The most toxic free radical appears responsible for much of the lung damage that can result from oxygen therapy in the critically ill or injured, Medical College of Georgia researchers report.
Within just a few days, ventilators and oxygen chambers used to significantly increase oxygen levels can also dramatically increase levels of peroxynitrite, an oxidant powerful enough to break down DNA and cause proteins to malfunction, said Dr. Yunchao Su, pharmacologist in the MCG Schools of Medicine and Graduate Studies.
Oxygen toxicity is the most severe side effect of oxygen therapy in newborns and adults. The lungs take the brunt of the damage, which can include inflammation, hemorrhaging and swelling that may result in death or chronic lung problems, said Su, corresponding author of the study published in the Journal of Biological Chemistry.
"We knew it was bad but we did not know why," Su said. The good news is they may also have a solution.
Researchers found that within five days, mice placed in small oxygen chambers that mimic oxygen levels given in intensive care have dramatically elevated levels of peroxynitrite in their lungs. Free radicals, such as peroxynitrite, result from oxygen use and are safe at low levels. While it's a given that oxygen therapy produces free radicals, the significant increase in peroxynitrite was not known.
The trouble begins when high oxygen levels prompt endothelial cells that line blood vessels and tiny airs sacs in the lung to make more nitric oxide, the precursor of peroxynitrite. At high levels, nitric oxide, most often a helpful compound, combines with other free radicals produced by excess oxygen use to form the powerful peroxynitrite. "As oxygen levels increase, nitric oxide levels increase and so peroxynitrite levels do as well," Su said.
But he appears to have identified a break point in the destructive cycle. Su found that in the face of high oxygen levels, the enzyme that makes nitric oxide binds with the protein actin to produce more nitric oxide. So he developed a compound, peptide 326, that interferes with their binding and the excess peroxynitrite levels that typically follow. Su used the binding site itself as a cue for the peptide design after trying many existing compounds, including smoke, to break the bond.
Su's long term goal is for peptide 326, or something similar, to be used in patients likely after the first few days of oxygen therapy. Much as health care providers monitor blood oxygen long term to ensure sufficient levels, they could also monitor peroxynitrite levels. "It's only after several days of steady increases that the level becomes destructive," Su noted.
MCG scientists are already using peptide 326 in mice receiving oxygen therapy.
The research was funded by the National Institutes of Health, the American Heart Association and the Flight Attendants Medical Research Institute.
Dr. Dmitry Kondrikov, assistant research scientist at MCG, is first author of the paper; graduate student Shawn Elms and vascular biologist Dr. David Fulton are co-authors.
Source:
Medical College of Georgia
среда, 11 мая 2011 г.
вторник, 10 мая 2011 г.
Shedding Light On Evolution Of Gene Regulation
Scientists at Penn State have shed light on some of the processes that regulate genes -- such as the processes that ensure that proteins are produced at the correct time, place, and amount in an organism -- and they also have shed light on the evolution of the DNA regions that regulate genes. The team focused on regulatory regions that, when bound to the protein GATA1, are thought to turn on genes that play an important role in the development of red blood cells. "Our findings could help others to develop drugs to treat people who suffer from sickle-cell anemia and other blood disorders," said Ross Hardison, the T. Ming Chu Professor of Biochemistry and Molecular Biology, and the team's leader. The results will be published on 1 December 2008 in the journal Genome Research.
Scientists once believed that nearly all DNA regulatory regions would be maintained, or conserved, in the DNA of related species over the course of their evolution because the regions contribute to essential biological functions. Scientists also believed that when bound to specific proteins, such as GATA1, DNA regulatory regions influence the expression of genes. But now researchers at Penn State have provided new evidence that not all of the DNA segments that are bound to GATA1 have been conserved in the genomes of related animals. They also found that the GATA1-bound DNA segments that are conserved among mammals do act to control the level of expression of certain genes.
To make their discovery the team used a technique called chromatin immunoprecipitation (ChIP) to identify all the DNA segments that bind to the GATA1 protein along most of a mouse chromosome. The technique works by using an antibody that specifically binds to GATA1 and pulls it from the genome along with the DNA segments to which the protein is bound. In this way, the researchers were able to isolate 63 DNA segments that are associated with GATA1 in the mouse chromosome. They then compared the DNA sequences in these segments to those in other species. The team found that only 45 percent of the GATA1-bound DNA sequences from the mouse were present in an identical form in other mammals. "We were surprised that so few of these GATA1-occupied regions, which could be involved in gene regulation in the mouse, are not present in the identical form in most other vertebrates," said Hardison.
