that most of the variants have an ancient origin. Many of the alterations we found occurred before early human populations migrated out of Africa," said first author Jan Korbel, a postdoctoral fellow in the Department of Molecular Biophysics & Biochemistry at Yale.
To look at structural variants that were shared or different, DNA from two females -- one of African descent and one of European descent -- was analyzed using a novel DNA-based methodology called Paired-End Mapping (PEM). Researchers broke up the genome DNA into manageable-sized pieces about 3000 bases long; tagged and rescued the paired ends of the fragments; and then analyzed their sequence with a high-throughput, rapid-sequencing method developed by 454 Life Sciences.
"454 Sequencing can generate hundreds of thousands of long read pairs that are unique within the human genome to quickly and accurately determine genomic variations," explained Michael Egholm, a co-author of the study and vice president of research and development at 454 Life Sciences.
"Previous work, based on point mutations estimated that there is a 0.1 percent difference between individuals, while this work points to a level of variation between two- and five-times higher," said Snyder.
"We also found 'hot spots' -- particular regions where there is a lot of variation," said Korbel. "While these regions may be still actively undergoing evolution, they are often regions associated with genetic disorder and disease."
"These results will have an impact on how people study genetic effects in disease," said Alex Eckehart Urban, a graduate student in Snyder's group, and one of the principal authors on the study. "It was previously assumed that 'landmarks,' like the SNPs mentioned earlier, were fairly evenly spread out in the genomes of different people. Now, when we are hunting for a disease gene, we have to take into account that structural variations can distort the map and differ between individual patients."
"While it may sound like a contradiction," says Snyder, "this study supports results we have previously reported about gene regulation as the primary cause of variation. Structural variation of large of spans of the genome will likely alter the regulation of individual genes within those sequences."
According to the authors, even in healthy people, there are variants in which part of a gene is deleted or sequences from two genes are fused together without destroying the cellular activity with which they are associated. They say these findings show that the "parts list" of the human genome may be more variable, and possibly more flexible, than previously thought.
Other authors from Yale in addition to primary authors Alex E Urban and Jan Korbel, who is also affiliated with the European Molecular Biology Laboratory in Heidelberg, Germany, are Fabian Grubert, Philip Kim, Dean Palejev, Nicholas Carriero, Andrea Tanzer, Eugenia Saunders, Sherman Weissman, and Mark Gerstein. The research was funded the National Institutes of Health, a Marie Curie Fellowship, the Alexander von Humboldt Foundation, The Wellcome Trust, Roche Applied Science and the Yale High Performance Computation Center.
Citation: Science: Science Express (on line) September 28, 2007.
Note: This story has been adapted from material provided by Yale University.

Fausto Intilla

www.oloscience.com

Personal Genomes: Mainstream In Five Years, But Who Should Have Access?

Source:

http://www.sciencedaily.com/releases/2007/09/070920145356.htm

Science Daily — Imagine this: you visit your clinician, undergo genetic testing, and then you are handed a miniature hard drive containing your personal genome sequence, which is subsequently uploaded onto publicly accessible databases. This may sound like science fiction, but it is scientific fact, and it is already happening.

In an article published in the upcoming issue of Science, University of Alberta researcher Tim Caulfield and co-authors highlight the need to proceed with caution when it comes to personal genomics projects that represent research milestones but are also fraught with ethical, social and clinical implications. Caulfield, who is the Canada Research Chair in Health Law at the U of A and professor and research director in public health sciences, is recognized as one of the foremost experts in health law research in Canada.
Scientists predict that within five years DNA sequencing technologies will be affordable enough that personal genomics will be integrated into routine clinical care. Companies are responding by offering their services for ancestry tracing, forensics, nutritional advice and reproductive assistance. It won't be long before companies are able to offer Facebook-like social networking services centred around our genomes.
Once we have our personal genomic information, what will we do with it and how might this information be used outside the medical context? How will physicians educate patients about the significance of genetic risk information? Will already-strained health-care systems be able to cope with the inevitable influx of "worried well" patients seeking follow-up investigations for genetic risks that are not clinically meaningful?
Caulfield and his colleagues pose these questions and warn that the routine generation of individual genome sequences will pose challenges to our health-care system.
They argue that only clinically meaningful genomic test results should be integrated into medical decision-making--however, this will require clear standards, multidisciplinary collaboration and careful consideration of the ethical, social and clinical implications.
Note: This story has been adapted from a news release issued by University of Alberta.

