PHILADELPHIA Rahul M. Kohli, MD, PhD, an assistant professor of Medicine and Biochemistry & Biophysics, is one of the recipients of a New Innovator Award from National Institutes of Health (NIH).

The NIH Directors New Innovator Award, totaling $1.5 million over five years, supports highly innovative research and creative, new investigators who exhibit strong potential to make great advances on a critical biomedical or behavioral research problem.

Kohlis lab will use the grant to study the enzymes that drive bacterial evolution, aiming to devise new methods to combat the emergence of drug-resistant bacteria.

The ability of pathogens to quickly build up resistance to the best available antibiotics leads to potentially devastating consequences to human health. Past responses to this concern have largely focused on modifying existing drugs, which can offer a brief reprieve, but eventually fosters more drug resistance. Kohlis research seeks to change the paradigm of attacking drug resistance, by targeting the very pathways that allow the pathogen to mutate.

Rather than focusing on drugs that kill bacteria, understanding and targeting bacterias ability to adapt could be an effective new approach to drug resistance, said Kohli. Given the clinical importance of the problem, Im excited about the opportunities we can pursue with this award.

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Penn Medicine is one of the world's leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of the Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System, which together form a $4.3 billion enterprise.

The Perelman School of Medicine is currently ranked #2 in U.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $479.3 million awarded in the 2011 fiscal year.

The University of Pennsylvania Health System's patient care facilities include: The Hospital of the University of Pennsylvania -- recognized as one of the nation's top "Honor Roll" hospitals by U.S. News & World Report; Penn Presbyterian Medical Center; and Pennsylvania Hospital the nation's first hospital, founded in 1751. Penn Medicine also includes additional patient care facilities and services throughout the Philadelphia region.

Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2011, Penn Medicine provided $854 million to benefit our community.

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Penn Medicine Researcher Receives New Innovator Award from National Institutes of Health

BYU biochemistry professor Emily Bates has made recent discoveries that may revolutionize medicine

BYU research has shed light on the cause and prevention of birth defects as well as cancer.

BYU biochemistry professor Emily Bates and a few of her students recently preformed and published research that may lead to a permanent answer for birth defects and impact how cancer is treated.

Fetal Alcohol Syndrome anda rare condition called Andersen-Tawil Syndrome both cause birth defects like cleft palates, small or missing teeth andmisshapedor connected fingers and toes. Andersen-Tawil Syndrome is caused by genetic changes in a potassium channel, which is also the same channel blocked by consumption of alcohol.

Bates and her students made the revolutionary discovery that potassium channels help cells receive instructions that tell them what they are and where they should be.

Dr. Bates in the research lab

The instructions for cells to divide and move need to be sent during pregnancy while a baby is developing, but those signals should turn off after the baby is born so the cells stay where they are. In cancer cells, the signal has turned back on, allowing cells to metastasize or invade other tissues and allow for growth of new tumors.

Not only are Bates and her students excited to have found some information about the causes of Andersen-Tawil and Fetal Alcohol Syndrome, they are also excited to test a possible therapy to stop the spread of cancer cells throughout the body.

What happens later on in life if someone gets cancer, is that this pathway turns on when its not supposed to turn on anymore, Bates said. The cancer cells start to metastasize, or invade another tissue causing more tumors. What we hope is that blocking this channel will block a signaling pathway that drives metastasis.

In other words, if Bates and her students can eventually find a way to block the channel after it opens back up, cancer cells will not spread throughout the body once the original tumor is removed.

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BYU breakthrough targets birth defects - BYU biochemistry professor Emily Bates has made recent discoveries that may ...

Public release date: 12-Sep-2012 [ | E-mail | Share ]

Contact: Jessica Studeny jessica.studeny@case.edu 216-368-4692 Case Western Reserve University

Menachem Shoham, PhD, associate professor of biochemistry at Case Western Reserve University School of Medicine, has discovered novel antivirulence drugs that, without killing the bacteria, render Methicillin Resistant Staphylococcus Aureus (MRSA) and Streptococcus pyogenes, commonly referred to as strep, harmless by preventing the production of toxins that cause disease. The promising discovery was presented this week at the Interscience Conference on Antimicrobial Agents and Chemotherapy in San Francisco.

MRSA infections are a growing public health concern, causing 20,000 to 40,000 deaths per year in the United States alone. It is the most prevalent bacterial pathogen in hospital settings and in the community at large, with about one million documented infections per year nationally, costing an estimated $8 billion annually to treat.

The problem has become increasingly severe as the bacteria have developed a resistance to antibiotics. As result, health care providers are running out of options to treat patients suffering from antibiotic-resistant infections, like MRSA and strep, creating a dire need for alternative treatments and approaches.

"Staph bacteria are ubiquitous and normally do not cause infections, however, occasionally these bacteria become harmful due to their secretion of toxins," says Dr. Shoham. "We have discovered potential antivirulence drugs that block the production of toxins, thus rendering the bacteria harmless. Contrary to antibiotics, these new antivirulence drugs do not kill the bacteria. Since the survival of the bacteria is not threatened by this approach, the development of resistance, like that to antibiotics, is not anticipated to be a serious problem."

Dr. Shoham identified a bacterial protein, known as AgrA, as the key molecule responsible for turning on the release of toxins. AgrA, however, needs to be activated to induce toxin production. His goal was to block the activation of AgrA with a drug, thus preventing the cascade of toxin release into the blood that can lead to serious infections throughout the body.

The screening for AgrA inhibitors was initially carried out in a computer by docking libraries of many thousands of "drug-like" compounds and finding out which compounds would fit best into the activation site on AgrA. Subsequently, about 100 of the best scoring compounds were tested in the laboratory for inhibition of the production of a toxin that ruptures red blood cells. Seven of these compounds were found to be active. Testing compounds bearing chemical similarity to the original compounds lead to the discovery of additional and more potent so-called "lead" compounds.

Optimization of the initial "lead" compounds was performed by chemical synthesis of 250 new compounds bearing small but important chemical modifications on one of the initial leads. More than a dozen active compounds have been discovered by this method. The best drug candidate reduces red blood cell rupture by 95 percent without affecting bacterial growth.

Beginning this fall, Dr. Shoham and colleagues will begin testing the drug candidate in animal models.

