Published: March 21, 2012

The Gairdner Foundation has announced the recipients of the 2012 Canada Gairdner Awards. Recognized for some of the most significant medical discoveries from around the world, this years winners showcase a broad range of new medical insights, from pioneering new ways to tackle childhood illness in developing countries to identifying how our biological clocks guide our everyday lives.

Among the worlds most esteemed medical research prizes, the awards distinguish Canada as a leader in science and provide a $100,000 prize to scientists whose work holds important potential. The 2012 winners are as follows:

Thomas M. Jessell, Ph.D.

Thomas M. Jessell, Ph.D., Howard Hughes Medical Institute, Kavli Institute for Brain Science, Columbia University Medical Center, New York, NY

The challenge: Through communication between the sensory neuron and the motor neuron in our bodies nervous system, we acquire the ability to move and react to the world around us. But little was known about how these neurons communicate with each other.

The work: Dr. Jessells work reveals the basic principles of nervous system communication. By studying the assembly and organization of the circuit that controls movement in the spinal cord nervous system, Dr. Jessell identified the direct connection between the sensory neuron, which is responsible for allowing us to process what is happening in the world around us, and the motor neuron, which allows us to control how our muscles move to react to what we sense in that world.

Why it matters: As a result of this discovery, we have the potential to create interventional strategies to treat and cure neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA), where a problem with the circuit connection between the sensory neuron and the motor neuron prevents our minds and bodies from reacting properly to what we sense around us. Similarly, we now have the potential to restore movement in patients with spinal cord injury or paralysis.

(To learn more about Dr. Jessell and his work, read The Promise of the Brain.)

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Thomas Jessell Receives 2012 Gairdner Award for Groundbreaking Insights on Nervous System

Mark Merchant, biochemistry professor at McNeese State University, spoke with Leesville High School students Tuesday to discuss his ongoing research project investigating naturally occurring antibacterial peptides in alligators to uncover a new class of antibiotics. Merchant said he was first interested in this research when he noticed alligators who sustained serious injuries, such as a missing limb or tail, would not only heal rapidly, but also without any infections. So he set out to investigate in marshes to collect blood samples from crocodilians, which includes all alligator, crocodile and caiman species, to study their tissue and immune systems. After extracting the white blood cells, Merchant infused them with bacteria and discovered holes where it did not grow, proving there is something inside their white blood cells that kill bacteria. Merchant derived the term Zone of Inhibition to explain the area where bacteria cannot grow as well as measure the zone towards a variety of bacteria. After experimenting with different bacteria such as pseudomonas aeruginosa, a bacterial found in soil, and citrobacter freundii and escherichia coli, bacteria found in humans, the white blood cells attacked and killed both. The reason he found this interesting he said, was because alligators' immune systems fought off bacteria, viruses and fungi they had never been exposed to. Another remarkable discovery he said, was that the cells also killed bacteria called candida albicans, yeast infections, and Methicillin-resistant Staphylococcus aureus (MRSA), staff infections, which claim numerous lives every year. He stated since humans are dying from these infections and alligator white blood cells are killing them, then they might be able to develop antibacterial, anti-viral or anti-fungal drugs for human medicine. "The way we think it works is that the outer coat of bacteria gives off a negative charge and the white blood cells give off a positive charge," he said. "So when opposites attract, the cells tear a hole in the membrane and therefore kills the bacteria." Merchant said his is really excited now that his research team has isolated these proteins and have determined their structure and now are trying to synthesize them. Students at LHS were surprised by a certain visitor Merchant brought with him; a four-year-old alligator. As the students exited the auditorium, they had the opportunity to touch and feel the texture of the alligator. Donell Evans, head of science department at LHS, said by having Merchant speak with the students, they hope to help them understand what's being offered outside of high school in terms of science related jobs and careers. Also, they are trying to bring more awareness to the Science, Technology, Engineer and Mathematics (STEM) programs that were recently introduced to Vernon Parish. The students in her AP biology class were so captivated with Merchant's research that they asked to discuss it more in depth during Friday's class. "I just think having a Louisiana college like McNeese State University being on the forefront with new antibiotics is amazing," Evans said. Merchant's researched has been funded by several grants including a four-year Research Competitiveness Subprogram grant from the Louisiana Board of Regents, EPSCoR travel grants to speak at five national and international conferences, EPSCoR Links with Industry and National Labs (LINK) grant to travel to Argentina as well as most recently, a grant from National Geographic.

Link:
Alligator cells prevail possible human medicine

The study appears in the Proceedings of the National Academy of Sciences.

Bacteria often engage in chemical warfare with one another, and many antibiotics used in medicine are modeled on the weapons they produce. But microbes also must protect themselves from their own toxins. The defenses they employ for protection can be acquired by other species, leading to antibiotic resistance.

The researchers focused on an enzyme, known as MccF, that they knew could disable a potent "Trojan horse" antibiotic that sneaks into cells disguised as a tasty protein meal. The bacterial antibiotic, called microcin C7 (McC7) is similar to a class of drugs used to treat bacterial infections of the skin.