Fausto Intilla

www.oloscience.com

Skin As A Living Coloring Book

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http://www.sciencedaily.com/releases/2007/09/070906132823.htm

Science Daily — The pigment melanin, which is responsible for skin and hair color in mammals, is produced in specialized cells called melanocytes and then distributed to other cells. But not every cell in the complex layers of skin becomes pigmented. The question of how melanin is delivered to appropriate locations may have been answered by a study from researchers at the Massachusetts General Hospital (MGH) Cutaneous Biology Research Center (CBRC).

"Pigment recipient cells essentially tell melanocytes where to deposit melanin, and the pattern of those recipients determines pigment patterns," says Janice Brissette, PhD, who led the study. "Recipient cells act like the outlines in a child's coloring book; as recipient cells develop, they form a 'picture' that is initially colorless but is then 'colored in' by the melanocytes."
In humans, melanin is deposited in both the skin and the hair; but in some other mammals such as mice, melanin is primarily deposited in the coat, leaving the skin beneath the coat unpigmented. Melanocytes deposit melanin via cellular extensions called dendrites that reach out to other cells in the epidermis (the outer layer of skin) or the hair follicles. But the mechanism determining whether melanin is delivered to a particular cell has been unknown.
The MGH-CBRC researchers theorized that a mouse gene known as Foxn1 might play a role. Lack of Foxn1 is responsible for so-called 'nude mice,' which have hair that is so brittle it breaks off, resulting in virtually total hairlessness, and other defects of the skin. A similar phenomenon exists in humans with inactivation of the corresponding gene.
When the researchers developed a strain of transgenic mice in which Foxn1 is misexpressed in cells that do not usually contain melanin, they found those normally colorless areas became pigmented. Examining the skin of the transgenic mice revealed that melanocytes were contacting and delivering melanin to the cells in which Foxn1 was abnormally activated. No pigment was observed in the corresponding tissues of normal mice. Examination of human skin samples showed that the human version of Foxn1 was also expressed in cells known to be pigment recipients. Further experiments revealed that Foxn1 signals melanocytes through a protein called Fgf2, levels of which rise as Foxn1 expression increases.
"Foxn1 makes epithelial cells into pigment recipients, which attract melanocytes and stimulate pigment transfer, engineering their own pigmentation," says Brissette, an associate professor of Dermatology at Harvard Medical School. She and her colleagues note that the Foxn1/Fgf2 pathway probably has additional functions in the skin and that it is probably not the only pathway responsible for the targeting of pigment.
"We know that Foxn1 and Fgf2 act in concert with other factors and function within a larger network of genes. Our next step will be to identify other genes that can confer the pigment recipient phenotype or control the targeting of pigment," Brissette adds. Her research may eventually be relevant to disorders such as vitiligo -- in which pigment disappears from patches of skin -- age spots, the greying of hair and even the deadly melanocyte-based skin cancer melanoma.
The report appears in the Sept. 7 issue of Cell.
The co-first authors of the Cell report are Lorin Weiner, PhD, and Rong Han, PhD, both of the MGH-CBRC. Additional co-authors are Jian Li, PhD, Kiyotaka Hasegawa, MS, and David Lee, MGH-CBRC; Bianca Scicchitano, PhD, now at La Sapienza/University of Rome; and Maddalena Grossi, PhD, University of Lausanne, Switzerland. The study was supported by the National Institutes of Health and by the CBRC.
Note: This story has been adapted from a news release issued by Massachusetts General Hospital.