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Novel non-antibiotic agents against MRSA and common strep infections

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

Acceleron Pharma, Inc., a biopharmaceutical company developing protein therapeutics for cancer and orphan diseases, announced that Tom Maniatis, Ph.D., an Acceleron co-founder and Professor and Chair of the Department of Biochemistry and Molecular Biophysics at the Columbia University College of Physicians and Surgeons, is to be honored with the 2012 Lasker-Koshland Special Achievement Award in Medical Science. The Albert and Mary Lasker foundation award is considered to be one of the most prestigious scientific prizes and the Special Achievement Award recognizes its recipients for exceptional leadership and citizenship in biomedical science. Dr. Maniatis will be presented with the Lasker-Koshland Special Achievement Award in Medical Science on September 21st in New York City.

Dr. Maniatis is a pioneer in the development of gene cloning technology, and he has published extensively in the field of eukaryotic gene regulation. In particular, he identified numerous genetic defects that underlie the inherited human illness -thalassemia. Dr. Maniatis is widely known for his seminal work developing gene cloning technologies and applying those methods to discovering the genetic bases of human diseases. His book, The Cloning Manual, has become a world-wide resource.

In addition to these scientific accomplishments, Dr. Maniatis has been instrumental in creating successful biotechnology companies. He was a co-founder of Genetics Institute, where he chaired the scientific board and served on the board of directors for more than 17 years. During this time, Genetic Institutes gained FDA approval for several protein-based drugs, including recombinant human erythropoietin, Factor VIII and Factor IX, as well as bone morphogenic proteins. Dr. Maniatis was also a co-founder of ProScript Inc., which discovered the drug Velcade (bortezomib). Dr. Maniatis is currently a member of the board of directors at Acceleron.

Mark Ptashne, Ph.D., the Ludwig Chair of Molecular Biology at Memorial Sloan-Kettering Cancer Center in New York, a co-founder of Genetics Institute and Acceleron, and a previous Lasker awardee said, Ive worked with Tom for many years in both basic science and biotechnology,he is simply the best.

Tom has had an enormous impact on the scientific community and an equally impressive contribution to the discovery and development of innovative medicines at several biotechnology companies, said John Knopf, Ph.D., Chief Executive Officer of Acceleron. I have had the distinct pleasure of knowing and working with Tom since I joined Genetics Institute 30 years ago. I personally continue to benefit significantly from his involvement at Acceleron as does our entire team of world-class scientists.

About Acceleron

Acceleron is a privately-held biopharmaceutical company committed to discover, develop, manufacture and commercialize novel protein therapeutics for orphan diseases and cancer. Accelerons scientific approach takes advantage of its unique insight to discover first-in-class therapies based on the TGF- protein superfamily. Acceleron utilizes proven biotherapeutic technologies and capitalizes on the companys internal GMP manufacturing capability to advance its therapeutic programs rapidly and efficiently. The investors in Acceleron include Advanced Technology Ventures, Alkermes, Avalon Ventures, Bessemer Ventures, Celgene, Flagship Ventures, MPM BioEquities, OrbiMed Advisors, Polaris Ventures, QVT Financial, Sutter Hill Ventures and Venrock. For further information on Acceleron, please visit http://www.acceleronpharma.com.

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Acceleron Founder Dr. Tom Maniatis To Receive The 2012 Lasker Award in Medical Science

Two Columbia professors have won prestigious Lasker Foundation Awards for their work in biological sciences.

Tom Maniatis, the Isidore S. Edelman Professor of Biochemistry and chair of the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center, will receive the 2012 Lasker-Koshland Special Achievement Award in Medical Science. Maniatis is known for both his research on the mechanisms of gene regulation and his Molecular Cloning Manual. The award, which he will share with the Carnegie Institutions Donald Brown, is given to scientists for exceptional leadership and citizenship in biomedical science.

I am deeply honored to receive the Lasker Special Achievement Award in Medical Science, said Maniatis. I became a scientist because of the excitement of making discoveries, but to see the impact of these discoveries on the treatment of human disease has been particularly gratifying.

On the Morningside campus, Michael Sheetz, the William R. Kenan Jr. Professor of Biological Sciences, won the Lasker Basic Medical Research Award for his part in discoveries concerning cytoskeletal motor proteins, machines that move cargos within cells, contract muscles, and enable cell movements. The basic research award is given to those scientists whose techniques or concepts to the elimination of major causes of disability and death, according to the Lasker Foundation.

He won it with two other scientists, Stanford Universitys James Spudich and Ronald Vale of the University of California, San Francisco, with whom hes been working for many years. I am deeply honored to receive the Lasker with friends and wish to thank the many people in my lab and our collaborators who contributed so much to the overall effort, said Sheetz.

The Lasker Awards, which carry an honorarium of $250,000 for each category, will be presented at a ceremony on Friday, September 21, in New York City. Since the inception of the Lasker Awards in 1945, 81 Lasker laureates have gone on to win the Nobel Prize, 29 in the last two decades.

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Two Columbia Professors Win Lasker Foundation Awards for Their Work in Biological Sciences

Public release date: 10-Sep-2012 [ | E-mail | Share ]

Contact: Karin Eskenazi ket2116@columbia.edu 212-342-0508 Columbia University Medical Center

NEW YORK (September 10, 2012) Tom Maniatis, PhD, the Isidore S. Edelman Professor of Biochemistry and chair of the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center, is to receive the 2012 Lasker-Koshland Special Achievement Award in Medical Science. Dr. Maniatis is known for both his research on the mechanisms of gene regulation and his Molecular Cloning Manual. Dr. Maniatis will receive the award on Sept. 21 in New York City.

"I am deeply honored to receive the Lasker Special Achievement Award in Medical Science," said Dr. Maniatis. "I became a scientist because of the excitement of making discoveries, but to see the impact of these discoveries on the treatment of human disease has been particularly gratifying."

"Tom Maniatis' work is the quintessential example of the path from basic science to clinical applications," said Lee Goldman, MD, executive vice president of Columbia University and dean of the faculties of health sciences and medicine at Columbia University Medical Center. "His cloning manual is used by researchers worldwide, while his research contributions are at the foundation of current thinking about genetics."

In 1980 James Watson, PhD, director of Cold Spring Harbor Laboratory (CSHL), asked Maniatiswho was on the Harvard faculty at the timeto teach new genetic engineering techniques during a summer course at CSHL and then to produce a manual. The resultant Molecular Cloning Manualpublished in 1982 and often referred to as "the Bible" by students and researcherscontained practically every technique biologists needed to manipulate DNA.