"How Trojan horse antibiotics work is that the antibiotic portion is coupled to something that's fairly innocuous in this case it's a peptide," said University of Illinois biochemistry professor Satish Nair, who led the study. "So susceptible bacteria see this peptide, think of it as food and internalize it."

The meal comes at a price, however: Once the bacterial enzymes chew up the amino acid disguise, the liberated antibiotic is free to attack a key component of protein synthesis in the bacterium, Nair said.

"That is why the organisms that make this thing have to protect themselves," he said.

In previous studies, researchers had found the genes that protect some bacteria from this class of antibiotic toxins, but they didn't know how they worked. These genes code for peptidases, which normally chew up proteins (polypeptides) and lack the ability to recognize anything else.

Before the new study, "it wasn't clear how a peptidase could destroy an antibiotic," Nair said.

To get a fuller picture of the structure of the peptidase, Illinois graduate student Vinayak Agarwal crystallized MccF while it was bound to other molecules, including the antibiotic. An analysis of the structure and its interaction with the antibiotic revealed that MccF looked a lot like other enzymes in its family, but with a twist or, rather, a loop. Somehow MccF has picked up an additional loop of amino acids that it uses to recognize the antibiotic, rendering it ineffective.

"Now we know that specific amino acid residues in this loop are responsible for making this from a normal housekeeping gene into something that's capable of degrading this class of antibiotics," Nair said.

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Study finds how bacteria resist a 'Trojan horse' antibiotic

Public release date: 19-Mar-2012 [ | E-mail | Share ]

Contact: Diana Yates diya@illinois.edu 217-333-5802 University of Illinois at Urbana-Champaign

CHAMPAIGN, lll. A new study describes how bacteria use a previously unknown means to defeat an antibiotic. The researchers found that the bacteria have modified a common "housekeeping" enzyme in a way that enables the enzyme to recognize and disarm the antibiotic.

The study appears in the Proceedings of the National Academy of Sciences.

Bacteria often engage in chemical warfare with one another, and many antibiotics used in medicine are modeled on the weapons they produce. But microbes also must protect themselves from their own toxins. The defenses they employ for protection can be acquired by other species, leading to antibiotic resistance.

The researchers focused on an enzyme, known as MccF, that they knew could disable a potent "Trojan horse" antibiotic that sneaks into cells disguised as a tasty protein meal. The bacterial antibiotic, called microcin C7 (McC7) is similar to a class of drugs used to treat bacterial infections of the skin.

"How Trojan horse antibiotics work is that the antibiotic portion is coupled to something that's fairly innocuous in this case it's a peptide," said University of Illinois biochemistry professor Satish Nair, who led the study. "So susceptible bacteria see this peptide, think of it as food and internalize it."

The meal comes at a price, however: Once the bacterial enzymes chew up the amino acid disguise, the liberated antibiotic is free to attack a key component of protein synthesis in the bacterium, Nair said.

"That is why the organisms that make this thing have to protect themselves," he said.

In previous studies, researchers had found the genes that protect some bacteria from this class of antibiotic toxins, but they didn't know how they worked. These genes code for peptidases, which normally chew up proteins (polypeptides) and lack the ability to recognize anything else.

Originally posted here:
Team discovers how bacteria resist a 'Trojan horse' antibiotic

BELLINGHAM - Scientific measurements of the biochemistry of Lake Whatcom showed some improvement in 2011, but that is probably the result of a cool summer, not human efforts to control polluting runoff.

So says Robin Matthews, the lead scientist on the annual lake water monitoring effort commissioned by the city. Matthews is director of the Institute for Watershed Studies at Huxley College of the Environment, Western Washington University.

"I think we got a break last summer," Matthews said.

Cold and cloudy conditions kept water temperatures lower, and that delayed and diminished the annual explosion of algae populations that have affected lake quality in previous summers.

In the hotter summer of 2009, the algae concentrations got so high that they caused a serious cut in the capacity of the city's water treatment plant, resulting in mandatory water use restrictions. But even in a cool year like 2011, the algae growth was still enough to reduce the system's capacity, Matthews said.

While the scientific measurements taken in 2011 did show a reduction in levels of phosphorus and algae, Matthews said she believes the reductions were minor, and the summer's lower temperatures probably account for those reductions.

"It (pollution measurement) is down a little but it's not down much," Matthews said. "It doesn't show an improvement from watershed changes."

Matthews refuses to draw conclusions from any single year's worth of lake water measurements. Instead, she points to the whole series of measurements going back to 1994. Those measurements show year-to-year fluctuations, but a general rising trend in both phosphorus concentrations and algae growth.

As Matthews explained it, the lake's problems stem from phosphorus-laden runoff that is made worse by human activities in the watershed. The phosphorus nourishes algae growth, and the dead algae become food for bacteria. The bacteria, in turn, deplete dissolved oxygen and make the lake less hospitable to fish.