Fausto Intilla

www.oloscience.com

'Skinny Gene' Exists

Source:

http://www.sciencedaily.com/releases/2007/09/070904122434.htm

Science Daily — Researchers at UT Southwestern Medical Center have found that a single gene might control whether or not individuals tend to pile on fat, a discovery that may point to new ways to fight obesity and diabetes.

"From worms to mammals, this gene controls fat formation," said Dr. Jonathan Graff, associate professor of developmental biology and internal medicine at UT Southwestern and senior author of a study appearing in the Sept. 5 issue of Cell Metabolism. "It could explain why so many people struggle to lose weight and suggests an entirely new direction for developing medical treatments that address the current epidemic of diabetes and obesity.
"People who want to fit in their jeans might someday be able to overcome their genes."
The gene, called adipose, was discovered in fat fruit flies more than 50 years ago by a graduate student at Yale University, but few people knew about it. Its mechanism was unknown, and whether it's important in other genes was a mystery.
In the current study, the UT Southwestern researchers examined how adipose works by analyzing fruit flies, tiny worms called C. elegans, cultured cells, and genetically engineered mice, as well as by exploiting sophisticated molecular techniques. Using several methods, they manipulated adipose in the various animals, turning the gene on and off at different stages in the animals' lives and in various parts of their bodies.
It was discovered that the gene, which is also present in humans, is likely to be a high-level master switch that tells the body whether to accumulate or burn fat.
In the mice, the researchers found that increasing adipose activity improved the animals' health in many ways. Mice with experimentally increased adipose activity ate as much or more than normal mice; however, they were leaner, had diabetes-resistant fat cells, and were better able to control insulin and blood-sugar metabolism.
In contrast, animals with reduced adipose activity were fatter, less healthy and had diabetes.
The researchers' work on flies showed that the gene is "dose-sensitive" -- that is, the various combinations of the gene's variants lead to a range of body types from slim to medium to obese.
"This is good news for potential obesity treatments, because it's like a volume control instead of a light switch; it can be turned up or down, not just on or off," Dr. Graff said. "Eventually, of course, the idea is to develop drugs to target this system, but that's in the years to come."
This genetic mechanism makes survival sense, he said, because if a population has many versions of the gene scattered among many different individuals, at least some will survive in different conditions. For instance, a fat fruit fly may be able to survive famine, but a sleeker model might be better at evading predators.
Dr. Graff said the next step is to understand better the exact mechanisms by which adipose exerts its control.
Although the current study finally identifies the adipose gene's function, the gene was discovered more than 50 years ago when Winifred Doane, now a professor emeritus at Arizona State University, was studying fruit flies and noticed that some contained more fat than others. She linked this trait to a gene she named adipose and hypothesized that this natural variation gave the chubbier flies an evolutionary advantage; they could hoard more fat on the same amount of food as their skinnier counterparts, allowing them to survive times of famine.
But for people in developed countries, this trait has backfired. It's all feast and no famine, so the fat builds and builds.
"Even a pound a year adds up over a lifetime," Dr. Graff said.
Other UT Southwestern researchers involved in the study were Dr. Jae Myoung Suh, postdoctoral researcher in developmental biology; Daniel Zeve, Robert Li and Michael Wang, students in the Medical Scientist Training Program; Dr. Renee McKay, instructor of developmental biology; Dr. Jin Seo, postdoctoral researcher in developmental biology; and Zack Salo, undergraduate at UT Arlington.
The work was supported by the National Institutes of Health.
Note: This story has been adapted from a news release issued by UT Southwestern Medical Center.

Fausto Intilla

www.oloscience.com

Fighting Malaria By Tricking Mosquito's Sense Of Smell

Source:

http://www.sciencedaily.com/releases/2007/08/070830122259.htm

Science Daily — By mapping a specialized sensory organ that the malaria mosquito uses to zero in on its human prey, an international team of researchers has taken an important step toward developing new and improved repellents and attractants that can be used to reduce the threat of malaria, generally considered the most prevalent life-threatening disease in the world.

