A team of Rutgers University scientists led by Richard H. Ebright and Eddy Arnold has identified a new antibiotic target and a new antibiotic mechanism that may enable the development of broad-spectrum antibacterial agents effective against bacterial pathogens resistant to current antibiotics. In particular, the results could lead the way to new treatments for tuberculosis (TB) that involve shorter courses of therapy and are effective against drug-resistant TB.
The researchers showed how three antibiotics - myxopyronin, corallopyronin and ripostatin - block the action of bacterial RNA polymerase (RNAP). RNAP is the enzyme that transcribes genetic information from DNA into RNA, which, in turn, directs the assembly of proteins, the building blocks of all biological systems. Blocking bacterial RNAP kills bacterial cells.
The research findings are reported in the journal Cell, published online Oct. 16 and in the Oct. 17 print issue of the journal.
The shape of the RNAP molecule is key to the action of the three antibiotics, Ebright explained. "RNAP has a shape reminiscent of a crab claw, with two prominent pincer-like projections," he said. "Just as with a real crab claw, one pincer stays fixed and one pincer moves - opening to allow DNA into the enzyme and closing to keep DNA in the enzyme. The pincer that moves does so by rotating about a hinge, termed the 'switch region,' located at its base."
The studies showed that the three antibiotics bind to this hinge and, further, that by jamming the hinge, they prevent the pincer from opening to let DNA into the enzyme, Ebright said.
Once the target and mechanism of the three antibiotics were elucidated, the researchers proceeded to determine the structure of RNAP bound to one of the three antibiotics. "This has allowed us to define how the enzyme and the antibiotic interact and to characterize how the enzyme changes shape in response to the antibiotic," Arnold said. "Perhaps more important, this has allowed us to explore ways to change the chemical structure of the antibiotic to make tighter interactions with the enzyme for higher potency."
The three antibiotics exhibit potent activity against a broad spectrum of bacterial species, including the bacterium that causes TB, and exhibit no cross resistance with current antibacterial agents.
"The three antibiotics are attractive candidates for development as broad spectrum antibacterial agents," Ebright said, "and their target within RNAP - the hinge or 'switch region' - is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents."
Arnold points out that the binding site for the three antibiotics has attractive features for design of new agents. "The target site is a pocket that accommodates a variety of chemical types. The nature of the binding site and mechanism of inhibition are analogous to those of the HIV-1 reverse transcriptase non-nucleoside inhibitors, which include four FDA-approved drugs for treating HIV-1 infections. The parallels are encouraging and suggest that multiple classes of agents can be developed to target the new site."
Ebright, a Howard Hughes Medical Institute investigator, is a professor in the Department of Chemistry and Chemical Biology and a member of the Waksman Institute of Microbiology at Rutgers, The State University of New Jersey. Arnold, also a professor of chemistry and chemical biology, is a member of the Center for Advanced Biotechnology and Medicine (CABM), jointly operated by Rutgers and the University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School.
Jayanta Mukhopadhyay from Ebright's laboratory and Kalyan Das from Arnold's laboratory carried out much of the work.
The research team also included Rolf Jansen and Herbert Irschik of the Helmholtz Center for Infection Research in Braunschweig, Germany.
Most antibacterial compounds are able to kill actively growing TB bacteria but are unable to kill resting, dormant TB bacteria. As a result, most antibacterial compounds can rapidly reduce populations of TB bacteria in infected patients to low numbers but cannot rapidly reduce these numbers to zero. Antibacterial compounds that target RNAP, however, are able to kill both active and dormant TB bacteria since RNAP plays essential roles in, and is required for survival of, both active and dormant TB bacteria.
A class of antibacterial compounds known as rifamycins, which target RNAP, are current first-line treatment of TB and are the sole current treatments that can relatively rapidly reduce populations of TB bacteria to zero. Unfortunately, rifamycins are too toxic to administer at doses that most rapidly clear infection. Also, resistance to rifamycins occurs frequently, due to mutations that alter their binding site on RNAP.
The three antibiotics studied by Ebright and co-workers also target RNAP; however, they target a new site on RNAP, different from the site on RNAP targeted by rifamycins. "A key point about these antibiotics is that their binding site on RNAP is different from, and does not overlap with, the binding site for rifamycins," Ebright said. "As a result, these antibiotics can function simultaneously with rifamycins and can be co-administered with rifamycins for more rapid clearance of infection. As a further result, these antibiotics do not exhibit cross-resistance with rifamycins. Mutations that alter the binding site for rifamycins on RNAP and confer resistance to rifamycins do not confer resistance to these antibiotics.
The standard course of therapy for most bacterial infections is about two weeks, but TB is different. The shortest course of therapy for TB is six to nine months. "That is, if you can use rifamycins," Ebright notes. "If you have a patient who cannot tolerate rifamycins, or if you have a patient whose infection is resistant to rifamycins, that patient is looking at 18 to 24 months of therapy."
"The Holy Grail in TB therapy is to reduce the course of therapy from six months to two weeks - to make treatment of TB like treatment of other bacterial infections," Ebright said. "If you could develop a two-week therapy for TB, you could eradicate TB. With a six-month course of therapy for a disease that is largely centered in the third world, the logistical problems of administering therapy over space and time make eradication a nonstarter. But if there were a two-week course of therapy, the logistics would be manageable, and the disease would be eradicated."
The hope is that the new findings will bring that goal closer.
Source: Joseph Blumberg
Rutgers University
четверг, 26 мая 2011 г.
Prenatal Drinking, Environmental Enrichment: Effects On Neurotrophins Are Independent Of Each Other
Prenatal alcohol exposure may be particularly destructive for neurotrophins, a family of peptides that influence the growth, development and functional plasticity of the fetal brain. A new rodent study of alcohol's effects on three key neurotrophins has found that, even though environmental enrichment may be able to improve some fetal-alcohol effects, those benefits do not appear to be mediated by neurotrophins.