DNA sequences that are maintained across species over the course of their evolution are said to be conserved. A portion of these conserved sequences shows a particularly high level of similarity across species, indicating that a process is at work, called purifying selection, in which changes in the DNA are rejected. Previously, scientists assumed that purifying selection maintains most regulatory regions in the genomes of animals because they are involved in important biological functions. However, recent research has shown that many of the DNA segments bound by proteins that can influence gene expression are not under strong purifying selection.
To find out if the DNA segments bound by GATA1 are capable of regulating genes, the scientists investigated the extent to which they could trigger the expression of a gene after introducing GATA1-bound DNA segments into red blood cells. The scientists cut these GATA1-bound DNA segments out of the mouse's genome and reintroduced them into mouse red blood cells along with a gene from a firefly that is responsible for the insect's ability to produce light. The team's goal was to determine if GATA1 would bind to the regulatory regions and turn on the activity of the firefly gene.
"We wanted to know if the level of gene activity would change and if it did change, how much it would change," said Hardison. The team found that 52 percent of the GATA1-bound regions increased gene activity two-fold and 28 percent of the regions increased gene activity three-fold. "We think that some of the regions that do not appear to be functional may function only together with other regulatory regions, or they could just be parking lots, or storage areas, for proteins," Hardison said.
The researchers hope that their findings will help other researchers to develop drugs to treat people who suffer from sickle-cell anemia and other blood disorders. In particular, the new results will help researchers to identify functional DNA segments from the large number that are bound by a particular protein. The GATA1 protein plays an important role in the development of red blood cells by controlling the switch from the fetal form of hemoglobin, which is produced during the second two trimesters of pregnancy, to the adult form, which begins to be produced after birth. Most adults do not produce the fetal form of hemoglobin, and it is the improper functioning of the adult form of hemoglobin that is responsible for many blood disorders.
"If someone could find a way to get the fetal forms to stay active in adults who suffer from blood disorders, it could really help them," said Hardison. "I am optimistic that our results will provide better information to researchers who specialize in developing drugs for people with blood disorders."
This research was funded by grants from the National Institutes of Health, the Pennsylvania Department of Health, and the Huck Institutes of the Life Sciences at Penn State.
Source: Barbara K. Kennedy
Penn State
Scientists once believed that nearly all DNA regulatory regions would be maintained, or conserved, in the DNA of related species over the course of their evolution because the regions contribute to essential biological functions. Scientists also believed that when bound to specific proteins, such as GATA1, DNA regulatory regions influence the expression of genes. But now researchers at Penn State have provided new evidence that not all of the DNA segments that are bound to GATA1 have been conserved in the genomes of related animals. They also found that the GATA1-bound DNA segments that are conserved among mammals do act to control the level of expression of certain genes.
To make their discovery the team used a technique called chromatin immunoprecipitation (ChIP) to identify all the DNA segments that bind to the GATA1 protein along most of a mouse chromosome. The technique works by using an antibody that specifically binds to GATA1 and pulls it from the genome along with the DNA segments to which the protein is bound. In this way, the researchers were able to isolate 63 DNA segments that are associated with GATA1 in the mouse chromosome. They then compared the DNA sequences in these segments to those in other species. The team found that only 45 percent of the GATA1-bound DNA sequences from the mouse were present in an identical form in other mammals. "We were surprised that so few of these GATA1-occupied regions, which could be involved in gene regulation in the mouse, are not present in the identical form in most other vertebrates," said Hardison.
DNA sequences that are maintained across species over the course of their evolution are said to be conserved. A portion of these conserved sequences shows a particularly high level of similarity across species, indicating that a process is at work, called purifying selection, in which changes in the DNA are rejected. Previously, scientists assumed that purifying selection maintains most regulatory regions in the genomes of animals because they are involved in important biological functions. However, recent research has shown that many of the DNA segments bound by proteins that can influence gene expression are not under strong purifying selection.
To find out if the DNA segments bound by GATA1 are capable of regulating genes, the scientists investigated the extent to which they could trigger the expression of a gene after introducing GATA1-bound DNA segments into red blood cells. The scientists cut these GATA1-bound DNA segments out of the mouse's genome and reintroduced them into mouse red blood cells along with a gene from a firefly that is responsible for the insect's ability to produce light. The team's goal was to determine if GATA1 would bind to the regulatory regions and turn on the activity of the firefly gene.