Scientists could now identify genes that cause disease and then produce new drugs such as human insulin; and the techniques were indispensable for the success of the Human Genome Project. Dr. Maniatis' laboratory developed many of the techniques in the manual, which he coauthored with his postdoctoral fellow Ed Fritsch, PhD, and Joe Sambrook, PhD, the scientific director at CSHL.

Using the new techniques, Dr. Maniatis was the first to isolate a human gene and to use the cloned gene to identify deletion and substitution mutations that cause disease. The gene beta globin, for example, is part of the hemoglobin complex, and the mutations Dr. Maniatis identified cause a blood disease called beta thalassemia.

Maniatis also created the first complete human "genomic" DNA librarya collection of DNA containing every human genewhich made it possible to isolate and study any human gene. As with his genetic engineering techniques, Maniatis freely shared this library with other researchers.

In other research, Dr. Maniatis and his students uncovered important details of how information in genes is turned into proteins, including the mechanisms of transcription and RNA splicing.

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Dr. Tom Maniatis honored with 2012 Lasker-Koshland Special Achievement Award in Medical Science

The work Richwoods High School grad Ryan Niemeier does would be impressive enough just on its face.

The biology student, now in his junior year at Bradley University, has spent the last three years working with nanofiber materials, trying to create "scaffold" systems to help concentrate the delivery of stem cells to help the body repair itself. It's research that could one day help facilitate repairs to damaged organs and lead to cures for conditions like Parkinson's disease.

And now he's taking the research on the road, with a prestigious nine-month fellowship to Galway, Ireland, to expand his work and come at it from a different perspective and with the advice of different scientists.

Niemeier stands out among students at Bradley, said mentor Craig Cady, a Bradley biology professor whose research is directed in similar areas.

"It's unusual for a student ... to see him advance that much at that age," he said. "Some students are intimidated at that age - a lot of research, a lot of stress. But Ryan was very much at ease. He can make decisions on his own," Cady said.

In fact, though still a student, he's frequently been the one in the driver's seat when it comes to determining where he wants to take his studies.

"Ryan basically was involved in implementing and creating a design to literally do the research" that led him to where he is today, Cady said.

"I've been able to set up and design all my experiments from the ground up," Niemeier said shortly before leaving last month for the Emerald Isle.

And that's precisely what he said he was looking for in choosing a course of study, first at Bradley and then with the fellowship: "Am I going to be able to get into a lab and am I going to be able to do meaningful research?"

The two share a student-mentor relationship, but because of the direction of their research and the amount of time they have spent together since the summer after Niemeier's junior year of high school, Cady said, they can also work as collaborators.

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Bradley biology student takes his research on the road

Removing molecular 'garbage' may be key to successful aging, Clarke says

(Attention editors: Photo Attached)

Newswise Steven G. Clarke, a distinguished professor in the department of chemistry and biochemistry in UCLA's College of Letters and Science, has been named to UCLA's Elizabeth and Thomas Plott Chair in Gerontology.

The endowed chair, held for a five-year term, is intended for a scholar who conducts research and education activities related to aging and longevity in the areas of molecular biology, neuroscience and immunology.

An authority in his field, Clarke focuses on the biochemistry of the aging process and conducts research aimed at understanding, on a molecular level, how human functions are maintained during aging.

His research team has proposed that a major factor in the successful aging of all organisms is how well age-generated molecular "garbage" damaged proteins, nucleic acids, lipids and small molecules can either be repaired or eliminated from the body. His lab has analyzed protein-repair systems and novel types of enzymes that may contribute to reducing this buildup of damage in aging organisms.

Specifically, Clarke's team discovered and characterized the repair system involving the enzyme L-isoaspartyl methyltransferase, or PCMT. Early research on this enzyme's ability to repair defective proteins demonstrated that mice lacking sufficient PCMT had a significant increase in the number of damaged proteins in their tissues, particularly in the brain. Deficiencies in this enzyme have been linked to epilepsy and may also play a role in several degenerative diseases.

According to Clarke, understanding such pathways may help spur the future development of interventions to enhance these repair systems in the elderly, helping address declines in muscle strength, lung capacity, mental status, eye-lens clarity, heart output and other losses of function.

Clarke added that we may now be at the tip of the iceberg in our understanding of how many repair activities exist and how these activities may be manipulated for healthy living, particularly with diet and pharmaceuticals.

"I'm excited to accept the appointment to the Plott Chair and to continue our research in this critical field," said Clarke, who also directs UCLA's Cellular and Molecular Biology Training Program.

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UCLA Chemist Steven G. Clarke Named to Endowed Chair in Gerontology

SAN DIEGO Open an undergraduate biochemistry textbook and you will learn that enzymes are highly efficient and specific in catalyzing chemical reactions in living organisms, and that they evolved to this state from their sloppy and promiscuous ancestors to allow cells to grow more efficiently. This fundamental paradigm is being challenged in a new study by bioengineers at the University of California, San Diego, who reported in the journal Science what a few enzymologists have suspected for years: Many enzymes are still pretty sloppy and promiscuous, catalyzing multiple chemical reactions in living cells, for reasons that were previously not well understood.

In this study, the research team, led by Bernhard Palsson, Galetti Professor of Bioengineering at the UC San Diego Jacobs School of Engineering, brought together decades of work on the behavior of individual enzymes to produce a genome-scale model of E. coli metabolism and report that at least 37 percent of its enzymes catalyze multiple metabolic reactions that occur in an actively growing cell.

Weve been able to stitch all of the enzymes together into one giant model, giving us a holistic view of what has been driving the evolution of enzymes and found that it isnt quite what weve thought it to be, said Palsson.

When organisms evolve, it is the genes or proteins that change. Therefore, gene and protein evolution has classically been studied one gene at a time. However in this work, Palsson and his colleagues, introduce an important paradigm shift by demonstrating that the evolution of individual proteins and enzymes is influenced by the function of all of the other enzymes in an organism, and how they all work together to support the growth rate of the cell.

Using a whole-cell model of metabolism, the research team found that the more essential an enzyme is to the growth of the cell, the more efficient it needs to be; meanwhile, enzymes that only weakly contribute to cell growth can remain sloppy. The study found three major reasons why some enzymes have evolved to be so efficient, while others have not:

Our study found that the functions of promiscuous enzymes are still used in growing cells, but the sloppiness of these enzymes is not detrimental to growth. They are much less sensitive to changes in the environment and not as necessary for efficient cell growth, said Nathan Lewis, who earned a Ph.D. in bioengineering at the Jacobs School in March and is now a postdoctoral fellow at Harvard Medical School.