And it becomes a vicious circle, because the lower oxygen levels result in chemical changes that release additional phosphorus from compounds and make it usable for algae food.

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Cool 2011 summer helped Lake Whatcom water quality a bit

Public release date: 14-Mar-2012 [ | E-mail | Share ]

Contact: Clea Desjardins clea.desjardins@concordia.ca 514-848-2424 x5068 Concordia University

This press release is available in French.

Montreal -- Canada defines itself as a nation that stretches from coast to coast to coast. But can we keep those coasts healthy in the face of climate change? Yves Glinas, associate professor in Concordia's Department of Chemistry and Biochemistry, has found the solution in a surprising element: iron.

In a study published in Nature, Glinas along with Concordia PhD candidate Karine Lalonde and graduate Alexandre Ouellet, as well as McGill colleague Alfonso Mucci studies the chemical makeup of sediment samples from around the world ocean to show how iron oxides remove carbon dioxide from our atmosphere.

"People around the planet are fighting to reduce the amount of CO2 pumped into the atmosphere in the hopes of reducing climate change. But when it comes to getting rid of the CO2 that's already there, nature herself plays an important role," Glinas explains. CO2 is removed from the atmosphere and safely trapped on the ocean floor through a natural reaction that fixes the molecule to organic carbon on the surface of large bodies of water.

How exactly does that fixation process work? "For well over a decade, the scientific community has held onto the hypothesis that tiny clay minerals were responsible for preserving that specific fraction of organic carbon once it had sunk to the seabed," explains Mucci, whose related research was picked as one of the top 10 Scientific Discoveries of the year by Qubec Science. Through careful analysis of sediments from all over the world, Glinas and his team found that iron oxides were in fact responsible for trapping one fifth of all the organic carbon deposited on the ocean floor.

With this new knowledge comes increased concern: iron oxides are turning into what might be termed endangered molecules. As their name suggests, iron oxides can only form in the presence of oxygen, meaning that a well-oxygenated coastal ecosystem is necessary for the iron oxides to do their work in helping to remove carbon dioxide from the atmosphere. But there has been a worrying decrease in dissolved oxygen concentrations found in certain coastal environments and this trend is expanding. Locations once teeming with life are slowly becoming what are known as "dead zones" in which oxygen levels in the surface sediment are becoming increasingly depleted. That familiar culprit, man-made pollution, is behind the change.

Major rivers regularly discharge pollutants from agricultural fertilizers and human waste directly into lake and coastal environments, leading to a greater abundance of plankton. These living organisms are killed off at a greater rate and more organic carbon is sinking to the bottom waters, causing even greater consumption of dissolved oxygen. This makes the problem of low dissolved oxygen levels even worse. If the amount of oxygen in an aquatic environment decreases beyond a certain point, iron oxides stop being produced, thus robbing that environment of a large fraction of its natural ability to extract carbon dioxide from the atmosphere.

But there is hope. "This study also represents an indirect plea towards reducing the quantities of fertilizers and other nutrient-rich contaminants discharged in aquatic systems" explains Lalonde, who Glinas credits with much of the work behind this elemental study. She hopes that better understanding the iron-organic carbon stabilizing mechanism could "eventually lead to new ways of increasing the rate of organic carbon burial in sediments."

Read this article:
Fielding questions about climate change

To Bob Rose and his colleagues, evolution isn't just a theoryit's the basis for their whole career.

"The idea of evolution is seminal to biochemistry," Rose, professor of biochemistry, said. Rose is currently working with the University, researching the gene that promotes insulin-production in various species.

"We do a lot of comparisons between species, which is very evolution-based." Rose said.

Rose is currently working on comparing the insulin promoter between humans, rats and mice in order to understand what things are conserved between the species. One of the key differences between these species is that mice have two insulin genes, whereas humans only have one.

"For some reason, the function was important enough to warrant two genes we see variations like that a lot," Rose said.

Despite those differences, enough is conserved between the proteins that regulate the genes and even the genes themselves that researchers can examine them as an important evolutionarily-preserved function.

According to Paul Wollenzien, professor of biochemistry, the first signs of evolution came at the earliest stages of life. Originally, polymers of RNA, nucleic acids that can code genetic information, self-competed for replication. Next came proteins translated from that primary genetic code, and finally life began to emerge.

Even in modern organisms, there are clues to these early events. For example, there are sequences within ribosomal RNA that are shared between the three domains of life: eukaryotes, prokaryotes and achaea. This means that the sequences were present within the progenitor of these domainsa common ancestor.

"Because we can recognize these universally-conserved sequences, we take that to mean that they were established early on in evolution," Wollenzien said. Because the sequences were established very early on, it indicates a great importance for the basic functions of life.

Evolution influences the emerging field of biochemistry with something called "Instant Evolution."