Results will be published in the October issue of Alcoholism: Clinical & Experimental Research and are currently available at Early View.
"Neurotrophins are produced in the nervous system and are critical for normal development of the brain," explained Robert F. Berman, a professor in the department of neurological surgery and at the Center for Neuroscience at the University of California - Davis, as well as corresponding author for the study.
"Neurotrophins also play important roles in learning and memory, and contribute to the repair of the brain following injury or stress. We chose to examine three - nerve growth factor (NGF), neurotrophin-3 (NT-3), and brain-derived neurotrophic factor (BDNF) - because previous research had shown that prenatal alcohol exposure alters their levels in the brain, and that treatment of other types of brain injury with NGF or BDNF can be beneficial."
Researchers divided 22 pregnant Sprague-Dawley rats into four groups: Zero (receiving 0 g of alcohol), Low (4 g/kg/day), High (6 g/kg/day) and NaГЇve (untreated pregnant rats). The two alcohol groups were given alcohol on gestational days eight to 20. After weaning on postnatal day 21, the 228 offspring were housed for six weeks in one of three conditions: Isolated, Social or Enriched. Levels of NGF, NT-3 and BDNF were then measured in the offsprings' frontal cortex, occipital cortex, hippocampus, and cerebellar vermis.
"We found that prenatal alcohol exposure generally increased brain neurotrophin levels in adult rats," said Berman. "This suggests that neurotrophin levels increased as compensation for damage to the developing brain from prenatal alcohol exposure. Results also demonstrated that the effects of prenatal alcohol exposure can be enduring and last into adulthood."
Previous rodent research conducted by Berman had shown that rearing rats in an enriched environment following prenatal alcohol exposure improved their motor function as well as learning and memory. "In this study, we found that being raised in an enriched environment, with ample opportunities for motor and sensory stimulation, and social interactions, unexpectedly resulted in reduced levels of neurotrophins in some areas of the cortex, but not in other areas which are well known to be affected by prenatal alcohol exposure," he said.
When both sets of findings are considered together, he added, they indicate that the effects of prenatal alcohol exposure and environmental rearing conditions on neurotrophin levels are largely independent, with little evidence that one directly influenced the other's effects on neurotrophin levels. "In other words," he said, "our results did not support our hypothesis that the beneficial effects of early environmental enrichment in rats exposed prenatally to alcohol were mediated directly by the three neurotrophins we examined in four specific brain areas."
This means that the molecular and cellular mechanisms underlying environmental enrichment effects after prenatal alcohol exposure are still not understood, said Berman. "While the importance of the postnatal rearing environment for brain development is clear, we need additional research to aid in devising rational treatment strategies for Fetal Alcohol Spectrum Disorders, including fetal alcohol syndrome," he said.
Alcoholism: Clinical & Experimental Research (ACER) is the official journal of the Research Society on Alcoholism and the International Society for Biomedical Research on Alcoholism. Co-authors of the ACER paper, "Environmental Enrichment Alters Neurotrophin Levels after Fetal Alcohol Exposure in Rats," were: Elizabeth A. Parks of the Neuroscience Program and Department of Neurological Surgery at the University of California - Davis; and Andrew P. McMechan and John H. Hannigan of the Department of Obstetrics & Gynecology and the C.S. Mott Center for Human Growth and Development in the School of Medicine, and the Department of Psychology at Wayne State University. The study was funded by the National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism.
Additional contact:
John H. Hannigan, Ph.D.
Wayne State University
Source: Robert F. Berman, Ph.D.
University of California - Davis
Alcoholism: Clinical & Experimental Research
Results will be published in the October issue of Alcoholism: Clinical & Experimental Research and are currently available at Early View.
"Neurotrophins are produced in the nervous system and are critical for normal development of the brain," explained Robert F. Berman, a professor in the department of neurological surgery and at the Center for Neuroscience at the University of California - Davis, as well as corresponding author for the study.
"Neurotrophins also play important roles in learning and memory, and contribute to the repair of the brain following injury or stress. We chose to examine three - nerve growth factor (NGF), neurotrophin-3 (NT-3), and brain-derived neurotrophic factor (BDNF) - because previous research had shown that prenatal alcohol exposure alters their levels in the brain, and that treatment of other types of brain injury with NGF or BDNF can be beneficial."
Researchers divided 22 pregnant Sprague-Dawley rats into four groups: Zero (receiving 0 g of alcohol), Low (4 g/kg/day), High (6 g/kg/day) and NaГЇve (untreated pregnant rats). The two alcohol groups were given alcohol on gestational days eight to 20. After weaning on postnatal day 21, the 228 offspring were housed for six weeks in one of three conditions: Isolated, Social or Enriched. Levels of NGF, NT-3 and BDNF were then measured in the offsprings' frontal cortex, occipital cortex, hippocampus, and cerebellar vermis.
"We found that prenatal alcohol exposure generally increased brain neurotrophin levels in adult rats," said Berman. "This suggests that neurotrophin levels increased as compensation for damage to the developing brain from prenatal alcohol exposure. Results also demonstrated that the effects of prenatal alcohol exposure can be enduring and last into adulthood."
Previous rodent research conducted by Berman had shown that rearing rats in an enriched environment following prenatal alcohol exposure improved their motor function as well as learning and memory. "In this study, we found that being raised in an enriched environment, with ample opportunities for motor and sensory stimulation, and social interactions, unexpectedly resulted in reduced levels of neurotrophins in some areas of the cortex, but not in other areas which are well known to be affected by prenatal alcohol exposure," he said.
When both sets of findings are considered together, he added, they indicate that the effects of prenatal alcohol exposure and environmental rearing conditions on neurotrophin levels are largely independent, with little evidence that one directly influenced the other's effects on neurotrophin levels. "In other words," he said, "our results did not support our hypothesis that the beneficial effects of early environmental enrichment in rats exposed prenatally to alcohol were mediated directly by the three neurotrophins we examined in four specific brain areas."