This study is also a triumph in the emerging field of systems biology, which leverages the power of high-performance computing and an enormous amount of available data from the life sciences to simulate activities such as the rates of reactions that break down nutrients to make energy and new cell parts. This study sheds light on the vast number of promiscuous enzymes in living organisms and shifts the paradigm of research in biochemistry to a holistic level, said Lewis. The insights found in our work also clearly show that fine-grained knowledge can be obtained about individual proteins while using large-scale models. This concept will yield immediate and more distant results.

Our teams findings could also inform other research efforts into which enzymes require further study for overlooked promiscuous activities, said Hojung Nam, a postdoctoral researcher in Palssons lab. Besides testing and characterizing more enzymes for potential promiscuous activities, enzyme promiscuity could have far-reaching impacts as scientists try to understand how unexpected promiscuous activities of enzymes contribute to diseases such as leukemia and brain tumors, said Nam.

Funding was provided by the U.S. Department of Energy and National Institutes of Health (DE-SC0004917, DE-FG02-09ER25917, and 2R01GM057089-13) and a fellowship from the National Science Foundation (NSF GK-12 742551).

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‘Promiscuous’ enzymes still common in metabolism

Sangeeta Tohani, 19, of Longwood Gardens, Barkingside performed a special dance routine in front of 80,000 people in the Olympic Stadium alongside fellow dancers from Sakthi Fine Arts, The Crescent, Gants Hill.

The Queen Mary University student auditioned back in February and she was soon told she had been selected after learning Indian classical dancing since she was about five years old.

She said: From the very beginning the whole experience has been incredible. We saw people auditioning with disabilities, who were all catered for, which was really inspiring.

I was determined to get involved in the Paralymics after missing out on the Olympics, which I watched constantly. And knowing that Id be performing just around the corner from where I live was amazing.

Miss Tohani, who also performed during the Torch Relay in Redbridge, was part of the Navigation segment of the ceremony representing the sea.

She said: Despite the steps being fairly simple I forgot them in the dress rehearsal because everything was so overwhelming and to see everything come together in the stadium left me gobsmacked.

Miss Tohani, who described the experience as surreal had been practising with the large group of dancers for ten hours a day for the past three weeks in preparation for the performance.

She added: It started to rain during our section, which was quite late on, leaving the floor really wet; but we didnt even think about it.

Once our part was almost over everyone got really emotional because we didnt want it to end. I have met so many people who I wouldnt normally get a chance to meet.

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Public release date: 5-Sep-2012 [ | E-mail | Share ]

Contact: Angela Hopp ahopp@asbmb.org 240-283-6614 American Society for Biochemistry and Molecular Biology

The National Human Genome Research Institute today announced the results of a five-year international study of the regulation and organization of the human genome. The project is named ENCODE, which stands for the Encyclopedia of DNA Elements. In conjunction with the release of those results, the Journal of Biological Chemistry has published a series of reviews that focus on several aspects of the findings.

"The ENCODE project not only generated an enormous body of data about our genome, but it also analyzed many issues to better understand how the genome functions in different types of cells. These insights from integrative analyses are really stories about how molecular machines interact with each other and work on DNA to produce the proteins and RNAs needed for each cell to function within our bodies," explains Ross Hardison of Pennsylvania State University, one of the JBC authors.

Hardison continued: "The Journal of Biological Chemistry recognized that the results from the ENCODE project also would catalyze much new research from biochemists and molecular biologists around the world. Hence, the journal commissioned these articles not only to communicate the insights from the papers now being published but also to stimulate more research in the broader community."

The human genome consists of about 3 billion DNA base pairs, but only a small percentage of DNA actually codes for proteins. The roles and functions of the remaining genetic information were unclear to scientists and even referred to as "junk DNA." But the results of the ENCODE project is filling this knowledge gap. The findings revealed that more than 80 percent of the human genome is associated with biological function.

The study showed in a comprehensive way that proteins switch genes on and off regularly and can do so at distances far from the genes they regulate and it determined sites on chromosomes that interact, the locations where chemical modifications to DNA can influence gene expression, and how the functional forms of RNA can regulate the expression of genetic information.

The results establish the ways in which genetic information is controlled and expressed in specific cell types and distinguish particular regulatory regions that may contribute to diseases.

"The deeper knowledge of gene regulation coming from the ENCODE project will have a positive impact on medical science," Hardison emphasizes. For example, recent genetic studies have revealed many genomic locations that can affect a person's susceptibility to common diseases. The ENCODE data show that many of these regions are involved in gene regulation, and the data provide hypotheses for how variations in these regions can affect disease susceptibility, adds Hardison.

The effort behind the ENCODE project was extraordinary. More than 440 scientists in 32 labs in United States, the United Kingdom, Spain, Singapore and Japan performed more than 1,600 sets of experiments on 147 types of tissue. The results were published today in one main integrative paper and five other papers in the journal Nature, 18 papers in Genome Research and six papers in Genome Biology.

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Major advances in understanding the regulation and organization of the human genome

Enzymes are often thought to be specific, catalyzing only one reaction in a cell (left). However, some more promiscuous enzymes have many functions and catalyze many reactions in a cell. This study shows that promiscuous enzymes play a larger part in cell growth than previously thought. Credit: Courtesy of Systems Biology Research Group, UC San Diego, Jacobs School of Engineering

Open an undergraduate biochemistry textbook and you will learn that enzymes are highly efficient and specific in catalyzing chemical reactions in living organisms, and that they evolved to this state from their "sloppy" and "promiscuous" ancestors to allow cells to grow more efficiently. This fundamental paradigm is being challenged in a new study by bioengineers at the University of California, San Diego, who reported in the journal Science what a few enzymologists have suspected for years: many enzymes are still pretty sloppy and promiscuous, catalyzing multiple chemical reactions in living cells, for reasons that were previously not well understood.

In this study, the research team, led by Bernhard Palsson, Galetti Professor of Bioengineering at the UC San Diego Jacobs School of Engineering, brought together decades of work on the behavior of individual enzymes to produce a genome-scale model of E. coli metabolism and report that at least 37 percent of its enzymes catalyze multiple metabolic reactions that occur in an actively growing cell.