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Darwin peering through the molecular level

UTHSCT researchers receive five seed grants totaling $115,000

Five seed grants totaling $115,000 have been awarded to researchers at The University of Texas Health Science Center at Tyler. The locally raised money will help UTHSCT researchers explore new cures for serious diseases, saidSteven Idell, MD, Ph.D., UTHSCTs vice president for research.

Hong-Long Ji, Ph.D., associate professor of biochemistry, was awarded a $40,000 grant to study the relationship between abnormal genes and chronic obstructive pulmonary disease (COPD).

Usha Pendurthi, Ph.D., professor of molecular biology, received $40,000 to fund her work into how certain proteins that curb blood clotting affect the growth of cancerous tumors.

Proteins are required for the structure, function, and regulation of the bodys cells, tissues, and organs; each protein has unique functions. Hormones, enzymes, and antibodies are all examples of proteins.

Buka Samten, Ph.D., associate professor of microbiology and immunology, and Malini Madiraju, Ph.D., professor of biochemistry, were awarded $20,000 for preliminary research that could lead to a better vaccine against tuberculosis. Thats important, because TB kills more than a million people each year, according to the World Health Organization.

Anna Kurdowska, Ph.D., professor of biochemistry, received $10,000 for her research into a new way to treat acute lung injury, also known as acute respiratory distress syndrome (ARDS). And Amir Shams, Ph.D., associate professor of microbiology and immunology, received $5,000 to examine how to keep treatments for injured lungs inside those lungs.

These grants enable our scientists to pursue new and exciting research that could change our understanding of how serious diseases develop, as well as transform how we treat them. They help our researchers acquire the preliminary data they need to successfully compete for funding from the National Institutes of Health, the gold standard in biomedical research, Dr. Idell said, calling this years projects outstanding.

Funding for the seed grants comes from UTHSCs Research Council and the Texas Lung Injury Institute. Since 2002, scientists in the Center for Biomedical Research have been awarded $118.6 million in research dollars.

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UTHSCT researchers receive five seed grants totaling $115,000

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/b561c1/biochemistry_for_s) has announced the addition of John Wiley and Sons Ltd's new book "Biochemistry for Sport and Exercise Metabolism" to their offering.

How do our muscles produce energy for exercise and what are the underlying biochemical principles involved? These are questions that students need to be able to answer when studying for a number of sport related degrees. This can prove to be a difficult task for those with a relatively limited scientific background. Biochemistry for Sport and Exercise Metabolism addresses this problem by placing the primary emphasis on sport, and describing the relevant biochemistry within this context.

The book opens with some basic information on the subject, including an overview of energy metabolism, some key aspects of skeletal muscle structure and function, and some simple biochemical concepts. It continues by looking at the three macromolecules which provide energy and structure to skeletal muscle - carbohydrates, lipids, and protein. The last section moves beyond biochemistry to examine key aspects of metabolism - the regulation of energy production and storage. Beginning with a chapter on basic principles of regulation of metabolism it continues by exploring how metabolism is influenced during high-intensity, prolonged, and intermittent exercise by intensity, duration, and nutrition.

Key Features:

Biochemistry for Sport and Exercise Metabolism will prove invaluable to students across a range of sport-related courses, who need to get to grips with how exercise mode, intensity, duration, training status and nutritional status can all affect the regulation of energy producing pathways and, more important, apply this understanding to develop training and nutrition programmes to maximise athletic performance.

Key Topics Covered:

For more information visit http://www.researchandmarkets.com/research/b561c1/biochemistry_for_s

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Research and Markets: Biochemistry for Sport and Exercise Metabolism

We bring you a guest post today from Faraz Hussain, who studies biochemistry at Illinois Institute of Technology. Faraz is a student of Joseph Orgel, the biologist researching preserved dinosaur tissue whom we profiled in the latest episode of Clever Apes. Here, Faraz introduces us to a completely different way of bridging the eons to bring dinosaurs into the present day. Gabriel Spitzer

Dinosaurs 180 million-odd year reign may be considered a lively old romp by most, but some clever apes would prefer to study these fossils in the flesh. One particular suborder, the theropods, never really went extinct at all. The birds that descended from them are the nearest living relatives today of both raptors and tyrannosaursperhaps none more so than the humble hen. Paleontologist Jack Horner, one of the most vocal exponents of avian dinosaurs being all around us, would rather that hens' more imposing ancestors had not evolutionarily "chickened out" in the first place.

Instead of messing about with amber-encased mosquitoes gorged on dino-DNA and playing fill-in-the-blanks with frog and bird genomes la Jurassic Park, Horner has been rallying his paleontologist pals and evolutionary developmental biologists to try a fresh tack on resurrecting a dinosaur: He wants to reverse-engineer a chickenosaurus. Hey, why start from scratch when you already have a fully-formed dinosaur in need of just a few minor genetic modifications? What follows is not your grandma's stuffed chicken recipe:

Chicken fingers:

While birds may have opted for wings instead of claws, both the T. rex and the chicken have only three digits at the end of each. In birds, however, these fingers have fused together. Hans Larsson at McGill University's Redpath Museum is looking for ways to short-circuit the genetic pathway responsible for this process in the chicken's embryonic stage and allowing the digits to separate so that, instead of those delicious wings, it ends up with far deadlier talons instead.