This means that the molecular and cellular mechanisms underlying environmental enrichment effects after prenatal alcohol exposure are still not understood, said Berman. "While the importance of the postnatal rearing environment for brain development is clear, we need additional research to aid in devising rational treatment strategies for Fetal Alcohol Spectrum Disorders, including fetal alcohol syndrome," he said.
Alcoholism: Clinical & Experimental Research (ACER) is the official journal of the Research Society on Alcoholism and the International Society for Biomedical Research on Alcoholism. Co-authors of the ACER paper, "Environmental Enrichment Alters Neurotrophin Levels after Fetal Alcohol Exposure in Rats," were: Elizabeth A. Parks of the Neuroscience Program and Department of Neurological Surgery at the University of California - Davis; and Andrew P. McMechan and John H. Hannigan of the Department of Obstetrics & Gynecology and the C.S. Mott Center for Human Growth and Development in the School of Medicine, and the Department of Psychology at Wayne State University. The study was funded by the National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism.
Additional contact:
John H. Hannigan, Ph.D.
Wayne State University
Source: Robert F. Berman, Ph.D.
University of California - Davis
Alcoholism: Clinical & Experimental Research
How Enzymes Break Down Cellulose; Study By Iowa State Researcher
Peter Reilly pointed to the framed journal covers decorating his office.
Each of the six showed the swirling, twisting, complicated structure of an enzyme. Those bright and colorful illustrations are the work of his lab. And they're part of Reilly's work to understand how the structure of an enzyme influences its mechanism and its activity.
In other words, he's trying to figure out "how is it that these things work," said Reilly, a professor of chemical and biological engineering and an Anson Marston Distinguished Professor of Engineering at Iowa State University.
That's important because enzymes do a lot for all of us.
Enzymes are proteins produced by living organisms that accelerate chemical reactions. They, for example, work inside the human digestive system to break starch or protein molecules into smaller pieces that can be absorbed by the intestines. Enzymes are also used to produce bread, they're added to detergents to clean stains and they're used to treat leather. And because enzymes break down cellulose into simple sugars that can be fermented into alcohol, they're a big part of producing ethanol from cellulose.
Reilly is particularly interested in the enzymes that work on cellulose. He has a three-year, $306,000 grant from the U.S. Department of Agriculture to develop a basic understanding of how they work.
Those enzymes are known as cellulases. They're commonly produced by fungi and bacteria. And they've got a very hard job.
Cellulose is tough stuff. It's in the cell walls of plants. It's what gives a plant its structure.
"It's why trees stand up," Reilly said.
He also said, "Nature has done its best to break down cellulose."
So different enzymes have developed different ways of attacking cellulose.
One enzyme Reilly has studied and illustrated - a cellobiohydrolase enzyme - has an extension that works like a little plow. It rips up one cellulose chain from a cellulose crystal and feeds it into a tunnel on the main enzyme surface so that it can be chopped up.
Reilly, who can't resist a lesson in biochemistry, likes to explain how enzymes attack and break chemical bonds. He'll display diagrams on his office computer that show the bonds in cellulose molecules. He'll point out where enzymes attack some of those bonds. He'll say the chemical reactions create high-energy transition states that scientists are working hard to understand. And he'll get back to the bottom line.
"These different enzymes all do the same thing," Reilly said. "They all break down bonds between the sugars that make up cellulose."
And, he said, "For something that's not alive, enzymes are awfully sophisticated."
Reilly's students use a lot of computing power to figure out how enzymes are put together. They routinely work with CyBlue, Iowa State's supercomputer capable of 5.7 trillion calculations per second, and Lightning, an Iowa State high-performance computer capable of 1.8 trillion calculations per second.
By adding to the basic understanding of enzymes, Reilly is opening doors for new and better applications of enzymes. Better enzymes, for example, could be the key to making the production of cellulosic ethanol more efficient and more economical.
There's still a lot for chemical engineers to learn about the specialized proteins.
After all, Reilly said, "Nature has tried over and over to find ways to break down cellulose."
Source: Peter Reilly
Iowa State University
Each of the six showed the swirling, twisting, complicated structure of an enzyme. Those bright and colorful illustrations are the work of his lab. And they're part of Reilly's work to understand how the structure of an enzyme influences its mechanism and its activity.
In other words, he's trying to figure out "how is it that these things work," said Reilly, a professor of chemical and biological engineering and an Anson Marston Distinguished Professor of Engineering at Iowa State University.
That's important because enzymes do a lot for all of us.
Enzymes are proteins produced by living organisms that accelerate chemical reactions. They, for example, work inside the human digestive system to break starch or protein molecules into smaller pieces that can be absorbed by the intestines. Enzymes are also used to produce bread, they're added to detergents to clean stains and they're used to treat leather. And because enzymes break down cellulose into simple sugars that can be fermented into alcohol, they're a big part of producing ethanol from cellulose.
Reilly is particularly interested in the enzymes that work on cellulose. He has a three-year, $306,000 grant from the U.S. Department of Agriculture to develop a basic understanding of how they work.
Those enzymes are known as cellulases. They're commonly produced by fungi and bacteria. And they've got a very hard job.
Cellulose is tough stuff. It's in the cell walls of plants. It's what gives a plant its structure.
"It's why trees stand up," Reilly said.
He also said, "Nature has done its best to break down cellulose."
So different enzymes have developed different ways of attacking cellulose.
One enzyme Reilly has studied and illustrated - a cellobiohydrolase enzyme - has an extension that works like a little plow. It rips up one cellulose chain from a cellulose crystal and feeds it into a tunnel on the main enzyme surface so that it can be chopped up.
Reilly, who can't resist a lesson in biochemistry, likes to explain how enzymes attack and break chemical bonds. He'll display diagrams on his office computer that show the bonds in cellulose molecules. He'll point out where enzymes attack some of those bonds. He'll say the chemical reactions create high-energy transition states that scientists are working hard to understand. And he'll get back to the bottom line.