The sensory organ is the maxillary palp. It is one of three structures extending from the mosquito's head that together provide it with its sense of smell and taste. The other two are the feathery antennae that serve as general-purpose olfactory organs and respond to a wide range of different chemicals and the proboscis that contains sensors designed for close-in odor and taste detection.
The detailed map of the maxillary palp, which was published online in the journal Current Biology on Aug. 30, has determined that it contains a unique array of highly specialized receptor cells that detect carbon dioxide and octenol, key chemical signals that the insects use to find human prey.
"These receptors are highly sensitive, which suggests that the maxillary palps may serve as the malaria mosquito's long-range detection system," says Tan Lu, a graduate student at Vanderbilt who is the paper's first author.
"We haven't proven it yet, but the implication is that if you took away the maxillary palp the mosquito would not do nearly as well at finding human prey," adds Laurence J. Zwiebel, professor of biological sciences at Vanderbilt, who headed the study.
The research was performed by collaborators from Vanderbilt, Yale and Wageningen University in the Netherlands. They are part of a team that also includes researchers from the Ifakara Health Research and Development Centre in Tanzania and the Medical Research Council Laboratories in the Gambia that is funded by a grant from the Foundation for the National Institutes of Health through the Grand Challenges to Global Health Initiative in 2005 to develop a chemical strategy to combat the spread of malaria by the Anopheles mosquito.
"This paper marks a threshold in our grand challenge project because it provides a biological context and then strips it down to a few molecular targets that we are using to develop chemical modifiers that should have direct impacts on the mosquito's behavior," says Zwiebel.
The study fills a major gap in the scientific understanding of the malaria mosquito's olfactory system. Although considerable research has been done on the physiology and molecular biology of Anopheles gambiae's antennae and proboscis, there have been few studies of its maxillary palps. Most of the previous work that had been done on this "accessory olfactory appendage" was performed in another species of mosquito, Aedes aeqypti, the carrier of dengue and yellow fever.
Previous work found that the maxillary palps of the A. aeqypti were sensitive to carbon dioxide and octenol. So the discovery that this was also the case in An. gambiae did not come as a big surprise. However, the researchers found that the malaria mosquito uses different sets of receptors for this purpose which help explain why it appears to rely less on carbon dioxide and more on human-specific chemical compounds in seeking out hosts than does A. aegypti.
The mosquito's elaborate "nose" consists of hundreds of hollow hair-like structures called sensilla attached to its antennae, maxillary palps and proboscis. The tips of these structures are perforated with thousands of tiny holes that let aromatic compounds penetrate to their interior, where they encounter thread-like extensions from neurons which are tuned to detect specific molecules.
Compared to the mosquito's antennae, which are designed to detect hundreds of different compounds, the study found that the maxillary palps are highly specialized. "The amazing thing that we found was that all the sensory hairs that line the bottom of the maxillary palps are identical," says Zwiebel. They are all attached to three neurons: one which is tuned to detect carbon dioxide; one which is tuned to detect octenol; and one which serves to enhance general olfactory reception.
In addition to Zwiebel and Lu, the Vanderbilt researchers who contributed to the study are Quirong Wang, Michael Rutzler, Hyung-Wook Kwon and R. Jason Pitts. The Wageningen team consists of Yu Tong Qiu, Joop J.A. van Loon and Willem Takken. The Yale contributors are Jae Young Kwon and John R. Carlson. The research was funded by a Gates Foundation Grand Challenges in Global Health Initiative grant and by grants from the National Institutes of Health. Note: This story has been adapted from a news release issued by Vanderbilt University.