"We wanted to know if the level of gene activity would change and if it did change, how much it would change," said Hardison. The team found that 52 percent of the GATA1-bound regions increased gene activity two-fold and 28 percent of the regions increased gene activity three-fold. "We think that some of the regions that do not appear to be functional may function only together with other regulatory regions, or they could just be parking lots, or storage areas, for proteins," Hardison said.
The researchers hope that their findings will help other researchers to develop drugs to treat people who suffer from sickle-cell anemia and other blood disorders. In particular, the new results will help researchers to identify functional DNA segments from the large number that are bound by a particular protein. The GATA1 protein plays an important role in the development of red blood cells by controlling the switch from the fetal form of hemoglobin, which is produced during the second two trimesters of pregnancy, to the adult form, which begins to be produced after birth. Most adults do not produce the fetal form of hemoglobin, and it is the improper functioning of the adult form of hemoglobin that is responsible for many blood disorders.
"If someone could find a way to get the fetal forms to stay active in adults who suffer from blood disorders, it could really help them," said Hardison. "I am optimistic that our results will provide better information to researchers who specialize in developing drugs for people with blood disorders."
This research was funded by grants from the National Institutes of Health, the Pennsylvania Department of Health, and the Huck Institutes of the Life Sciences at Penn State.
Source: Barbara K. Kennedy
Penn State
понедельник, 9 мая 2011 г.
Brain's Mechanisms Governing Exploration Are Among Those That Malfunction In Addiction And Mental Illness
Researchers have found the brain region that controls the decision to halt your midnight exploration of the refrigerator and commence enjoyment of that leftover chicken leg. What's more, they said, such mechanisms governing exploration are among those that malfunction in addiction and mental illness.
Emmanuel Procyk and colleagues published their findings in the January 24, 2008, issue of the journal Neuron, published by Cell Press.
In their experiments, the researchers presented monkeys with a choice of touch targets on a computer screen, requiring the monkeys to spend time exploring which target would trigger a juice reward. Once the monkeys discovered the reward target, the researchers then gave the animals a period during which they could repeatedly touch the reward target to obtain more juice.
During the trials, the researchers recorded the electrical activity of hundreds of neurons in the anterior cingulate cortex (ACC), a brain region known to be active in adaptive behaviors such as the shift between exploring and exploiting.
In their analysis, the researchers measured the electrophysiological activity of cells during four different types of feedback - incorrect choices, first reward, repetition of the reward, and the ending of a trial by breaking fixation on the targets.
Analyzing the results, the researchers concluded that "Our data show that ACC discriminates between different types of feedback, allowing appropriate behavioral adaptations."
They wrote that "Thus, the function we attribute to ACC activations is clearly not only to evaluate feedbacks but is also to participate in monitoring the different steps of the task at hand to optimize action adaptation and valuation. A dysfunction of these mechanisms represents the core feature of cognitive alterations observed in addiction and mental illness."
Wrote Procyk and colleagues, "The ACC produces signals that discriminate between various behaviorally relevant positive and negative feedbacks, suggesting a role in triggering appropriate adaptations. Our data reinforce the proposal that ACC is important for establishing action valuations. But they also emphasize a combined role in monitoring events/actions for behavioral regulation when task control is high, underlining the intimate link between control and action valuation."
The researchers include ReneВґ Quilodran, Marie Rothe, and Emmanuel Procyk, of both the Inserm, U846, Stem Cell and Brain Research Institute, Bron, France, and UniversiteВґ de Lyon, Lyon, France.
Source: Cathleen Genova
Cell Press
Emmanuel Procyk and colleagues published their findings in the January 24, 2008, issue of the journal Neuron, published by Cell Press.
In their experiments, the researchers presented monkeys with a choice of touch targets on a computer screen, requiring the monkeys to spend time exploring which target would trigger a juice reward. Once the monkeys discovered the reward target, the researchers then gave the animals a period during which they could repeatedly touch the reward target to obtain more juice.
During the trials, the researchers recorded the electrical activity of hundreds of neurons in the anterior cingulate cortex (ACC), a brain region known to be active in adaptive behaviors such as the shift between exploring and exploiting.
In their analysis, the researchers measured the electrophysiological activity of cells during four different types of feedback - incorrect choices, first reward, repetition of the reward, and the ending of a trial by breaking fixation on the targets.
Analyzing the results, the researchers concluded that "Our data show that ACC discriminates between different types of feedback, allowing appropriate behavioral adaptations."
They wrote that "Thus, the function we attribute to ACC activations is clearly not only to evaluate feedbacks but is also to participate in monitoring the different steps of the task at hand to optimize action adaptation and valuation. A dysfunction of these mechanisms represents the core feature of cognitive alterations observed in addiction and mental illness."