"These different enzymes all do the same thing," Reilly said. "They all break down bonds between the sugars that make up cellulose."
And, he said, "For something that's not alive, enzymes are awfully sophisticated."
Reilly's students use a lot of computing power to figure out how enzymes are put together. They routinely work with CyBlue, Iowa State's supercomputer capable of 5.7 trillion calculations per second, and Lightning, an Iowa State high-performance computer capable of 1.8 trillion calculations per second.
By adding to the basic understanding of enzymes, Reilly is opening doors for new and better applications of enzymes. Better enzymes, for example, could be the key to making the production of cellulosic ethanol more efficient and more economical.
There's still a lot for chemical engineers to learn about the specialized proteins.
After all, Reilly said, "Nature has tried over and over to find ways to break down cellulose."
Source: Peter Reilly
Iowa State University
Data Acquisition And Coordination Key To Human Microbiome Project
At birth, your body was 100-percent human in terms of cells. At death, about 10-percent of the cells in your body will be human and the remaining 90-percent will be microorganisms. That makes you a "supraorganism," and it is the interactions between your human and microbial cells that go a long way towards determining your health and physical well-being, especially your resistance to infectious diseases.
To learn more about the community of symbiotic microbes that outnumber our own somatic and germ cells by a 10:1 ratio, the National Institutes of Health (NIH) in 2008 launched the Human Microbiome Project (HMP) - a microbiome is the full complement of microorganisms populating a supraorganism. The goal of the HMP is to sequence the genomes of 1,000 or more of these microbial species and assemble the information in a "project catalog" as a reference for future investigations. The project catalog is housed at the HMP Data Acquisition and Coordination Center (DACC), which was created and is maintained by researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab).
"The HMP project catalog is a unique worldwide resource," says molecular biologist Nikos Kyrpides of Berkeley Lab's Genomics Division, who heads the Genome Biology and Metagenomics Programs for the Joint Genome Institute (JGI) and is the co-principal investigator of the DACC. "It has a central role in the HMP, not only in maintaining the list and status of over 1,400 individual human microbiome projects, but also as a data managements system for the metadata associated with these projects, such as information on the microbial isolation sites and the sites in the human body where these microbes can be found, and information on the phenotypic properties of these microbes."
At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for "Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any sequenced genome. The results identify gene-calling errors such as potentially incorrect gene start and end positions, large overlaps between genes, and fragmented or missed genes. GOLD provides comprehensive information on genome sequencing projects, including metagenomes and metadata from around the world. The HMP project catalog is powered by the GOLD database and provides a specialized user interface by which the data stored in GOLD can be read.
The other co-principal investigator of the DACC is Victor Markowitz who heads Berkeley Lab's Biological Data Management and Technology Center in the Computational Research Division, and also serves as the Chief Informatics Officer and Associate Director at JGI. Markowitz oversees the development and maintenance of the Integrated Microbial Genomics with Microbiome samples (IMG/M) system, which provides comparative analysis tools for the study of metagenomes вЂ" the collective genetic material of a given microbiome. First released in 2006, IMG/M contains millions of annotated microbial gene sequences, recovered from wild varieties of microbial communities. IMG/M is now being applied to the HMP.
"Resources such as GenePRIMP, GOLD and IMG/M are among the best in the world when it comes to providing comparative analysis tools for microbial genomes and metagenomes," Markowitz says. "As the HMP moves forward, these resources will provide support for the annotation and analysis of HMP datasets, in particular via the metagenome annotation pipeline at JGI and a HMP specific version of the IMG/M system."
The first 178 reference microbial genomes have now been analyzed and catalogued by the HMP. The results were published in the journal Science in a paper titled, "A Catalog of Reference Genomes from the Human Microbiome."
In this paper, HMP researchers report comparing data from the sequenced reference genomes to human metagenomic data in the public domain to identify proteins, determine gene functionality and link metagenomic data to individual microbial species. From an analysis of 547,968 predicted proteins, the HMP researchers report 29,987 unique proteins, which suggests a far greater diversity in the human microbiome than previously suspected.
"The Science paper is a milestone in the human microbiome research with the release to the public of 178 finished or high quality draft genomes from organisms isolated from various sites in the human body," says Kyrpides. "It signals the beginning of a much larger effort that aims to provide a more comprehensive genetic catalog of the microbes living in the human body. The impact of understanding what is the normal microbial flora, what is its core genetic content, and how perturbations of the normal microbial flora of the human body can shift from protecting our bodies into causing diseases will eventually be enormous."
Kyrpides, Markowitz and their colleagues at the DACC are playing a critical role in fulfilling an NIH call for development of common sequencing and annotation standards that have not existed before. Lack of common language and a clearing house for genome data have been among the most daunting problems in genomics research.
Says Markowitz, "The greatest challenge ahead will be handling hundred of metagenomic datasets generated as part of the HMP, which will represent several orders of magnitude more data than the datasets presented in the current paper. We need to develop novel analysis and visualization methods to handle this massive increase in data."
Adds Kyrpides, "New sequencing technologies and our ability to generate orders of magnitude more data compared to only a year or two ago are changing the field entirely, and are mandating a social shift among the scientists involved to a more collaborative rather than competitive spirit. None of us can provide solutions alone any more, and joint efforts such as the HMP are the only way we'll succeed."
Other Berkeley Lab/JGI researchers with prominent roles in the HMP include Gary Andersen, Todd DeSantis, Amy Chen, Konstantinos Liolios, Amrita Pati and Konstantinos Mavrommatis.
Berkeley Lab is a U.S. Department of Energy (DOE) national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the DOE Office of Science.