"We've been able to stitch all of the enzymes together into one giant model, giving us a holistic view of what has been driving the evolution of enzymes and found that it isn't quite what we've thought it to be," said Palsson.

When organisms evolve, it is the genes or proteins that change. Therefore, gene and protein evolution has classically been studied one gene at a time. However in this work, Palsson and his colleagues, introduce an important paradigm shift by demonstrating that the evolution of individual proteins and enzymes is influenced by the function of all of the other enzymes in an organism, and how they all work together to support the growth rate of the cell.

Enlarge

Each gene and protein in a cell has a function, and many of these functions are linked to each other. Thus, as organisms evolve, the collective functions of all genes and proteins in the cells influence the evolution of each gene or protein. Credit: Courtesy of Systems Biology Research Group, UC San Diego, Jacobs School of Engineering

"Our study found that the functions of promiscuous enzymes are still used in growing cells, but the sloppiness of these enzymes is not detrimental to growth. They are much less sensitive to changes in the environment and not as necessary for efficient cell growth," said Nathan Lewis, who earned a Ph.D. in bioengineering at the Jacobs School in March and is now a postdoctoral fellow at Harvard Medical School.

This study is also a triumph in the emerging field of systems biology, which leverages the power of high-performance computing and an enormous amount of available data from the life sciences to simulate activities such as the rates of reactions that break down nutrients to make energy and new cell parts. "This study sheds light on the vast number of promiscuous enzymes in living organisms and shifts the paradigm of research in biochemistry to a holistic level," said Lewis. "The insights found in our work also clearly show that fine-grained knowledge can be obtained about individual proteins while using large-scale models." This concept will yield immediate and more distant results.

"Our team's findings could also inform other research efforts into which enzymes require further study for overlooked promiscuous activities," said Hojung Nam, a postdoctoral researcher in Palsson's lab. "Besides testing and characterizing more enzymes for potential promiscuous activities, enzyme promiscuity could have far-reaching impacts as scientists try to understand how unexpected promiscuous activities of enzymes contribute to diseases such as leukemia and brain tumors," said Nam.

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'Promiscuous' enzymes still prevalent in metabolism

Newswise Svetlana Kilina, Ph.D., assistant professor of chemistry and biochemistry at North Dakota State University, Fargo, has received a $750,000 five-year award from the U.S. Department of Energy Office of Science Early Career Research Program. Funding will be used to conduct research outlined in Dr. Kilinas proposal titled Modeling of Photoexcited Process at Interfaces of Functionalized Quantum Dots.

Dr. Kilinas research occurs at the intersection of renewable energy, high-performance computing, nanotechnology and chemistry. Only 68 awardees were selected from a pool of about 850 university- and national laboratory-based applicants, based on peer review by outside scientific experts.

Quantum dots are nanocrystals discovered by scientists in the 1980s. Ranging in size from two to 10 nanometers, billions of them could fit on the head of a pin. Their tiny sizes belie the Herculean impact they could make in semiconductors and energy. Dr. Kilinas work centers on new generation solar cells and fuel cells using quantum-dot-based materials.

Materials at the nanoscale level behave differently than at larger scales. Energized quantum dots absorb and emit light. The color of the light depends on the size of the dot. In addition, one quant of light can generate more than two carriers of electric current (two electrons-hole pairs instead of one) in quantum dots. As a result, quantum dots could convert energy to light or vice versa more efficiently than conventional energy materials based on bulk semiconductors such as silicon. That makes quantum dots very promising materials for solar cells and other energy applications.

One of the main obstacles in the synthesis of quantum dots is the controllable chemistry of the quantum dot surface, said Dr. Kilina. Due to their nanosize, the dots are extremely chemically reactive, and different organic molecules from solvent/air environment interact with the surface of the quantum dot during and after synthesis. These molecules cover the surface of the quantum dot like a shell, influencing its optical and electronic properties.

Dr. Kilina uses supercomputers to conduct computer-simulated experiments, investigate and advance her research in this field. Her goal is to generate theoretical insights to the surface chemistry of quantum dots, which are critical to design efficient quantum-dot-based materials for solar energy conversion and lighting applications.

To apply her model and algorithmic methods, Dr. Kilinas research group uses supercomputers at the NDSU Center for Computationally Assisted Science and Technology, in addition to Department of Energy and Los Alamos National Laboratory leadership-class, high-performance computing facilities. The combination of NDSU supercomputing and government facilities substantially reduces the amount of time needed for the massive calculations used in this research.

Dr. Kilinas research aims to gain fundamental understanding of nanomaterials at the molecular and electronic level, said Dr. Greg Cook, chair of NDSUs Department of Chemistry and Biochemistry. Insights gained from this research will enable the progression of solar energy technology to help solve the worlds energy challenges. The Department of Energy award recognizes Dr. Kilinas unique expertise in the area of theoretical modeling of these materials critical for the future, said Cook.

Dr. Kilinas research addresses fundamental questions of modern materials science that affect the design and manufacture of new-generation energy conversion devices. To design and manufacture such devices requires developing new multi-functional materials with controllable properties. As part of Dr. Kilinas work centered around new generation solar cells and fuel cells, she develops and applies a new generation non-adiabatic photoinduced dynamics methodology that simultaneously includes electron-hole coupling response for excitonic effects and exciton-phonon coupling critical in photoexcitation and couplings between electronics and crystal-lattice vibrations responsible for energy-to-heat losses.

It is anticipated that the acquired theoretical knowledge gained from the research at NDSU will help better explain and interpret experimental data and could facilitate rational design of new nanostructures with desired optical, transport, and light harvesting properties that are fundamental to a myriad of clean energy technologies.

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NDSU Research Connects the Dots to Renewable Energy Future

Brain imaging helps to understand how the brain works, aids in the diagnosis of neurological diseases and guides treatments. Positron emission tomography or PET is an imaging technique that uses trace amounts of radioactive drugs to visualize the function and biochemistry of the brain.

Imaging researchers now have developed new PET tracers to detect changes in the brain caused by Alzheimer's dementia and other neurodegenerative disease. These diseases damage and ultimately kill large numbers of brain cells (neurons) and thus lead to severe disability and death.

Neurodegenerative diseases cause specific patterns of injury and biochemical abnormalities in the brain. Until recently, these changes could only be measured after death by examining brain tissue using a microscope. One of the exciting developments in PET imaging is the availability of new agents that can detect beta-amyloid plaques, one of the key abnormalities in Alzheimer's disease, in the living human brain. Plaques may develop in the brain over a decade before Alzheimer's symptoms develop.