Rump:

A chicken has only a handful of vertebrae at the end of its spine that fuse to form what passes for its tail. In 2007, Larsson observed a tail in a developing chick embryo that had 16, although by the time it hatched these had dwindled to five. Turn off the genetic mechanism that triggers the breakdown and absorption of the tail, and voilyou're well on your way to the 40 or so vertebrae found in some of the heftiest hindquarters ever: the T. rex tail.

Teeth:

Matthew Harris discovered the rudiments of teeth on a frankenchicken embryo called the talpid2 usually known for its polydactyl fingers. While a far cry from the toothy old tyrannosaur grin that we know and lovethe genome of a chicken doesnt contain genes coding for enamel, nor can they produce dentin, which made up the bulk of those formidable fangsits finally a fighting chance for poultry to bite back!

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Clever Apes: Cooking up a dino-chicken

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

Contact: Kim Irwin kirwin@mednet.ucla.edu 310-206-2805 University of California - Los Angeles Health Sciences

Researchers at the UCLA stem cell center and the departments of chemistry and biochemistry and pathology and laboratory medicine have identified, for the first time, a generic way to correct mutations in human mitochondrial DNA by targeting corrective RNAs, a finding with implications for treating a host of mitochondrial diseases.

Mutations in the human mitochondrial genome are implicated in neuromuscular diseases, metabolic defects and aging. There currently are no methods to successfully repair or compensate for these mutations, said study co-senior author Dr. Michael Teitell, a professor of pathology and laboratory medicine and a researcher with the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA.

Between 1,000 and 4,000 children per year in the United States are born with a mitochondrial disease and up to one in 4,000 children in the U.S. will develop a mitochondrial disease by the age of 10, according to Mito Action, a nonprofit organization supporting research into mitochondrial diseases. In adults, many diseases of aging have been associated with defects of mitochondrial function, including diabetes, Parkinson's disease, heart disease, stroke, Alzheimer's disease and cancer.

"I think this is a finding that could change the field," Teitell said. "We've been looking to do this for a long time and we had a very reasoned approach, but some key steps were missing. Now we have developed this method and the next step is to show that what we can do in human cell lines with mutant mitochondria can translate into animal models and, ultimately, into humans."

The study appears March 12, 2012 in the peer-reviewed journal Proceedings of the National Academy of Sciences.

The current study builds on previous work published in 2010 in the peer-reviewed journal Cell, in which Teitell, Carla Koehler, a professor of chemistry and biochemistry and a Broad Stem Cell Research Center scientist, and their team uncovered a role for an essential protein that acts to shuttle RNA into the mitochondria, the energy-producing "power plant" of a cell.

Mitochondria are described as cellular power plants because they generate most of the energy supply within a cell. In addition to supplying energy, mitochondria also are involved in a broad range of other cellular processes including signaling, differentiation, death, control of the cell cycle and growth.

The import of nucleus-encoded small RNAs into mitochondria is essential for the replication, transcription and translation of the mitochondrial genome, but the mechanisms that deliver RNA into mitochondria have remained poorly understood.

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Correcting human mitochondrial mutations

LOS ANGELES Researchers at the UCLA stem cell center and the departments of chemistry and biochemistry and pathology and laboratory medicine have identified, for the first time, a generic way to correct mutations in human mitochondrial DNA by targeting corrective RNAs, a finding with implications for treating a host of mitochondrial diseases.

Mutations in the human mitochondrial genome are implicated in neuromuscular diseases, metabolic defects and aging. There currently are no methods to successfully repair or compensate for these mutations, said study co-senior author Dr. Michael Teitell, a professor of pathology and laboratory medicine and a researcher with the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA.

Between 1,000 and 4,000 children per year in the United States are born with a mitochondrial disease and up to one in 4,000 children in the U.S. will develop a mitochondrial disease by the age of 10, according to Mito Action, a nonprofit organization supporting research into mitochondrial diseases. In adults, many diseases of aging have been associated with defects of mitochondrial function, including diabetes, Parkinson's disease, heart disease, stroke, Alzheimer's disease and cancer.

"I think this is a finding that could change the field," Teitell said. "We've been looking to do this for a long time and we had a very reasoned approach, but some key steps were missing. Now we have developed this method and the next step is to show that what we can do in human cell lines with mutant mitochondria can translate into animal models and, ultimately, into humans."

The study appears today in the peer-reviewed journal Proceedings of the National Academy of Sciences.

The current study builds on previous work published in 2010 in the peer-reviewed journal Cell, in which Teitell, Carla Koehler, a professor of chemistry and biochemistry and a Broad stem cell research center scientist, and their team uncovered a role for an essential protein that acts to shuttle RNA into the mitochondria, the energy-producing "power plant" of a cell.