Source:
Lynn Yarris
DOE/Lawrence Berkeley National Laboratory
To learn more about the community of symbiotic microbes that outnumber our own somatic and germ cells by a 10:1 ratio, the National Institutes of Health (NIH) in 2008 launched the Human Microbiome Project (HMP) - a microbiome is the full complement of microorganisms populating a supraorganism. The goal of the HMP is to sequence the genomes of 1,000 or more of these microbial species and assemble the information in a "project catalog" as a reference for future investigations. The project catalog is housed at the HMP Data Acquisition and Coordination Center (DACC), which was created and is maintained by researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab).
"The HMP project catalog is a unique worldwide resource," says molecular biologist Nikos Kyrpides of Berkeley Lab's Genomics Division, who heads the Genome Biology and Metagenomics Programs for the Joint Genome Institute (JGI) and is the co-principal investigator of the DACC. "It has a central role in the HMP, not only in maintaining the list and status of over 1,400 individual human microbiome projects, but also as a data managements system for the metadata associated with these projects, such as information on the microbial isolation sites and the sites in the human body where these microbes can be found, and information on the phenotypic properties of these microbes."
At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for "Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any sequenced genome. The results identify gene-calling errors such as potentially incorrect gene start and end positions, large overlaps between genes, and fragmented or missed genes. GOLD provides comprehensive information on genome sequencing projects, including metagenomes and metadata from around the world. The HMP project catalog is powered by the GOLD database and provides a specialized user interface by which the data stored in GOLD can be read.
The other co-principal investigator of the DACC is Victor Markowitz who heads Berkeley Lab's Biological Data Management and Technology Center in the Computational Research Division, and also serves as the Chief Informatics Officer and Associate Director at JGI. Markowitz oversees the development and maintenance of the Integrated Microbial Genomics with Microbiome samples (IMG/M) system, which provides comparative analysis tools for the study of metagenomes вЂ" the collective genetic material of a given microbiome. First released in 2006, IMG/M contains millions of annotated microbial gene sequences, recovered from wild varieties of microbial communities. IMG/M is now being applied to the HMP.
"Resources such as GenePRIMP, GOLD and IMG/M are among the best in the world when it comes to providing comparative analysis tools for microbial genomes and metagenomes," Markowitz says. "As the HMP moves forward, these resources will provide support for the annotation and analysis of HMP datasets, in particular via the metagenome annotation pipeline at JGI and a HMP specific version of the IMG/M system."
The first 178 reference microbial genomes have now been analyzed and catalogued by the HMP. The results were published in the journal Science in a paper titled, "A Catalog of Reference Genomes from the Human Microbiome."
In this paper, HMP researchers report comparing data from the sequenced reference genomes to human metagenomic data in the public domain to identify proteins, determine gene functionality and link metagenomic data to individual microbial species. From an analysis of 547,968 predicted proteins, the HMP researchers report 29,987 unique proteins, which suggests a far greater diversity in the human microbiome than previously suspected.
"The Science paper is a milestone in the human microbiome research with the release to the public of 178 finished or high quality draft genomes from organisms isolated from various sites in the human body," says Kyrpides. "It signals the beginning of a much larger effort that aims to provide a more comprehensive genetic catalog of the microbes living in the human body. The impact of understanding what is the normal microbial flora, what is its core genetic content, and how perturbations of the normal microbial flora of the human body can shift from protecting our bodies into causing diseases will eventually be enormous."
Kyrpides, Markowitz and their colleagues at the DACC are playing a critical role in fulfilling an NIH call for development of common sequencing and annotation standards that have not existed before. Lack of common language and a clearing house for genome data have been among the most daunting problems in genomics research.
Says Markowitz, "The greatest challenge ahead will be handling hundred of metagenomic datasets generated as part of the HMP, which will represent several orders of magnitude more data than the datasets presented in the current paper. We need to develop novel analysis and visualization methods to handle this massive increase in data."
Adds Kyrpides, "New sequencing technologies and our ability to generate orders of magnitude more data compared to only a year or two ago are changing the field entirely, and are mandating a social shift among the scientists involved to a more collaborative rather than competitive spirit. None of us can provide solutions alone any more, and joint efforts such as the HMP are the only way we'll succeed."
Other Berkeley Lab/JGI researchers with prominent roles in the HMP include Gary Andersen, Todd DeSantis, Amy Chen, Konstantinos Liolios, Amrita Pati and Konstantinos Mavrommatis.
Berkeley Lab is a U.S. Department of Energy (DOE) national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the DOE Office of Science.
Source:
Lynn Yarris
DOE/Lawrence Berkeley National Laboratory
Advances In Proteomics Bring Scientists Closer To Infertility Cures
Proteins found in sperm are central to understanding male infertility and could be used to determine new diagnostic methods and fertility treatments according to a paper published by the journal Molecular and Cellular Proteomics (MCP). The article demonstrates how proteomics, a relatively new field focusing on the function of proteins in a cell, can be successfully applied to infertility, helping identify which proteins in sperm cells are dysfunctional.
"Up to 50 percent of male-factor infertility cases in the clinic have no known cause, and therefore no direct treatment. In-depth study of the molecular basis of infertility has great potential to inform the development of sensitive diagnostic tools and effective therapies," write co-authors Diana Chu, assistant professor of biology at San Francisco State University and Tammy Wu, post-doctoral fellow at SF State. The study is included in a special Oct. 10 issue of MCP dedicated to the clinical application of proteomics.
"We suggest how the study of proteins is useful in the clinic, to help people move from infertile to fertile and ultimately to help couples have a baby," Chu said. "The ultimate goal is that a doctor could be able to say to a patient, 'this is the protein that is misregulated in your sperm and this is the drug that corrects it or decreases the level of that protein.' Understanding sperm proteins also means that a doctor could be able to inform patients of the likely success rates of different fertility therapies, an important factor given the high cost of fertility treatments."
More than 2 million couples in the U.S. are facing infertility. While many scientific studies examine the supply of sperm, its mobility and its ability to fertilize, Chu argues that a wider array of sensitive tests - including studies of cell proteins - are needed to determine the root causes of male infertility.
Proteins found in sperm cells are unique. This means therapies can be developed that target only these proteins and do not produce side effects in the patient or defects in the resulting offspring.