Wrote Procyk and colleagues, "The ACC produces signals that discriminate between various behaviorally relevant positive and negative feedbacks, suggesting a role in triggering appropriate adaptations. Our data reinforce the proposal that ACC is important for establishing action valuations. But they also emphasize a combined role in monitoring events/actions for behavioral regulation when task control is high, underlining the intimate link between control and action valuation."
The researchers include ReneВґ Quilodran, Marie Rothe, and Emmanuel Procyk, of both the Inserm, U846, Stem Cell and Brain Research Institute, Bron, France, and UniversiteВґ de Lyon, Lyon, France.
Source: Cathleen Genova
Cell Press
воскресенье, 8 мая 2011 г.
Predicting The Fate Of A Living Fossil: How Will Global Warming Affect Sex Determination And Hatching Phenology In Tuatara?
Climate warming will affect animals in many ways, including the sex of some species' offspring. For tuatara, unique and ancient reptiles from New Zealand, warmer nest temperatures produce male-biased clutches.
We predicted sex ratios and hatching times of tuatara clutches under future climate scenarios by linking egg development data with sophisticated models of soil microclimates.
Under extreme climate change only males would hatch from nests of the rarest tuatara species by the mid 2080s.
Our novel approach will help in assessing future translocation sites for tuatara, and for predicting climatic impacts on other species where sex is determined by temperature.
Proceedings of the Royal Society B: Biological Sciences
Proceedings B is the Royal Society's flagship biological research journal, dedicated to the rapid publication and broad dissemination of high-quality research papers, reviews and comment and reply papers. The scope of journal is diverse and is especially strong in organismal biology.
publishing.royalsociety/proceedingsb
We predicted sex ratios and hatching times of tuatara clutches under future climate scenarios by linking egg development data with sophisticated models of soil microclimates.
Under extreme climate change only males would hatch from nests of the rarest tuatara species by the mid 2080s.
Our novel approach will help in assessing future translocation sites for tuatara, and for predicting climatic impacts on other species where sex is determined by temperature.
Proceedings of the Royal Society B: Biological Sciences
Proceedings B is the Royal Society's flagship biological research journal, dedicated to the rapid publication and broad dissemination of high-quality research papers, reviews and comment and reply papers. The scope of journal is diverse and is especially strong in organismal biology.
publishing.royalsociety/proceedingsb
суббота, 7 мая 2011 г.
New Forecasting Tool Could Reduce Drug Development Costs
It now costs more than $800 million to develop a new drug. But what if pharmaceutical companies had a way to predict which experimental drugs will ultimately get FDA approval, giving them the confidence to invest money in them, and which drugs will ultimately fail, allowing them to cut their losses early?
In the February issue of Nature Reviews Drug Discovery, researchers from the Children's Hospital Boston Informatics Program (CHIP) present a forecasting model that may increase the efficiency of drug R&D and save hundreds of millions of dollars per new drug. They also argue that more data sharing by the drug industry - particularly of "negative" data - would greatly improve the accuracy of forecasting and benefit industry and patients alike, allowing more medical discoveries to be brought to the bedside.
Asher Schachter, MD, MMSc, MS, and Marco Ramoni, PhD, both of CHIP, constructed a Bayesian network model to calculate the probability that a given new drug would pass successfully through Phase III trials and receive New Drug Application (NDA) approval. Their approach differs from convention in modeling populations of drugs rather than populations of patients. They used publicly available safety and efficacy data for about 500 successful and failed new drugs, broken down by therapeutic category, then confirmed the validity of their model by testing it with a group of cancer drugs whose fates are already known.
To gauge the model's potential economic impact, Schachter and Ramoni then performed a pharmaco-economic analysis in collaboration with Stan Finkelstein, MD, Senior Research Scientist at the MIT Sloan School of Management. This analysis, using summary data on industry-reported expenditures and revenues, indicated that application of the model would reduce mean capitalized expenditures by an average of $283 million per successful new drug (from $727 to $444), and increase revenues by an average of $160 million per Phase III trial (from $347 to $507 million) during the drug's first seven years on the market.
Schachter, also a pediatric nephrologist at Children's Hospital Boston, believes that more data sharing by the pharmaceutical industry would enable the industry to learn more from its own failures. "There's a tendency in the industry to bury data on failed drugs and forget about them," Schachter says. "We hope our model will add fuel to efforts to show that data-sharing could be beneficial to everybody."