Neurologists and other dementia specialists currently rely primarily on information gathered from the patient and family, physical examination and cognitive tests to diagnose Alzheimer's dementia. In some cases, determining the cause of a patient's cognitive problems can be challenging, and now PET imaging can help doctors and patients be more confident in the diagnosis.

Two clinically used PET imaging tests for patients are being evaluated for dementia. A PET tracer called FDG measures the brain's use of glucose, a simple sugar that serves as the brain's major source of energy. In dementia due to Alzheimer's disease, decreased glucose metabolism in specific brain regions supports a diagnosis of Alzheimer's disease.

The other PET imaging test for patients with cognitive impairment uses a different PET tracer, florbetapir, which binds to beta-amyloid plaques that occur in Alzheimer's disease. This PET tracer was approved for clinical use by the Food and Drug Administration in April 2012. Amyloid PET imaging can show the presence or absence of abnormally increased plaques in the brain. Low plaque levels (a negative amyloid PET study) reduce the likelihood that a patient's cognitive problems are due to Alzheimer's disease. Higher plaque levels are present in Alzheimer's disease, but a positive amyloid PET scan can occur with other neurologic diseases and in older people without cognitive problems.

Both FDG and amyloid PET are only part of the evaluation of patients with dementia or other cognitive disorders. Neither of these tests alone can make specific diagnoses. PET imaging in patients with cognitive impairment should be ordered by physicians experienced in the diagnosis and treatment of patients of these conditions when the results will help in clinical decision making.

Dr. Jonathan McConathy is an assistant professor of radiology at Washington University who is board certified in diagnostic radiology and nuclear medicine. For information about brain PET studies at Washington University, call 314-362-4738.

The rest is here:
Senior Focus: New imaging device helps detect brain changes

ScienceDaily (Aug. 30, 2012) Open an undergraduate biochemistry textbook and you will learn that enzymes are highly efficient and specific in catalyzing chemical reactions in living organisms, and that they evolved to this state from their "sloppy" and "promiscuous" ancestors to allow cells to grow more efficiently. This fundamental paradigm is being challenged in a new study by bioengineers at the University of California, San Diego, who reported in the journal Science what a few enzymologists have suspected for years: many enzymes are still pretty sloppy and promiscuous, catalyzing multiple chemical reactions in living cells, for reasons that were previously not well understood.

In this study, the research team, led by Bernhard Palsson, Galetti Professor of Bioengineering at the UC San Diego Jacobs School of Engineering, brought together decades of work on the behavior of individual enzymes to produce a genome-scale model of E. coli metabolism and report that at least 37 percent of its enzymes catalyze multiple metabolic reactions that occur in an actively growing cell.

"We've been able to stitch all of the enzymes together into one giant model, giving us a holistic view of what has been driving the evolution of enzymes and found that it isn't quite what we've thought it to be," said Palsson.

When organisms evolve, it is the genes or proteins that change. Therefore, gene and protein evolution has classically been studied one gene at a time. However in this work, Palsson and his colleagues, introduce an important paradigm shift by demonstrating that the evolution of individual proteins and enzymes is influenced by the function of all of the other enzymes in an organism, and how they all work together to support the growth rate of the cell.

Using a whole-cell model of metabolism, the research team found that the more essential an enzyme is to the growth of the cell, the more efficient it needs to be; meanwhile, enzymes that only weakly contribute to cell growth can remain 'sloppy.' The study found three major reasons why some enzymes have evolved to be so efficient, while others have not:

Enzymes that are used more extensively by the organism need to be more efficient to avoid waste. To increase efficiency, they evolve to catalyze one specific metabolic reaction. When enzymes are responsible for catalyzing reactions that are necessary for cell growth and survival, they are specific in order to avoid interference from molecules that are not needed for cell growth and survival.

Since organisms have to adapt to dynamic and noisy environments, they sometimes need to have careful control of certain enzyme activities in order to avoid wasting energy and prepare for anticipated nutrient changes. Evolving higher specificity makes these enzymes easier to control.

"Our study found that the functions of promiscuous enzymes are still used in growing cells, but the sloppiness of these enzymes is not detrimental to growth. They are much less sensitive to changes in the environment and not as necessary for efficient cell growth," said Nathan Lewis, who earned a Ph.D. in bioengineering at the Jacobs School in March and is now a postdoctoral fellow at Harvard Medical School.

This study is also a triumph in the emerging field of systems biology, which leverages the power of high-performance computing and an enormous amount of available data from the life sciences to simulate activities such as the rates of reactions that break down nutrients to make energy and new cell parts. "This study sheds light on the vast number of promiscuous enzymes in living organisms and shifts the paradigm of research in biochemistry to a holistic level," said Lewis. "The insights found in our work also clearly show that fine-grained knowledge can be obtained about individual proteins while using large-scale models." This concept will yield immediate and more distant results.

"Our team's findings could also inform other research efforts into which enzymes require further study for overlooked promiscuous activities," said Hojung Nam, a postdoctoral researcher in Palsson's lab. "Besides testing and characterizing more enzymes for potential promiscuous activities, enzyme promiscuity could have far-reaching impacts as scientists try to understand how unexpected promiscuous activities of enzymes contribute to diseases such as leukemia and brain tumors," said Nam.

Originally posted here:
'Promiscuous' enzymes still prevalent in metabolism: Challenges fundamental notion of enzyme specificity and efficiency

Newswise Open an undergraduate biochemistry textbook and you will learn that enzymes are highly efficient and specific in catalyzing chemical reactions in living organisms, and that they evolved to this state from their sloppy and promiscuous ancestors to allow cells to grow more efficiently. This fundamental paradigm is being challenged in a new study by bioengineers at the University of California, San Diego, who reported in the journal Science what a few enzymologists have suspected for years: many enzymes are still pretty sloppy and promiscuous, catalyzing multiple chemical reactions in living cells, for reasons that were previously not well understood.

In this study, the research team, led by Bernhard Palsson, Galetti Professor of Bioengineering at the UC San Diego Jacobs School of Engineering, brought together decades of work on the behavior of individual enzymes to produce a genome-scale model of E. coli metabolism and report that at least 37 percent of its enzymes catalyze multiple metabolic reactions that occur in an actively growing cell.