Mitochondria are described as cellular power plants because they generate most of the energy supply within a cell. In addition to supplying energy, mitochondria also are involved in a broad range of other cellular processes including signaling, differentiation, death, control of the cell cycle and growth.

The import of nucleus-encoded small RNAs into mitochondria is essential for the replication, transcription and translation of the mitochondrial genome, but the mechanisms that deliver RNA into mitochondria have remained poorly understood.

The study in Cell outlined a new role for a protein called polynucleotide phosphorylase (PNPASE) in regulating the import of RNA into mitochondria. Reducing the expression or output of PNPASE decreased RNA import, which impaired the processing of mitochondrial genome-encoded RNAs. Reduced RNA processing inhibited the translation of proteins required to maintain the mitochondrial electron transport chain that consumes oxygen during cell respiration to produce energy. With reduced PNPASE, unprocessed mitochondrial-encoded RNAs accumulated, protein translation was inhibited and energy production was compromised, leading to stalled cell growth.

The findings from the current study provide a form of gene therapy for mitochondria by compensating for mutations that cause a wide range of diseases, said study co-senior author Koehler.

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Repairing mutations in human mitochondria

In a report that appears online in the journal Structure, the BCM team describes the development of the semi-automated protocol that enables researchers to "rapidly generate an ensemble of initial models for individual proteins, which can later be optimized to produce full atomic models."

Taking the 3-D images generated through the process of electron cryo-microscopy and X-ray crystallography, the team developed this computational approach to produce these first-generation models of the proteins' structure or fold without prior knowledge of the protein's sequence or other information.

"This is important in working with big complexes made up of 10 to 30 proteins," said Dr. Matthew Baker, instructor in biochemistry and molecular biology at BCM and the paper's corresponding author. "You might know the structure of one or two proteins, but you want to know how all of those proteins interact with each other. As long as you can separate one protein from another, you can use this technique to make a model of each of the proteins in the complex."

"We borrowed from a classic computer science problem called the 'traveling salesman problem,'" said Dr. Mariah Baker, the paper's first author and a postdoctoral fellow at BCM. "It is in effect a connect-the-dots puzzle without the numbers."

In the traveling salesman problem, computer programmers are asked to figure the best route for a salesman who wants to visits all the cities where he sells just once while minimizing the distance traveled. Pathwalking solves a similar problem for proteins by looking for the optimal path through a 3-D image that connects C-alpha atoms, rather than cities, to form the protein's structure.

The tool is the answer to the dilemma presented by the near-atomic structures that are in the "middle" not of the highest resolution or the lowest resolution, said Matthew Baker.

As many as 25 percent of all structures imaged by electron cryo-microscopy and one-third of large protein complexes solved by X-ray crystallography are in the 3 to 10 angstroms range, said Matthew Baker.

Until now, the methodology used to annotate or trace the structure of protein from these density maps was usually tailored to specific cases, said Mariah Baker.

"They involved a lot of user intervention and the possibility to include bias," she said. That sparked a determination to automate the process with better routines that required less specific information.

"The question we asked was, can we trace a protein fold in a density map without a priori knowledge," she said. "The answer is that we can."

Continue reading here:
Semi-automated 'pathwalking' to build a protein model

Renowned Scientist receives IRL Industry and Outreach Fellowship

IRL has appointed Professor Juliet Gerrard, a biochemist and leader in the industrial application of biochemistry in New Zealand as its second Industry and Outreach Fellow.

IRLs Industry and Outreach Fellowships have been established as part of IRLs drive to strengthen links between the research and high-value manufacturing organisations.

New Zealands economic success depends on our ability to get greater coordination and alignment across our research and industry sectors. One area of significant potential is through greater mobility of highly talented people, says Shaun Coffey, IRL Chief Executive.

The Industry and Outreach Fellowships attract leaders from the research sector into IRL to develop areas of scientific research and assist with their application to industry.

Professor Gerrard, who runs the Biomolecular Interaction Centre at the University of Canterbury, has held a number of significant positions in recognition of her scientific work and has recently been appointed Chair of the Marsden Council.

Professor Gerrard sees the overall strategic aim of the Industry and Outreach Fellowship programme as boosting collaboration.

"There is a lot of research being done in both universities and industry and Id like to bridge that gap between fundamental and applied work," she says. "By collaborating with IRL I believe that we will be able to achieve this."

Professor Gerards track record includes stints working for Crop and Food Research Ltd, and conducting research for the likes of Fonterra. She is also a principal investigator at the MacDiarmid Institute and Riddet Institute and has been on a number of editorial boards for scientific journals. She has written over 100 journal articles.

IRL Industry and Outreach Fellows are initially appointed for a five-year term and are mandated to resolve industry-related problems while building links between research institutions and business.

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Renowned Scientist receives IRL Industry and Outreach Fellow

A University associate research scientist in the Department of Biochemistry and Molecular Biology was arrested Saturday night and charged with driving under the influence of alcohol, failure to maintain lane and open container, according to an Athens-Clarke County police report.