Such efforts include legislation introduced in the Senate last year (S3807) that would establish a clinical trial registry database that would report the results of later-stage clinical trials, both good and bad.
In their report in Nature Reviews Drug Discovery, Schachter and Ramoni also argue that more accurate clinical forecasting would eliminate unsafe investigational new drugs; avoid subjecting patients to unnecessary drug trials; reduce the cost of prescription drugs for consumers; and empower the industry to take risks on truly innovative new drugs, so that more get to market.
The need for pharmaceutical industry involvement in early trials is especially acute for pediatric drugs, Schachter adds. Companies are reluctant to conduct clinical trials in children, fearing a negative impact on marketability. Instead, doctors often resort to giving adult drugs to children off-label, outside the context of a controlled, safety-monitored study.
For more information on the model and related issues, visit: phorecaster/.
The Children's Hospital Informatics Program (CHIP) is a multidisciplinary applied research program at Children's Hospital Boston and the Harvard-MIT Division of Health, Sciences and Technology. CHIP focuses in three areas: bioinformatics, public health informatics (including biosurveillance), and clinical informatics. Its diverse faculty includes physicians trained in information science, computer scientists with expertise in the biomedical sciences, mathematicians, and epidemiologists. CHIP provides shared resources to develop innovative information technologies with the goal of both enhancing biomedical research and improving patient care. CHIP also serves as the bioinformatics core for several national genomics investigations. For more information, visit: chip/.
Founded in 1869 as a 20-bed hospital for children, Children's Hospital Boston today is the nation's leading pediatric medical center, the largest provider of health care to Massachusetts children, and the primary pediatric teaching hospital of Harvard Medical School. In addition to 347 pediatric and adolescent inpatient beds and comprehensive outpatient programs, Children's houses the world's largest research enterprise based at a pediatric medical center, where its discoveries benefit both children and adults. More than 500 scientists, including eight members of the National Academy of Sciences, 11 members of the Institute of Medicine and 10 members of the Howard Hughes Medical Institute comprise Children's research community. For more information about the hospital visit: childrenshospital/newsroom.
Contact: Anna Gonski
Children's Hospital Boston
In the February issue of Nature Reviews Drug Discovery, researchers from the Children's Hospital Boston Informatics Program (CHIP) present a forecasting model that may increase the efficiency of drug R&D and save hundreds of millions of dollars per new drug. They also argue that more data sharing by the drug industry - particularly of "negative" data - would greatly improve the accuracy of forecasting and benefit industry and patients alike, allowing more medical discoveries to be brought to the bedside.
Asher Schachter, MD, MMSc, MS, and Marco Ramoni, PhD, both of CHIP, constructed a Bayesian network model to calculate the probability that a given new drug would pass successfully through Phase III trials and receive New Drug Application (NDA) approval. Their approach differs from convention in modeling populations of drugs rather than populations of patients. They used publicly available safety and efficacy data for about 500 successful and failed new drugs, broken down by therapeutic category, then confirmed the validity of their model by testing it with a group of cancer drugs whose fates are already known.
To gauge the model's potential economic impact, Schachter and Ramoni then performed a pharmaco-economic analysis in collaboration with Stan Finkelstein, MD, Senior Research Scientist at the MIT Sloan School of Management. This analysis, using summary data on industry-reported expenditures and revenues, indicated that application of the model would reduce mean capitalized expenditures by an average of $283 million per successful new drug (from $727 to $444), and increase revenues by an average of $160 million per Phase III trial (from $347 to $507 million) during the drug's first seven years on the market.
Schachter, also a pediatric nephrologist at Children's Hospital Boston, believes that more data sharing by the pharmaceutical industry would enable the industry to learn more from its own failures. "There's a tendency in the industry to bury data on failed drugs and forget about them," Schachter says. "We hope our model will add fuel to efforts to show that data-sharing could be beneficial to everybody."
Such efforts include legislation introduced in the Senate last year (S3807) that would establish a clinical trial registry database that would report the results of later-stage clinical trials, both good and bad.
In their report in Nature Reviews Drug Discovery, Schachter and Ramoni also argue that more accurate clinical forecasting would eliminate unsafe investigational new drugs; avoid subjecting patients to unnecessary drug trials; reduce the cost of prescription drugs for consumers; and empower the industry to take risks on truly innovative new drugs, so that more get to market.
The need for pharmaceutical industry involvement in early trials is especially acute for pediatric drugs, Schachter adds. Companies are reluctant to conduct clinical trials in children, fearing a negative impact on marketability. Instead, doctors often resort to giving adult drugs to children off-label, outside the context of a controlled, safety-monitored study.