Weve been able to stitch all of the enzymes together into one giant model, giving us a holistic view of what has been driving the evolution of enzymes and found that it isnt quite what weve thought it to be, said Palsson.

When organisms evolve, it is the genes or proteins that change. Therefore, gene and protein evolution has classically been studied one gene at a time. However in this work, Palsson and his colleagues, introduce an important paradigm shift by demonstrating that the evolution of individual proteins and enzymes is influenced by the function of all of the other enzymes in an organism, and how they all work together to support the growth rate of the cell.

Using a whole-cell model of metabolism, the research team found that the more essential an enzyme is to the growth of the cell, the more efficient it needs to be; meanwhile, enzymes that only weakly contribute to cell growth can remain sloppy. The study found three major reasons why some enzymes have evolved to be so efficient, while others have not:

Enzymes that are used more extensively by the organism need to be more efficient to avoid waste. To increase efficiency, they evolve to catalyze one specific metabolic reaction. When enzymes are responsible for catalyzing reactions that are necessary for cell growth and survival, they are specific in order to avoid interference from molecules that are not needed for cell growth and survival.

Since organisms have to adapt to dynamic and noisy environments, they sometimes need to have careful control of certain enzyme activities in order to avoid wasting energy and prepare for anticipated nutrient changes. Evolving higher specificity makes these enzymes easier to control.

Our study found that the functions of promiscuous enzymes are still used in growing cells, but the sloppiness of these enzymes is not detrimental to growth. They are much less sensitive to changes in the environment and not as necessary for efficient cell growth, said Nathan Lewis, who earned a Ph.D. in bioengineering at the Jacobs School in March and is now a postdoctoral fellow at Harvard Medical School.

This study is also a triumph in the emerging field of systems biology, which leverages the power of high-performance computing and an enormous amount of available data from the life sciences to simulate activities such as the rates of reactions that break down nutrients to make energy and new cell parts. This study sheds light on the vast number of promiscuous enzymes in living organisms and shifts the paradigm of research in biochemistry to a holistic level, said Lewis. The insights found in our work also clearly show that fine-grained knowledge can be obtained about individual proteins while using large-scale models. This concept will yield immediate and more distant results.

Our teams findings could also inform other research efforts into which enzymes require further study for overlooked promiscuous activities, said Hojung Nam, a postdoctoral researcher in Palssons lab. Besides testing and characterizing more enzymes for potential promiscuous activities, enzyme promiscuity could have far-reaching impacts as scientists try to understand how unexpected promiscuous activities of enzymes contribute to diseases such as leukemia and brain tumors, said Nam.

Here is the original post:
Science Study Shows 'Promiscuous' Enzymes Still Prevalent in Metabolism

29.08.2012 - (idw) Ruhr-Universitt Bochum

First place in an EU competitive call on Unconventional Computing was awarded to a collaborative proposal coordinated by Prof. John McCaskill from the RUB Faculty of Chemistry and Biochemistry. The project MICREAgents plans to build autonomous self-assembling electronic microreagents that are almost as small as cells. They will exchange chemical and electronic information to jointly direct complex chemical reactions and analyses in the solutions they are poured into. The EU supports the project within the FP7 programme with 3.4 million Euros for three years. Turning chemistry inside-out Self-assembling smart microscopic reagents to pioneer pourable electronics 3.4 million Euros from EU programme for international research project

First place in an EU competitive call on Unconventional Computing was awarded to a collaborative proposal coordinated by Prof. John McCaskill from the RUB Faculty of Chemistry and Biochemistry. The project MICREAgents plans to build autonomous self-assembling electronic microreagents that are almost as small as cells. They will exchange chemical and electronic information to jointly direct complex chemical reactions and analyses in the solutions they are poured into. This is a form of embedded computation to compute is to construct in which for example the output is a particular catalyst or coating needed in the (input) local chemical environment. The EU supports the project within the FP7 programme with 3.4 million Euros for three years. Four research groups at RUB will join forces with top teams across Europe, from Israel and New Zealand.

Self-assembling electronic agents

In order to create this programmable microscale electronic chemistry, MICREAgents (Microscopic Chemically Reactive Electronic Agents) will contain electronic circuits on 3D microchips, called lablets. The lablets have a diameter of less than 100 m and self-assemble in pairs or like dominos to enclose transient reaction compartments. They can selectively concentrate, process, and release chemicals into the surrounding solution, under local electronic control, in a similar way to which the genetic information in cells controls local chemical processes. The reversible pairwise association allows the lablets to transfer information from one to another.

Translating electronic signals into chemical processes

The lablet devices will integrate transistors, supercapacitors, energy transducers, sensors and actuators, and will translate electronic signals into constructive chemical processing as well as record the results of this processing. Instead of making chemical reactors to contain chemicals, the smart MICREAgents will be poured into chemical mixtures, to organize the chemistry from within. Ultimately, such microreactors, like cells in the bloodstream, will open up the possibility of controlling complex chemistry from the inside out.

The self-assembling smart micro reactors can be programmed for molecular amplification and other chemical processing pathways that start from complex mixtures, concentrate and purify chemicals, perform reactions in programmed cascades, sense reaction completion, and transport and release products to defined locations. MICREAgents represent a novel form of computation intertwined with construction. By embracing self-assembly and evolution, they are a step towards a robust and evolvable realization of John von Neumanns universal construction machine vision. Although these nanoscale structures will soon be sufficiently complex to allow self-replication of their chemical and electronic information, they will not present a proliferative threat to the environment, because they depend for their function on the electronic circuit layer that is fabricated as part of their substrate.

RUB collaborators

For the project, Prof. Dr. John S. McCaskill (Microsystems Chemistry and Biological Information Technology) collaborates with Prof. Dr. Gnter von Kiedrowski (Bioorganic Chemistry), Prof. Dr. Jrgen Oehm (Analog Integrated Circuits) and Dr. Pierre Mayr (Integrated Digital Circuits). McCaskills and von Kiedrowskis labs at RUB have already joined forces in previous European Projects forging a path towards artificial cells. The ECCell project, for example, that finished in February this year, has laid the foundation for an electronic chemical cell. There, the electronics and microfluidics were exterior to the chemistry: in MICREAgents this is being turned inside out.