Irina Kataeva, 55, was pulled over by an officer on West Broad Street after he noticed her vehicle cross into the left lane and go across the fog line, according to the report.

Kataeva reportedly told the officer she had difficulty seeing at night, and the officer then noticed her eyes were extremely red and watery and there was the smell of alcohol on her breath.

The officer then asked her how much she had to drink, and she said she had one beer, according to the report.

While the officer was speaking to Kataeva, another officer noticed an open container of alcohol in the passenger seat.

When she exited the car, the officer noticed she was swaying when she walked and asked her if she had any alcohol in the car.

Kataeva reportedly said she did not have any alcohol in the vehicle. But when the officer asked to search her car, she said she did mind and had a bottle of liquor in the front seat.

An officer recovered an opened bottle of root beer flavored vodka from the car, according to the report.

Kataeva declined to perform field sobriety tests, and she reportedly asked the officer to just let her go and told him she was not far away from her house.

Her breath tested positive for alcohol, and she was placed under arrest and taken to the ACC Police Substation on Baxter Street, according to the report.

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University associate research scientist arrested with root beer flavored vodka in front seat (w/Documents)

PHILADELPHIA Mark A. Lemmon, PhD, chair of the Department of Biochemistry and Biophysics at the Perelman School of Medicine, University of Pennsylvania, is the 2012 recipient of the Dorothy Crowfoot Hodgkin Award by The Protein Society. The award will be presented at the 26th Annual Symposium of The Protein Society in August, during the Plenary Awards Session.

The Dorothy Crowfoot Hodgkin Award, is given in recognition of exceptional contributions in protein science, which profoundly influence our understanding of biology. Dr. Lemmon is being recognized for major contributions to the field of signal transduction and transmembrane signaling mechanisms of receptor tyrosine kinases. Crystallographic, biochemical, and genetic studies from his laboratory have provided sophisticated understanding of EGFR cell signaling. His discoveries of the mechanisms for the epidermal growth factor receptor family offer new ideas for developing therapies targeting cancer and other human diseases.

"Of course, it's not really my work that this award honors, but really that of several fantastic Penn postdocs and students," says Lemmon. "First, I'd particularly like to single out Diego Alvarado, Daryl Klein, Sung Hee Choi, Jeannine Mendrola and Fumin Shi for the EGF receptor work that the award cites. They are all great examples of the superb scientists that Penn Medicine attracts and reasons why it's so great to be here.

"Second, Dorothy Crowfoot Hodgkin has always been a hero of mine. She did much of her secondary education in the part of England where I grew up and was already a legend at Oxford when I went there. Her crystallographic studies of insulin -- well after her 1964 Nobel Prize -- inspired much of our structural work in EGF signaling. I always found it interesting too given her politics - that Margaret Thatcher was one of Professor Hodgkin's most famous students."

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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 billion enterprise.

Penn's Perelman School of Medicine is currently ranked #2 in U.S. News & World Report's survey of research-oriented medical schools and among the top 10 schools for primary care. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $507.6 million awarded in the 2010 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 10 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 2010, Penn Medicine provided $788 million to benefit our community.

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Penn Biochemist Receives Hodgkin Award from The Protein Society

Public release date: 1-Mar-2012 [ | E-mail | Share ]

Contact: Erin Pope Erin.Pope@NationwideChildrens.org 614-355-0495 Nationwide Children's Hospital

In 2010, the Center for Gene Therapy at Nationwide Children's Hospital launched a monthly podcast entitled, "This Month in Muscular Dystrophy," featuring internationally known scientists discussing the latest research in muscular dystrophy and other neuromuscular disorders. Now, these podcasts will be available for users on iTunes and at http://www.NationwideChildrens.org/muscular-dystrophy-podcast.

The podcasts are geared toward patients, their families and primary care physicians who take care of patients with neuromuscular diseases. Hosted by Kevin Flanigan, MD, an attending physician in Neurology at Nationwide Children's Hospital, and a principal investigator in the Center for Gene Therapy in The Research Institute at Nationwide Children's, the programs include interviews with authors of recent scientific publications discussing how their work improves understanding of inherited neuromuscular diseases and what their findings might mean for treatment.

New programs available for download on iTunes include:

Podcasts from previous months have also been uploaded to iTunes and are available for download.

"There is a lot of exciting work going on in the field of neuromuscular disease, and for patients and their families, it may be hard to get access to information about new results," said Dr. Flanigan, also a professor of Pediatrics and Neurology at The Ohio State University College of Medicine. "Our goal in offering this monthly podcast is to provide a way for people affected by the muscular dystrophies and related disorders to hear directly from top researchers about their latest results. It's my job to converse in understandable terms with these researchers about what is useful or exciting in their work."

Patients and their families are eager to find reliable information, especially about what new therapies are entering trials. With these podcasts available on iTunes, patients and their families have access to this information at their fingertips. These monthly podcasts provide reliable information directly from leading scientists and physicians in the field to empower patients to take the information they learn into their own clinics to discuss with their doctors. The podcasts also serve to provide reliable information to primary care physicians who often have the most contact with patients who have neuromuscular disorders.