Fausto Intilla

www.oloscience.com

Genome Study Shines Light On Genetic Link To Height

Source:

http://www.sciencedaily.com/releases/2007/09/070902193734.htm

Science Daily — It became clear nearly a century ago that many genes likely influence how tall a person grows, though little progress, if any, has followed in defining the myriad genes. Now an international research team brings light to this age-old question by pinpointing a genetic variant associated with human height -- the first consistent genetic link to be reported.

The findings, published in Nature Genetics, stem from a large-scale effort led by scientists at the Broad Institute of Harvard and MIT, Children's Hospital Boston, the University of Oxford and Peninsula Medical School, Exeter.
Using a new "genome-wide association" method, the research team searched the human genome for single letter differences in the genetic code that appear more often in tall individuals compared to shorter individuals. By analyzing DNA from nearly 35,000 people, the researchers zeroed in on a difference in the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T'. Inheriting the 'C'-containing copy of the gene often makes people taller: one copy can add about a half centimeter in height while two copies can add almost a full centimeter.
"This is the first convincing result that explains how DNA can affect normal variation in human height," said co-senior author Joel Hirschhorn, an associate member of the Broad Institute, a pediatric endocrinologist at Children's Hospital Boston, and an associate professor of genetics at Harvard Medical School. "Because height is a complex trait, involving a variety of genetic and non-genetic factors, it can teach us valuable lessons about the genetic framework of other complex traits -- such as diabetes, cancer and other common human diseases."
In addition to being a textbook example of a complex trait, height is a common reason children are referred to medical specialists. Although short stature by itself typically does not signal cause for concern, delayed growth can sometimes reflect a serious underlying health condition. "By defining the genes that normally affect stature, we might someday be able to better reassure parents that their child's height is within the range predicted by DNA, rather than a consequence of disease," said Hirschhorn.
Nearly 90% of the variation in height among most human populations can be attributed to DNA. The remainder is due to environmental and lifestyle factors, such as nutrition. Although a few genes have been uncovered through studies of rare, single-gene stature disorders, most do not seem to be associated with height in the general population. Recent advances, including the completion of the HapMap project and the availability of large-scale research tools, enabled the scientists to take a systematic approach to understand how common genetic differences can impact a person's height.
The results of the research team, which also includes co-senior authors Timothy Frayling of the Peninsula Medical School, Exeter and Mark McCarthy of the University of Oxford, spring from data made available in two recent genome-wide association studies of type 2 diabetes. The studies, one led by the Diabetes Genetics Initiative and the other by the Wellcome Trust Case Control Consortium, involved nearly 5,000 patients who generously volunteered DNA samples as well as pertinent clinical information, such as height and weight.
After scrutinizing the initial data, the scientists identified a single letter change -- known as a single nucleotide polymorphism or SNP -- in the HMGA2 gene as the most promising result. They collaborated with additional researchers to study this SNP through a second phase of analysis that encompassed nearly 30,000 individuals: adults and children from the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Exeter Family Study of Childhood Health (EFSOCH),
European adults taking part in a study of type 2 diabetes risk (UKT2D GCC), Finnish individuals participating in the FINRISK1997 health survey, and a set of tall and short European American and Polish adults assembled for studies of height. This two-pronged approach enabled co-first author Guillaume Lettre, a researcher at the Broad Institute and Children's Hospital Boston, and his colleagues to convincingly prove that the DNA variation in HMGA2 influences height.
The genomic find, though, is not the only indication that HMGA2 affects height. Previous studies in mice and humans revealed that a handful of rare stature disorders result from severe mutations in the gene. Taken together, the findings provide strong evidence for a role for HMGA2 in height. However, the identified SNP accounts for just 0.3% of the normal variability in human stature, which means there are probably many others yet to be found. To do this, researchers will need to study even larger groups of individuals.
"Unlike most other complex traits, height is something that can be easily defined and measured in very large numbers of people," said Hirschhorn. "Soon the scientific community will have access to many more large-scale genomic data sets, making it feasible to identify additional genes involved in height."
While surprisingly little is known about how genes hardwire humans for growth, some initial clues have already surfaced as a result of the HMGA2 discovery. The gene is active in the first months of fetal growth and shuts off shortly before birth, suggesting it orchestrates growth-related events early in human development. Moreover, it appears to influence the overall longitudinal growth of the skeleton, as scientists found that the T-to-C change in the gene's DNA sequence correlates with an increased length of both the limbs and spine in young children. HMGA2 has also been implicated in certain forms of cancer. Thus, further studies may help dissect the relationship between normal growth and the deranged growth central to cancer.
Citation: Weedon MN et al. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nature Genetics; DOI:10.1038/ng2121
Note: This story has been adapted from a news release issued by Broad Institute of MIT and Harvard.