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Project MICREAgents: self-assembling smart microscopic reagents to pioneer pourable electronics

A tiny resonating beam, just 10 millionths of a meter in length, can measure the mass of a molecule or nanoparticle in real time

By John Matson

WEIGHTY MATTERS: The diagonal beam in this image can detect the presence of single molecules and determine their mass. Image: Caltech/Scott Kelber and Michael Roukes

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Dieters and exercise buffs might feel better about their progress if they tracked their weight loss in daltons. Even a short jog can help you shed a few septillion daltons, a unit of mass often used in biochemistry that is equivalent to the atomic mass unit. (Of course, no weight-conscious individual would want to know their full weight in this unitthe average American male weighs approximately 5 X 1028 daltons.)

Even the megadalton, or one million daltons, is a tiny unit of measurea gold particle five nanometers across weighs in at just a few megadaltons. (One nanometer is a billionth of a meter.) But researchers at the California Institute of Technology and CEALeti, a government-funded research organization in Grenoble, France, have built a scale that weighs single objects even lighter than a megadalton, including nanoparticles and human antibody molecules. The device is the first of its kind to determine the masses of individual molecules and nanoparticles in real time, the researchers reported in a study published online August 26 in Nature Nanotechnology. (Scientific American is part of Nature Publishing Group.)

The heart of the device is a nanoelectromechanical resonatora tiny beam of silicon vibrating at two tones simultaneously. "It's like vibrating a guitar string at the fundamental and a harmonic," says study co-author Michael Roukes, a Caltech physicist. "We're continuously strumming it with an electrostatic excitation." The beam runs diagonally across the photo (above); it measures 10 microns long and 300 nanometers wide. (A micron is one millionth of a meter.)

Tiny arms connecting the ends of the beam to the rest of the device convert the resonator's vibrations into an electrical signal via a phenomenon known as the piezoresistive effect. "The smallest pieces there are flexed slightly, and when they're flexed their resistance changes," Roukes says. "And so we can read out the motion as a change in resistance." A single molecule landing on the beam shifts the frequency of the two tones downward, and from the accompanying change in resistance the researchers can deduce both the mass of the particle and where it landed along the beam.

The device's sensitivity to single molecules allowed the researchers to perform mass spectroscopyidentifying the various particles in a mixture by their masseson collections of gold nanoparticles five and 10 nanometers in diameter, as well as on the antibody molecule immunoglobulin M, which weighs just under one megadalton. (The natural molecules proved much more consistent in their construction than did the man-made nanoparticles, whose masses fluctuated by a factor of five or so from particle to particle.)

View original post here:
Scaled-Down: New Nano Device Can Weigh Single Molecules

Oak Hill High staff is commended

I would like to commend the staff at Oak Hill High School for the excellent education you provided our children. Our son returned to Marshall University as a senior and graduate with a biochemistry degree, then will move on to graduate or medical school. Our daughter moved in on Aug. 22 with 25 credit hours achieved through the hard work and dedication of those professionals at Oak Hill High School. She will begin her journey towards receiving her biochemistry degree and becoming a pediatric oncologist.

I am writing this article not only to commend educators who strive to make a difference, but also to help young people realize that dreams are not impossible. Sometimes they are hard to achieve because of the dedication and hard work that is needed to accomplish the goal, but if its worth the effort to make Gods world a better place, then do it.

My question to all of the wonderful students I have been blessed by is simply this: Why did God create you and what is your purpose in life? If you cant answer this question, then our world has no future.

Cathy Broughman

Oak Hill

Avoid buying puppies from roadside peddlers

If you have been to the Fayette Town Center more than a few times, you have surely seen people in the median selling pure-bred or designer breed puppies from their vehicles with a handmade sign. I would like to encourage readers not to walk, but run away from these people.

The plaza tried to solve the problem with signage, but the signs soon disappeared and the puppy peddlers returned. A puppy mill or a backyard breeder is an extremely common business that often operates underground, and right here in Fayette County.

The operator chooses a breed of the current fad (often a toy breed) and forces dogs of that breed or breeds to reproduce at an unhealthy frequency in deplorable conditions. The mothers do not receive adequate care, socialization, recreation or affection in order to keep operating costs at a minimum. Some spend most of their lives in a cage the size of your dishwasher.

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Tribune Readers’ Views for Thursday, Aug. 23

Public release date: 23-Aug-2012 [ | E-mail | Share ]

Contact: Steve Graff stephen.graff@jefferson.edu 215-955-5291 Thomas Jefferson University

PHILADELPHIAIt's widely accepted that molecular mechanisms mediating epigenetics include DNA methylation and histone modifications, but a team from Thomas Jefferson University has evidence to the contrary regarding the role of histone modifications.

A study of Drosophila embryos from Jefferson's Department of Biochemistry and Molecular Biology published ahead of print in Cell August 23 found that parental methylated histones are not transferred to daughter DNA. Rather, after DNA replication, new nucleosomes are assembled from newly synthesized unmodified histones.

"Essentially, all histones are going away during DNA replication and new histones, which are not modified, are coming in," said Alexander M. Mazo, Ph.D., professor of Biochemistry and Molecular Biology at Jefferson, and a member of Jefferson's Kimmel Cancer Center. "In other words, what we found is that histone modifying proteins are hiding on the way over replicating DNA, instead of histones 'jumping' over as currently thought."

"What this paper tells us," he continues, "is that these histone modifying proteins somehow are able to withstand the passage of the DNA replication machinery. They remained seated on their responsive binding sites, and in all likelihood they will re-establish histone modification and finalize the chromatin structure that allows either activation or repression of the target gene."

The team suggests that since it appears these histone modifying proteinsthe Trithorax-group (TrxG), which maintain gene expression, and the Polycomb-group (PcG), which plays a role in epigenetic silencing of genesre-establish the histone code on newly assembled unmethylated histones, they may act as epigenetic marks.

Epigenetics is the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. Epigenetic marks have become an important focus in recent years because they are thought to have the potential to explain mechanisms of aging, human development, and the origins of diseases, like cancer, heart disease, and mental illness.

According to widely-accepted models applied today, the tails of methylated histones turn genes in DNA "on" or "off" by loosening or tightening nucleosome structure, thus changing the accessibility of transcription factors and other proteins to DNA.

"People believe that everything gets worked off of DNA during the replication process and that these methylated histones act as epigenetic marks, since they are believed to rapidly jump from parental to daughter DNA" said Dr. Mazo. "But there is no experimental evidence to back this up."

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Histone-modifying proteins, not histones, remain associated with DNA through replication