Chu's paper highlights a selection of recent advances in the study of proteins in sperm cells, citing studies that have identified specific proteins that correlate with infertility.
Chu argues that further large-scale clinical studies are needed to identify patterns in the proteins found in the sperm of infertile patients. This would help scientists to better understand which proteins to focus on, since each sperm cell contains more than 2,000 proteins and each patient's sperm varies slightly in its protein content.
Understanding the function of individual proteins in sperm cells may not only aid scientists' understanding of fertility, but can also explain the causes of miscarriages, 50 percent of which have unexplained causes. Chu also suggests that further studies of the proteins found in sperm cells will have a significant impact on our understanding of the paternal protein contribution that can have long lasting effects on future generations.
Diana Chu is assistant professor of biology at San Francisco State University where she uses proteomic approaches to research the function of proteins associated to sperm chromatin. San Francisco State University's biology department is the largest in the California State University system. SF State ranks second among all U.S. comprehensive universities whose graduates successfully enroll in Ph.D. programs.
Source: Diana Chu
San Francisco State University
"Up to 50 percent of male-factor infertility cases in the clinic have no known cause, and therefore no direct treatment. In-depth study of the molecular basis of infertility has great potential to inform the development of sensitive diagnostic tools and effective therapies," write co-authors Diana Chu, assistant professor of biology at San Francisco State University and Tammy Wu, post-doctoral fellow at SF State. The study is included in a special Oct. 10 issue of MCP dedicated to the clinical application of proteomics.
"We suggest how the study of proteins is useful in the clinic, to help people move from infertile to fertile and ultimately to help couples have a baby," Chu said. "The ultimate goal is that a doctor could be able to say to a patient, 'this is the protein that is misregulated in your sperm and this is the drug that corrects it or decreases the level of that protein.' Understanding sperm proteins also means that a doctor could be able to inform patients of the likely success rates of different fertility therapies, an important factor given the high cost of fertility treatments."
More than 2 million couples in the U.S. are facing infertility. While many scientific studies examine the supply of sperm, its mobility and its ability to fertilize, Chu argues that a wider array of sensitive tests - including studies of cell proteins - are needed to determine the root causes of male infertility.
Proteins found in sperm cells are unique. This means therapies can be developed that target only these proteins and do not produce side effects in the patient or defects in the resulting offspring.
Chu's paper highlights a selection of recent advances in the study of proteins in sperm cells, citing studies that have identified specific proteins that correlate with infertility.
Chu argues that further large-scale clinical studies are needed to identify patterns in the proteins found in the sperm of infertile patients. This would help scientists to better understand which proteins to focus on, since each sperm cell contains more than 2,000 proteins and each patient's sperm varies slightly in its protein content.
Understanding the function of individual proteins in sperm cells may not only aid scientists' understanding of fertility, but can also explain the causes of miscarriages, 50 percent of which have unexplained causes. Chu also suggests that further studies of the proteins found in sperm cells will have a significant impact on our understanding of the paternal protein contribution that can have long lasting effects on future generations.
Diana Chu is assistant professor of biology at San Francisco State University where she uses proteomic approaches to research the function of proteins associated to sperm chromatin. San Francisco State University's biology department is the largest in the California State University system. SF State ranks second among all U.S. comprehensive universities whose graduates successfully enroll in Ph.D. programs.
Source: Diana Chu
San Francisco State University
Failing Mouse Hearts Safely Regenerated With Programmed Embryonic Stem Cells
Mayo Clinic researchers have safely transplanted cardiac preprogrammed embryonic stem cells into diseased hearts of mice successfully regenerating infarcted heart muscle without precipitating the growth of a cancerous tumor -- which, so far, has impeded successful translation into practice of embryonic stem cell research.
The Mayo study is the first known report establishing a successful, tumor-resistant approach to growing new heart tissue from an embryonic stem cell source. The study is published in the February issue of the Journal of Experimental Medicine.
Embryonic stem cells have the potential to become any cell type in the body. But directing the stem cells to regenerate targeted tissue is a process that hasn't yet been perfected. Scientists continue to closely scrutinize stem cell strategies to establish even safer and more effective treatments for disease.
"Embryonic stem cells are like a stealth fighter jet that flies virtually undetectable by radar," says the study's first author, Atta Behfar, M.D., Ph.D., a clinician-investigator fellow in the Mayo Graduate School of Medicine. "The host body doesn't recognize embryonic stem cells, which it allows to multiply freely in an unimpeded fashion."
The Mayo study is the first known report of a successful strategy for programming embryonic stem cells to suppress cancer genes, to mature into heart cells (also known as cardiomyocytes) and to successfully fix injured hearts without causing tumors to develop. The study removes a critical obstacle towards translation of regenerative technology into developing new therapies for people with heart disease.
"Embryonic stem cells have an unequaled potential for repair, yet it has been uncertain whether we can drive them to safely regenerate the tissue we would like to replace," says Andre Terzic, M.D., Ph.D., a stem cell specialist and lead investigator of the study. "Our objective was to repair heart muscle by avoiding the limitations intrinsic to embryonic stem cells, i.e., potential tumor growth."
"In this study, we have successfully programmed embryonic stem cells to safely generate new cardiac muscle tissue, leading potentially to new therapy," Dr. Terzic says.
The Study
Researchers transplanted mouse embryonic stem cells into infarcted hearts of mice. Consistent with the risk for uncontrolled growth, a significant number of recipient mouse hearts developed tumors. To avoid tumor formation, researchers secured guided differentiation of stem cells to produce cardiopoietic cells, or cardiac specified cell precursors rather than any cell type. Treatment with cardiopoietic cells proved to have no tendency to develop into cancer. Tumor-free heart repair occurred in all treated mice. Two months after cardiopoietic stem cell transplantation, scientists reported a 35 percent improved output in treated hearts.