"Through these podcasts, I think we can reinforce the hope shared by all families, and let them know that many pathways that may lead to meaningful treatments are being explored," Dr. Flanigan added.

Dr. Flanigan's primary research interest is in the genetic and molecular characterization of inherited neuromuscular diseases particularly muscular dystrophies and in the development of therapies directed toward these diseases.

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Nationwide Children's Hospital neuromuscular disorder podcasts now available on iTunes

Nobel Laureate in Chemistry Roger Tsien discussed current research on fluorescent proteins, or proteins that emit bright colors when exposed to ultraviolet blue light, and their uses in surgery at Emory on Thursday.

The Department of Biochemistry held the lecture, titled Breeding and Building molecules to Spy on Cells and Disease Processes, at the Woodruff Health Sciences building as part of the Department of Biochemistrys annual Donald B. McCormick Lecture. The annual lecture honors McCormick, who served as the chair of the department from 1979 to 1994 and is currently professor emeritus at Emorys School of Medicine.

McCormick is recognized for his many achievements including the publication of more than 500 papers, leading expertise in nutritional biochemistry, and membership in notable committees such as the National Institutes of Health (NIH).

In 2008, Tsien received the Nobel Prize in Chemistry for his discovery of the green fluorescent protein (GFP) with his colleagues Osamu Shimomura and Martin Chalfie. He is a Howard Hughes Medical Institute Investigator and professor at the University of California-San Diego.

He focused on proteins called miniSOGs, which are single oxygen-generating miniproteins and genetic tags used in electron microscopy (EM). He said electrons are beamed at an object to produce a highly magnified image. These miniSOGs are sequences of amino acids that can be attached to proteins, Tsien noted. When miniSOGs are exposed to blue light, they produce a type of molecular oxygen that is visible in EM. The use of EM creates an amplified image under the microscope which is of a greater resolution than the image produced by light microscopy.

It is really amazing how many different applications there are for the tag, James Roed, post doctorate fellow at the School of Medicine noted. The design is simple yet so complex and is really going to revolutionize cancer treatment but has potential in being used to tether probes to drugs as well.

Tsien explained the clinical applications of fluorescent dyes in cancer research and treatment. This is a very nonselective process. Tsien explained. When you try to do this with a fluorescent tag IV injection into a mouse, you get a fluorescent tail, because it sticks to the epithelia, which is the skin of the animal, at the site of the injection.

It then travels to different regions of the body but practically never reaches the tumor that you care about, Tsien said.

We decided in our lab that what was necessary was a way of making this process selective, not just indiscriminate, he said.

He then showed images of tumors in mice and explained the difficulty the human eye experiences in differentiating a tumor from the surrounding flesh. When the tissue was exposed via fluorescent illumination, the boundaries of the tumor became easily distinguishable as the fluorescent light blue mass stood out.

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Nobel Laureate Explores Proteins, Surgery

03-08-2011 12:03 (11/17/10) Lecture by Kevin Ahern of Oregon State University discussing Biochemistry Basics in BB 450. See the full course at oregonstate.edu Highlights Glycolysis II 1. Reaction #9 is catalyzed by enolase and involves removal of water from 2PG to form PEP, which is a highly energetic compound. 2. Reaction #10 is the "Big Bang" of glycolysis. It is catalyzed by the enzyme pyruvate kinase and in the reaction, a substrate level phosphorylation yields ATP. Note that the Delta G zero prime is very strongly negative, helping to pull all the reactions preceding it to a large extent. The enzyme is allosterically inactivated by ATP and allosterically activated by F1,6BP. The latter activation is an example of "feed forward" activation. Pyruvate kinase is also inactivated by phosphorylation, as will be seen in glycogen metabolism. 3. The phenomenon of redox balancing is important for glycolysis. Redox balancing relates to the relative amount of NAD+ and NADH in the cell. Remember that reaction 6 is very sensitive to the ratio of NAD+/NADH. 4. Pyruvate has three separate fates, depending on conditions and the cell type. When oxygen is present, there is plenty of NAD+, so aerobic cells convert pyruvate to acetyl-CoA for oxidation in the citric acid cycle. When oxygen is absent, NAD+ levels can go down, so to prevent that from happening, pyruvate is converted to either lactate (animals) or ethanol (bacteria/yeast). Either of these last two conversions REQUIRES NADH and produces NAD+ ...

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Bite-Sized Biochemistry #22 - Glycolysis II / Carbohydrate Metabolism - Video

30-01-2012 12:16 And thus begins the most revolutionary biology course in history. Come and learn about covalent, ionic, and hydrogen bonds. What about electron orbitals, the octet rule, and what does it all have to do with a mad man named Gilbert Lewis? It's all contained within. Like Crash Course on...

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That's Why Carbon Is A Tramp: Biology #1 - Video