For more information on the model and related issues, visit: phorecaster/.
The Children's Hospital Informatics Program (CHIP) is a multidisciplinary applied research program at Children's Hospital Boston and the Harvard-MIT Division of Health, Sciences and Technology. CHIP focuses in three areas: bioinformatics, public health informatics (including biosurveillance), and clinical informatics. Its diverse faculty includes physicians trained in information science, computer scientists with expertise in the biomedical sciences, mathematicians, and epidemiologists. CHIP provides shared resources to develop innovative information technologies with the goal of both enhancing biomedical research and improving patient care. CHIP also serves as the bioinformatics core for several national genomics investigations. For more information, visit: chip/.
Founded in 1869 as a 20-bed hospital for children, Children's Hospital Boston today is the nation's leading pediatric medical center, the largest provider of health care to Massachusetts children, and the primary pediatric teaching hospital of Harvard Medical School. In addition to 347 pediatric and adolescent inpatient beds and comprehensive outpatient programs, Children's houses the world's largest research enterprise based at a pediatric medical center, where its discoveries benefit both children and adults. More than 500 scientists, including eight members of the National Academy of Sciences, 11 members of the Institute of Medicine and 10 members of the Howard Hughes Medical Institute comprise Children's research community. For more information about the hospital visit: childrenshospital/newsroom.
Contact: Anna Gonski
Children's Hospital Boston
пятница, 6 мая 2011 г.
Caltech Scientists Show Why Anti-HIV Antibodies Are Ineffective At Blocking Infection
-Some 25 years after the AIDS epidemic spawned a worldwide search for an effective vaccine against the human immunodeficiency virus (HIV), progress in the field seems to have effectively become stalled. The reason? According to new findings from a team of researchers from the California Institute of Technology (Caltech), it's at least partly due to the fact that our body's natural HIV antibodies simply don't have a long enough reach to effectively neutralize the viruses they are meant to target.
Their findings were published last week in the online early edition of the Proceedings of the National Academy of Sciences (PNAS).
"This study helps to clarify the obstacles that antibodies face in blocking infection," says Pamela Bjorkman, the Max DelbrГјck Professor of Biology at Caltech and a Howard Hughes Medical Institute Investigator, "and will hopefully shed more light on why developing an effective vaccine for HIV has proven so elusive."
Y-shaped antibodies are best at neutralizing viruses--i.e., blocking their entry into cells and preventing infection--when both arms of the Y are able to reach out and bind to their target proteins at more or less the same time. In the case of HIV, antibodies that can block infection target the proteins that stud the surface of the virus, which stick out like spikes from the viral membrane. But an antibody can only bind to two spikes at the same time if those spikes fall within its span--the distance the antibody's structure allows it to stretch its two arms.
"When both arms of an antibody are able to bind to a virus at the same time," says Joshua Klein, a Caltech graduate student in biochemistry and molecular biophysics and the PNAS paper's first author, "there can be a hundred- to thousandfold increase in the strength of the interaction, which can sometimes translate into an equally dramatic increase in its ability to neutralize a virus. Having antibodies with two arms is nature's way of ensuring a strong binding interaction."
As it turns out, this sort of double-armed binding is easier said than done--at least in the case of HIV.
In their PNAS paper, Bjorkman and Klein looked at the neutralization capabilities of two different monoclonal antibodies isolated from HIV-infected individuals. One, called b12, binds a protein known as gp120, which forms the upper portion of an HIV's protein spike. The other, 4E10, binds to gp41, which is found on a lower portion of the spike known as the stalk.
The researchers broke each of the antibodies down into their component parts and compared their abilities to bind and neutralize the virus. They found, as expected, that one-armed versions of the b12 antibody were less effective at neutralizing HIV than two-armed versions. When they looked at the 4E10 antibody, by comparison, they found that having two arms conferred almost no advantage over having only one arm. In addition, they found that larger versions of 4E10 were less effective than smaller ones. These results highlight potential obstacles that vaccines designed to elicit antibodies similar to 4E10 might face.
But b12 has its own obstacles to overcome as well. In fact, when the researchers looked more closely at their data, they realized that the benefits of having two arms--even for b12--were much smaller than those seen for antibodies against viruses like influenza. In other words, the body's natural anti-HIV antibodies are much less effective at neutralizing HIV than they should be.
But why?
"The story really starts to get interesting when we think about what the human immunodeficiency virus actually looks like," says Klein. Whereas a single influenza virus's surface is studded with approximately 450 spikes, he explains, the similarly sized HIV may have fewer than 15 spikes.