The threat of tumor growth associated with embryonic stem cell transplants was eliminated by restricting expression of oncogenes and pluripotency genes through transgenic manipulation of tumor necrosis factor alpha (TNFa), a genome reprogramming protein. Researchers found that over-expressed TNFa promoted guided control of cardiac embryonic stem cells to drive the cardiogenesis process.
Researchers discovered approximately 15 proteins whose production was dramatically increased after TNFa stimulation. These proteins, when combined into a 'cocktail,' secured guided differentiation of embryonic stem cells, producing cardiac progenitors called cardiopoietic cells. Such guided heart precursor cells did not form tumors, even though they were transplanted at doses that would otherwise carry a high risk for tumorigenesis with embryonic stem cells.
"Our goal is to apply these findings to adult stem cells, and in our next step create the first human cardioprogenitor stem cells as a tool for therapies in the future," Dr. Terzic says.
The study was funded by the National Institutes of Health, American Heart Association, Marriott Heart Disease Research Program, Marriott Foundation, Ted Nash Long Life Foundation, Ralph Wilson Medical Research Foundation, Heart and Stroke Foundation of Canada, and Asper Foundation. Dr. Behfar is supported by the Clinician-Investigator Program at Mayo Clinic.
The Mayo study was a multidisciplinary effort with investigators from the Mayo Clinic Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Physical Medicine and Rehabilitation. Other investigators include: Carmen Terzic, M.D., Ph.D.; Randolph Faustino, Ph.D.; D. Kent Arrell, Ph.D.; Denice Hodgson, Satsuki Yamada, M.D., Ph.D., Michel Puceat, Nicolas Niederl'nder, Ph.D.; Alexey Alekseev, Ph.D.; and Leonid Zingman, M.D.
Contact: Amy Reyes
Mayo Clinic
The Mayo study is the first known report establishing a successful, tumor-resistant approach to growing new heart tissue from an embryonic stem cell source. The study is published in the February issue of the Journal of Experimental Medicine.
Embryonic stem cells have the potential to become any cell type in the body. But directing the stem cells to regenerate targeted tissue is a process that hasn't yet been perfected. Scientists continue to closely scrutinize stem cell strategies to establish even safer and more effective treatments for disease.
"Embryonic stem cells are like a stealth fighter jet that flies virtually undetectable by radar," says the study's first author, Atta Behfar, M.D., Ph.D., a clinician-investigator fellow in the Mayo Graduate School of Medicine. "The host body doesn't recognize embryonic stem cells, which it allows to multiply freely in an unimpeded fashion."
The Mayo study is the first known report of a successful strategy for programming embryonic stem cells to suppress cancer genes, to mature into heart cells (also known as cardiomyocytes) and to successfully fix injured hearts without causing tumors to develop. The study removes a critical obstacle towards translation of regenerative technology into developing new therapies for people with heart disease.
"Embryonic stem cells have an unequaled potential for repair, yet it has been uncertain whether we can drive them to safely regenerate the tissue we would like to replace," says Andre Terzic, M.D., Ph.D., a stem cell specialist and lead investigator of the study. "Our objective was to repair heart muscle by avoiding the limitations intrinsic to embryonic stem cells, i.e., potential tumor growth."
"In this study, we have successfully programmed embryonic stem cells to safely generate new cardiac muscle tissue, leading potentially to new therapy," Dr. Terzic says.
The Study
Researchers transplanted mouse embryonic stem cells into infarcted hearts of mice. Consistent with the risk for uncontrolled growth, a significant number of recipient mouse hearts developed tumors. To avoid tumor formation, researchers secured guided differentiation of stem cells to produce cardiopoietic cells, or cardiac specified cell precursors rather than any cell type. Treatment with cardiopoietic cells proved to have no tendency to develop into cancer. Tumor-free heart repair occurred in all treated mice. Two months after cardiopoietic stem cell transplantation, scientists reported a 35 percent improved output in treated hearts.
The threat of tumor growth associated with embryonic stem cell transplants was eliminated by restricting expression of oncogenes and pluripotency genes through transgenic manipulation of tumor necrosis factor alpha (TNFa), a genome reprogramming protein. Researchers found that over-expressed TNFa promoted guided control of cardiac embryonic stem cells to drive the cardiogenesis process.
Researchers discovered approximately 15 proteins whose production was dramatically increased after TNFa stimulation. These proteins, when combined into a 'cocktail,' secured guided differentiation of embryonic stem cells, producing cardiac progenitors called cardiopoietic cells. Such guided heart precursor cells did not form tumors, even though they were transplanted at doses that would otherwise carry a high risk for tumorigenesis with embryonic stem cells.
"Our goal is to apply these findings to adult stem cells, and in our next step create the first human cardioprogenitor stem cells as a tool for therapies in the future," Dr. Terzic says.
The study was funded by the National Institutes of Health, American Heart Association, Marriott Heart Disease Research Program, Marriott Foundation, Ted Nash Long Life Foundation, Ralph Wilson Medical Research Foundation, Heart and Stroke Foundation of Canada, and Asper Foundation. Dr. Behfar is supported by the Clinician-Investigator Program at Mayo Clinic.
The Mayo study was a multidisciplinary effort with investigators from the Mayo Clinic Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Physical Medicine and Rehabilitation. Other investigators include: Carmen Terzic, M.D., Ph.D.; Randolph Faustino, Ph.D.; D. Kent Arrell, Ph.D.; Denice Hodgson, Satsuki Yamada, M.D., Ph.D., Michel Puceat, Nicolas Niederl'nder, Ph.D.; Alexey Alekseev, Ph.D.; and Leonid Zingman, M.D.
Contact: Amy Reyes
Mayo Clinic
Scientists Identify A Molecule That Coordinates The Movement Of Cells
Even cells commute. To get from their birthplace to their work site, they sequentially attach to and detach from an elaborate track of exceptionally strong proteins known as the extracellular matrix. Now, in research to appear in the October 3 issue of Cell, scientists at the Howard Hughes Medical Institute and Rockefeller University show that a molecule, called ACF7, helps regulate and power this movement from the inside - findings that could have implications for understanding how cancer cells metastasize.