Fausto Intilla

www.oloscience.com

First Diploid Human Genome Sequence Shows We're Surprisingly Different

Source:

http://www.sciencedaily.com/releases/2007/09/070904072204.htm

Science Daily — Researchers at the J. Craig Venter Institute (JCVI), along with collaborators at The Hospital for Sick Children (Sick Kids) in Toronto and the University of California, San Diego (UCSD), have published a genome sequence of an individual, J. Craig Venter, Ph.D., that covers both of his chromosome pairs (or diploid genome), one set being inherited from each of his parents.

Two other versions of the human genome currently exist—one published in 2001 by Dr. Venter and colleagues at Celera Genomics, and another at the same time by a consortium of government and foundation-funded researchers. These genomes were not of any single individual, but rather were a mosaic of DNA sequences from various donors. In the case of Celera it was a consensus assembly from five individuals, while the publicly-funded version was based on patching together sequences from over 100 anonymous human sources. Both versions greatly underestimated human genetic diversity.
This new genome (called “HuRef”) represents the first time a true diploid genome from one individual—Dr. Venter, has been published. The research is available in the open access public journal, PLoS Biology.
Researchers at the JCVI have been sequencing and analyzing this version of Dr. Venter’s genome since 2003. Building on reanalyzed data from Dr. Venter’s genome that constituted 60% of the previously published Celera genome, the team had the goal of constructing a definitive reference human genome based on one individual. Using whole genome shotgun sequencing and highly accurate DNA sequencing using Sanger-based chemistry, the team produced additional data which constitutes the final 32 million sequence reads.
From the combined data of more than 20 billion base pairs of DNA, the team was able to assemble the majority of Dr. Venter's genome. Since this genome assembly uniquely catalogues the contributions of each of the parental chromosomes, for the first time the amount of variation existing between the two could be determined. Surprisingly, a higher than expected amount of genetic variation was found to exist between the two human chromosomes.
“Each time we peer deeper into the human genome we uncover more valuable insight into our intricate biology,” said Dr. Venter. “With this publication we have shown that human to human variation is five to seven-fold greater than earlier estimates proving that we are in fact more unique at the individual genetic level than we thought.” He added, “It is clear however that we are still at the earliest stages of discovery about ourselves and only with additional sequencing of more individual genomes will we garner a full understanding of how our genes influence our lives.”
Within the human genome there are several different kinds of DNA variants. The most studied type is single nucleotide polymorphisms or SNPs, which are thought to be the essential variants implicated in human traits and disease susceptibility. A total of 4.1 million variants covering 12.3 million base pairs of DNA were uncovered in this analysis of Dr. Venter’s genome. Of the 4.1 million variations between chromosome sets, 3.2 million were SNPs. This is a typical number expected to be found in any other human genome, but there were at least 1.2 million variants that had not been described before. Surprisingly, nearly one million were different kinds of variants including: insertion/deletions (“indels”), copy number variants, block substitutions and segmental duplications.
While the SNP events outnumbered the non-SNP variants, the latter class involved a larger portion (74%) of the variable component of Dr. Venter's genome. This data suggests that human-to-human variation is much greater than the 0.1% difference found in earlier genome sequencing projects. The new estimate based on this data is that genomes between individuals have at least 0.5% total genetic variation (or are 99.5% similar) The researchers suggest that much more research needs to be done on these non-SNP variants to better understand their role in individual genomics.
According to Samuel Levy, Ph.D., lead author and senior scientist at JCVI, “The ability to use unbiased, high throughput, sequencing methods coupled with advance computational analytic methods, enables us to characterize more comprehensively the wide variety of individual genetic variation. This offers us an unprecedented opportunity to study the prevalence and impact of these DNA variants on traits and diseases in human populations.”