With spikes so few and far between, finding two that both fall within the reach of a b12 or 4E10 antibody--the spans of which generally measure between 12 and 15 nanometers--becomes much more of a challenge.
"HIV may have evolved a way to escape one of the main strategies our immune system uses to defeat infections," says Klein. "Based on these data, it seems that the virus is circumventing the bivalent effect that is so key to the potency of antibodies."
"I consider this a very important paper because it changes the focus of the discussion about why anti-HIV antibodies are so poor," adds virologist David Baltimore, the Robert Andrews Millikan Professor of Biology and a Nobel Prize winner. "It brings attention to a long-recognized but often forgotten aspect of antibody attack--that they attack with two heads. What this paper shows is that anti-HIV antibodies are restricted to using one head at a time and that makes them bind much less well. Responding to this newly recognized challenge will be difficult because it identifies an intrinsic limitation on the effectiveness of almost any natural anti-HIV antibodies."
In addition to Bjorkman and Klein, the authors on the PNAS paper, "Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10," are Caltech research technicians Priyanthi Gnanapragasam, Rachel Galimidi, and Christopher Foglesong, and senior research specialist Anthony West, Jr.
The work described in the paper was supported by a Bill and Melinda Gates Foundation Grant through the Grand Challenges in Global Health Initiative and the Collaboration for AIDS Vaccine Discovery.
Source:
Lori Oliwenstein
California Institute of Technology
Their findings were published last week in the online early edition of the Proceedings of the National Academy of Sciences (PNAS).
"This study helps to clarify the obstacles that antibodies face in blocking infection," says Pamela Bjorkman, the Max DelbrГјck Professor of Biology at Caltech and a Howard Hughes Medical Institute Investigator, "and will hopefully shed more light on why developing an effective vaccine for HIV has proven so elusive."
Y-shaped antibodies are best at neutralizing viruses--i.e., blocking their entry into cells and preventing infection--when both arms of the Y are able to reach out and bind to their target proteins at more or less the same time. In the case of HIV, antibodies that can block infection target the proteins that stud the surface of the virus, which stick out like spikes from the viral membrane. But an antibody can only bind to two spikes at the same time if those spikes fall within its span--the distance the antibody's structure allows it to stretch its two arms.
"When both arms of an antibody are able to bind to a virus at the same time," says Joshua Klein, a Caltech graduate student in biochemistry and molecular biophysics and the PNAS paper's first author, "there can be a hundred- to thousandfold increase in the strength of the interaction, which can sometimes translate into an equally dramatic increase in its ability to neutralize a virus. Having antibodies with two arms is nature's way of ensuring a strong binding interaction."
As it turns out, this sort of double-armed binding is easier said than done--at least in the case of HIV.
In their PNAS paper, Bjorkman and Klein looked at the neutralization capabilities of two different monoclonal antibodies isolated from HIV-infected individuals. One, called b12, binds a protein known as gp120, which forms the upper portion of an HIV's protein spike. The other, 4E10, binds to gp41, which is found on a lower portion of the spike known as the stalk.
The researchers broke each of the antibodies down into their component parts and compared their abilities to bind and neutralize the virus. They found, as expected, that one-armed versions of the b12 antibody were less effective at neutralizing HIV than two-armed versions. When they looked at the 4E10 antibody, by comparison, they found that having two arms conferred almost no advantage over having only one arm. In addition, they found that larger versions of 4E10 were less effective than smaller ones. These results highlight potential obstacles that vaccines designed to elicit antibodies similar to 4E10 might face.
But b12 has its own obstacles to overcome as well. In fact, when the researchers looked more closely at their data, they realized that the benefits of having two arms--even for b12--were much smaller than those seen for antibodies against viruses like influenza. In other words, the body's natural anti-HIV antibodies are much less effective at neutralizing HIV than they should be.
But why?
"The story really starts to get interesting when we think about what the human immunodeficiency virus actually looks like," says Klein. Whereas a single influenza virus's surface is studded with approximately 450 spikes, he explains, the similarly sized HIV may have fewer than 15 spikes.
With spikes so few and far between, finding two that both fall within the reach of a b12 or 4E10 antibody--the spans of which generally measure between 12 and 15 nanometers--becomes much more of a challenge.
"HIV may have evolved a way to escape one of the main strategies our immune system uses to defeat infections," says Klein. "Based on these data, it seems that the virus is circumventing the bivalent effect that is so key to the potency of antibodies."