"The most dangerous part of cancer is that cancer cells migrate from their primary location and invade other parts of the body," says first author Xiaoyang Wu, a postdoc in Elaine Fuchs's Laboratory of Mammalian Cell Biology and Development. "ACF7 facilitates cell movement, so it's possible that the less ACF7 a cell has, the less malignant it would become. It's a really exciting question in cancer biology now."
To travel along the extracellular matrix, cells must stick to and unstick from it via focal adhesions, structures composed of molecules that connect the inside to the outside of the cell. (While some molecules connect to the matrix, others connect to a scaffold inside the cell called the cytoskeleton.) As these structures collectively assemble and disassemble, the cell walks forward. Fuchs and Wu show that ACF7 can not only access energy stores to power this movement from within but also coordinate it by linking two fiber-like proteins called f-actin and microtubules, which together form the cytoskeleton and help give cells their shape.
"Inside the cell, actin cables converge at focal adhesions at the cell's leading edge," Fuchs explains. "We found that ACF7 guides microtubules along a roadway of actin cables and leads them toward the focal adhesions at the cell's periphery. Among the cargo transported along microtubules are factors that disassemble focal adhesions. Hence by coupling microtubule, actin and focal adhesion dynamics within the cell, ACF7 becomes an orchestrator of directed cellular movement."
In particular, Wu and Fuchs, who is also a Howard Hughes Medical Institute investigator and Rebecca C. Lancefield Professor at Rockefeller, found that without ACF7, microtubules were no longer guided toward the focal adhesions in a directed manner. They also noticed that cellular movement slowed, suggesting that the sticky adhesive sites were no longer assembling and disassembling efficiently.
To figure out why, Fuchs and Wu studied how quickly wounds heal in mice. "During injury, stem cells proliferate and migrate to the affected site and replenish lost cells," explains Wu. "We saw that the cells without ACF7 proliferated normally, but they moved very, very slowly compared to normal skin cells. So the problem wasn't with abnormal proliferation but with cell migration." When the researchers mutated ACF7 so it couldn't release stored energy in cells, ACF7 linked f-actin and microtubules but the cells were also sluggish in their movement.
In previous work, the Fuchs team had already showed that ACF7 appeared side by side with focal adhesion molecules, but they never knew, until now, that ACF7 guides microtubules along actin cables to these sites. "Now, we have a better idea of why it's important for ACF7 to be there," says Fuchs. "In order to make the adhesive sites dynamically stick and unstick, assembly and disassembly factors need to be recruited there. The intracellular roadway governed by ACF7 makes that possible."
In the future, this information could be relevant in developing cancer therapeutics. "A major goal in the clinical arena is to halt cancer cells from migrating, a process important in metastasis," says Fuchs. By suppressing ACF7's function in cancer cells, it might be possible to slow metastasis.
This research was supported by the National Institutes of Health.
Source: Thania Benios
Rockefeller University
"The most dangerous part of cancer is that cancer cells migrate from their primary location and invade other parts of the body," says first author Xiaoyang Wu, a postdoc in Elaine Fuchs's Laboratory of Mammalian Cell Biology and Development. "ACF7 facilitates cell movement, so it's possible that the less ACF7 a cell has, the less malignant it would become. It's a really exciting question in cancer biology now."
To travel along the extracellular matrix, cells must stick to and unstick from it via focal adhesions, structures composed of molecules that connect the inside to the outside of the cell. (While some molecules connect to the matrix, others connect to a scaffold inside the cell called the cytoskeleton.) As these structures collectively assemble and disassemble, the cell walks forward. Fuchs and Wu show that ACF7 can not only access energy stores to power this movement from within but also coordinate it by linking two fiber-like proteins called f-actin and microtubules, which together form the cytoskeleton and help give cells their shape.
"Inside the cell, actin cables converge at focal adhesions at the cell's leading edge," Fuchs explains. "We found that ACF7 guides microtubules along a roadway of actin cables and leads them toward the focal adhesions at the cell's periphery. Among the cargo transported along microtubules are factors that disassemble focal adhesions. Hence by coupling microtubule, actin and focal adhesion dynamics within the cell, ACF7 becomes an orchestrator of directed cellular movement."
In particular, Wu and Fuchs, who is also a Howard Hughes Medical Institute investigator and Rebecca C. Lancefield Professor at Rockefeller, found that without ACF7, microtubules were no longer guided toward the focal adhesions in a directed manner. They also noticed that cellular movement slowed, suggesting that the sticky adhesive sites were no longer assembling and disassembling efficiently.
To figure out why, Fuchs and Wu studied how quickly wounds heal in mice. "During injury, stem cells proliferate and migrate to the affected site and replenish lost cells," explains Wu. "We saw that the cells without ACF7 proliferated normally, but they moved very, very slowly compared to normal skin cells. So the problem wasn't with abnormal proliferation but with cell migration." When the researchers mutated ACF7 so it couldn't release stored energy in cells, ACF7 linked f-actin and microtubules but the cells were also sluggish in their movement.
In previous work, the Fuchs team had already showed that ACF7 appeared side by side with focal adhesion molecules, but they never knew, until now, that ACF7 guides microtubules along actin cables to these sites. "Now, we have a better idea of why it's important for ACF7 to be there," says Fuchs. "In order to make the adhesive sites dynamically stick and unstick, assembly and disassembly factors need to be recruited there. The intracellular roadway governed by ACF7 makes that possible."
In the future, this information could be relevant in developing cancer therapeutics. "A major goal in the clinical arena is to halt cancer cells from migrating, a process important in metastasis," says Fuchs. By suppressing ACF7's function in cancer cells, it might be possible to slow metastasis.
This research was supported by the National Institutes of Health.
Source: Thania Benios
Rockefeller University
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