Another important feature that is made possible by having an individual, diploid genome is the ability to generate more informed haplotype assemblies. Haplotypes are groups of linked variations along the chromosomes. Other studies have generated many common haplotypes, however these are based on averages of large populations rather than individuals. Individual haplotypes enable scientists to study rare or 'private' variants that might explain and help predict traits and diseases in that particular person—allowing an individualized approach in genomic applications.
In the HuRef analysis, the team used the heterozygous portion of the 4.1 million variant set and new algorithms to build haplotype assemblies. These haplotype assemblies were typically an order of magnitude larger than what can be achieved by genotyping a single individual, with over half the genome contained in segments greater than 200,000 base pairs in length. The JCVI researchers expect this number to improve significantly as additional sequence coverage is added to HuRef using a variety of new sequencing technologies.
"In the future it will be possible to know the parental origin of DNA that is contributing, either alone or in combination, to various traits or disease," said co-author Stephen Scherer, Ph.D., senior scientist in Genetics and Genomic Biology at SickKids and professor of Molecular and Medical Genetics at the University of Toronto. "This study discovered that in an individual genome upwards of 44% of genes were variable in sequence, a number that geneticists have wondered about for 50 years. With this type of knowledge now in hand, the stage is set for an era of personalized medicine where genome sequence information becomes a critical reference to assist with health-related decisions", concluded Scherer.
Background
The publication of Dr. Venter’s genome represents the first publication of an individual’s genome and the first human genome publication since the first sequence and analysis of the human genome published in Science in 2001 by Dr. Venter and colleagues at Celera Genomics. The publicly funded genome project also published their version of the human genome at the same time in the journal Nature. At Celera there were five individuals whose genomes were used for that consensus human genome assembly. One of those individuals was Dr. Venter whose DNA constituted the majority of the DNA for that genome. The publicly funded genome project used DNA from a variety of individuals and is a composite version.
The new HuRef version of the human genome is the sequence and assembly of one individual in which the person’s two sets of chromosomes (one inherited from the mother and one set from the father) are represented. It is this kind of genome sequencing and analysis that will usher in the true era of individualized medicine.
Dr. Venter and the team at JCVI have long been proponents of finding new and improved methods for sequencing genomes since it is only through cost-effective and accurate sequencing methods that millions of human genomes can be sequenced. In September 2003, the JCVI announced a $500,000 prize for advances leading to the sequencing of one genome for $1,000 or less. The JCVI prize was eventually joined with the $10 million Archon X Prize for Genomics.
For the HuRef project, the team at JCVI used a more traditional method of sequencing—whole genome shotgun assembly which is built upon Sanger dideoxy sequencing. Then, Applied Biosystems 3730xl high-throughput DNA sequencing machines were employed since these methods still produce the longest and most accurate lengths of DNA. This project was designed to produce an accurate and more complete version of a single individual’s genome rather than producing a fast and potentially less expensive version. From the HuRef genome however the researchers believe that newer methods for sequencing can be used to enable more people to have their genome’s sequenced and analyzed. It is clear that the HuRef version is likely the last time that these more traditional methods of sequencing will be employed.
Funding for the research on the new HuRef diploid genome was from the J. Craig Venter Institute.
Note: This story has been adapted from a news release issued by J. Craig Venter Institute.

Fausto Intilla

www.oloscience.com