"I consider this a very important paper because it changes the focus of the discussion about why anti-HIV antibodies are so poor," adds virologist David Baltimore, the Robert Andrews Millikan Professor of Biology and a Nobel Prize winner. "It brings attention to a long-recognized but often forgotten aspect of antibody attack--that they attack with two heads. What this paper shows is that anti-HIV antibodies are restricted to using one head at a time and that makes them bind much less well. Responding to this newly recognized challenge will be difficult because it identifies an intrinsic limitation on the effectiveness of almost any natural anti-HIV antibodies."
In addition to Bjorkman and Klein, the authors on the PNAS paper, "Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10," are Caltech research technicians Priyanthi Gnanapragasam, Rachel Galimidi, and Christopher Foglesong, and senior research specialist Anthony West, Jr.
The work described in the paper was supported by a Bill and Melinda Gates Foundation Grant through the Grand Challenges in Global Health Initiative and the Collaboration for AIDS Vaccine Discovery.
Source:
Lori Oliwenstein
California Institute of Technology
четверг, 5 мая 2011 г.
New Anti-Inflammatory Compound Discovered
Scientists have discovered that a lipid known to protect the heart from inflammation and to cause skin allergic reactions also reduces inflammation of the kidneys. The discovery could help devise new ways of treating inflammatory kidney diseases.
The lipid, called sphingosylphosphorylcholine (SPC), has been shown to cause an increase in urine production in the kidneys and an abnormal accumulation of salt in the urine. But how SPC works in the kidneys is not completely understood.
Andrea Huwiler and colleagues examined the various proteins activated by SPC in kidney cells and showed for the first time that SPC triggers proteins known to reduce inflammation. Although more details will be needed to understand how these proteins and how SPC may interact with other anti-inflammatory proteins - such as transforming growth factor beta - SPC may be useful in the treatment of chronic inflammatory and fibrotic diseases of the kidneys, the scientists concluded.
Article: "Sphingosylphosphorylcholine acts in an anti-inflammatory manner in renal mesangial cells by reducing interleukin-1b-induced prostaglandin E2 formation," by Cuiyan Xin, Shuyu Ren, Wolfgang Eberhardt, Josef Pfeilschifter, and Andrea Huwiler.
The American Society for Biochemistry and Molecular Biology is a nonprofit scientific and educational organization with over 11,900 members in the United States and internationally. Most members teach and conduct research at colleges and universities. Others conduct research in various government laboratories, nonprofit research institutions and industry. The Society's student members attend undergraduate or graduate institutions.
Founded in 1906, the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology. The Society's purpose is to advance the science of biochemistry and molecular biology through publication of the Journal of Biological Chemistry, the Journal of Lipid Research, and Molecular and Cellular Proteomics, organization of scientific meetings, advocacy for funding of basic research and education, support of science education at all levels, and promoting the diversity of individuals entering the scientific work force.
For more information about ASBMB, see the Society's Web site at asbmb.
The lipid, called sphingosylphosphorylcholine (SPC), has been shown to cause an increase in urine production in the kidneys and an abnormal accumulation of salt in the urine. But how SPC works in the kidneys is not completely understood.
Andrea Huwiler and colleagues examined the various proteins activated by SPC in kidney cells and showed for the first time that SPC triggers proteins known to reduce inflammation. Although more details will be needed to understand how these proteins and how SPC may interact with other anti-inflammatory proteins - such as transforming growth factor beta - SPC may be useful in the treatment of chronic inflammatory and fibrotic diseases of the kidneys, the scientists concluded.
Article: "Sphingosylphosphorylcholine acts in an anti-inflammatory manner in renal mesangial cells by reducing interleukin-1b-induced prostaglandin E2 formation," by Cuiyan Xin, Shuyu Ren, Wolfgang Eberhardt, Josef Pfeilschifter, and Andrea Huwiler.
The American Society for Biochemistry and Molecular Biology is a nonprofit scientific and educational organization with over 11,900 members in the United States and internationally. Most members teach and conduct research at colleges and universities. Others conduct research in various government laboratories, nonprofit research institutions and industry. The Society's student members attend undergraduate or graduate institutions.
Founded in 1906, the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology. The Society's purpose is to advance the science of biochemistry and molecular biology through publication of the Journal of Biological Chemistry, the Journal of Lipid Research, and Molecular and Cellular Proteomics, organization of scientific meetings, advocacy for funding of basic research and education, support of science education at all levels, and promoting the diversity of individuals entering the scientific work force.
For more information about ASBMB, see the Society's Web site at asbmb.
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