Site of the day: http://milw0rm.com/
ScienceDaily (Feb. 3, 2010) — Medical researchers were shocked to discover that virtually all human embryonic stem cell lines being used in 2005 were contaminated. Animal byproducts used to line Petri dishes had left traces on the human cells. If those cells had been implanted in a human body they likely would have been rejected by the patient's immune system.
Even today, with new stem cell lines approved for use in medical research, there remains a risk that these cells will be contaminated in the same way. Most research labs still use animal-based "feeder layers" because it remains the cheapest and most reliable way to get stem cells to multiply.
Materials scientists at the University of Washington have now created an alternative. They built a three-dimensional scaffold out of a natural material that mimics the binding sites for stem cells, allowing the cells to reproduce on a clean, biodegradable structure. Results published in the journal Biomaterials show that human embryonic stem cells grow and multiply readily on the structure.
"The major challenge for stem cell therapy today is it's very difficult to make a lot of them with high purity," said lead author Miqin Zhang, a UW professor of materials science and engineering. "So far it seems like this material is very good for stem cell renewal."
Medical researchers hope to someday use stem cells to grow new tissues and organs. Key to the research is the fact that new cells maintain the property that holds medical promise -- the ability to differentiate into any of the more than 220 cell types in the adult human body.
Growing the cells in three dimensions better resembles conditions in the human body. It also allows mass production, which will be needed for any clinical applications.
"Three-dimensional scaffolds are an active area of research," said Carol Ware, a UW professor of comparative medicine and expert on stem cells. "They are not commonly used yet, but will be important to transition embryonic stem cells to the clinic. To date, nobody has found a perfect matrix."
Zhang's cylindrical scaffold is made of chitosan, found in the shells of crustaceans, and alginate, a gelatinous substance found in algae. Chitosan and alginate have a structure similar to the matrix that surrounds cells in the body, to which cells can attach. Different processing techniques can make the scaffold out of interconnected pores of almost any size, Zhang said.
Researchers first seeded the scaffold with 500,000 embryonic stem cells, and after 21 days the scaffold was completely saturated. The cells infiltrated the structure, Zhang added, unlike other materials where cells often grow only on the surface.
"This scaffold mimics the extracellular matrix at the atomic level, and so the cells are able to grow in this environment," Zhang said.
To retrieve the cells, researchers immersed the scaffold in a mild solution. The structure is biodegradable and so dissolved to release the stem cells. One also could implant the stem cell-covered scaffold directly into the body.
Analysis of gene activity and testing in the lab and in mice showed that the new stem cells retained the same properties as their predecessors.
Other researcher groups are also looking for alternatives to feeder layers. The leading contenders are scaffolds coated with custom proteins designed to mimic the key properties of the animal cells in the feeder layer. Such products are expensive and difficult to produce in a consistent manner, Zhang said. The proteins also get used up in a few days and have to be replaced, making them costly and time-consuming for everyday use.
"Our scaffold is made of natural materials that are already FDA-approved for food and biomedical applications. Also, these materials are unlimited, and the cost is cheap," she said.
Zhang's group is now working to build a scaffold larger than the current dime-sized prototype, and is collaborating with the UW's Institute for Stem Cells and Regenerative Medicine and UW School of Medicine to try growing different types of stem cells, including those from umbilical cord blood and bone marrow, in the material. They will try to get the resulting cells to differentiate into bone, neuron, muscle and liver cells.
Co-authors are Zhensheng Li and Matthew Leung, UW doctoral students in materials science and engineering; Dr. Richard Hopper, an associate professor at the UW School of Medicine; and Dr. Richard Ellenbogen, professor and chair of neurological surgery at the UW School of Medicine.
(http://www.sciencedaily.com/releases/2010/02/100202174743.htm)
Monday, February 8, 2010
Microbes Produce Fuels Directly from Biomass
Site of the day: http://milw0rm.com/
ScienceDaily (Jan. 31, 2010) — A collaboration led by researchers with the U.S. Department of Energy's Joint BioEnergy Institute (JBEI) has developed a microbe that can produce an advanced biofuel directly from biomass. Deploying the tools of synthetic biology, the JBEI researchers engineered a strain of Escherichia coli (E. coli) bacteria to produce biodiesel fuel and other important chemicals derived from fatty acids.
"The fact that our microbes can produce a diesel fuel directly from biomass with no additional chemical modifications is exciting and important," says Jay Keasling, the Chief Executive Officer for JBEI, and a leading scientific authority on synthetic biology. "Given that the costs of recovering biodiesel are nowhere near the costs required to distill ethanol, we believe our results can significantly contribute to the ultimate goal of producing scalable and cost effective advanced biofuels and renewable chemicals."
Keasling led the collaboration, which was was made up of a team from JBEI's Fuels Synthesis Division that included Eric Steen, Yisheng Kang and Gregory Bokinsky, and a team from LS9, a privately-held industrial biotechnology firm based in South San Francisco. The LS9 team was headed by Stephen del Cardayre and included Zhihao Hu, Andreas Schirmer and Amy McClure. The collaboration has published the results of their research in the January 28, 2010 edition of the journal Nature. The paper is titled, "Microbial Production of Fatty Acid-Derived Fuels and Chemicals from Plant Biomass."
A combination of ever-increasing energy costs and global warming concerns has created an international imperative for new transportation fuels that are renewable and can be produced in a sustainable fashion. Scientific studies have consistently shown that liquid fuels derived from plant biomass are one of the best alternatives if a cost-effective means of commercial production can be found. Major research efforts to this end are focused on fatty acids -- the energy-rich molecules in living cells that have been dubbed nature's petroleum.
Fuels and chemicals have been produced from the fatty acids in plant and animal oils for more than a century. These oils now serve as the raw materials not only for biodiesel fuel, but also for a wide range of important chemical products including surfactants, solvents and lubricants.
"The increased demand and limited supply of these oils has resulted in competition with food, higher prices, questionable land-use practices and environmental concerns associated with their production," Keasling says. "A more scalable, controllable, and economic alternative route to these fuels and chemicals would be through the microbial conversion of renewable feedstocks, such as biomass-derived carbohydrates."
E. coli isa well-studied microorganism whose natural ability to synthesize fatty acids and exceptional amenability to genetic manipulation make it an ideal target for biofuels research. The combination of E. coli with new biochemical reactions realized through synthetic biology, enabled Keasling, Steen and their colleagues to produce structurally tailored fatty esters (biodiesel), alcohols and waxes directly from simple sugars.
"Biosynthesis of microbial fatty acids produces fatty acids bound to a carrier protein, the accumulation of which inhibits the making of additional fatty acids," Steen says. "Normally E. coli doesn't waste energy making excess fat, but by cleaving fatty acids from their carrier proteins, we're able to unlock the natural regulation and make an abundance of fatty acids that can be converted into a number of valuable products. Further, we engineered our E. coli to no longer eat fatty acids or use them for energy."
After successfully diverting fatty acid metabolism toward the production of fuels and other chemicals from glucose, the JBEI researchers engineered their new strain of E. coli to produce hemicellulases -- enzymes that are able to ferment hemicellulose, the complex sugars that are a major constituent of cellulosic biomass and a prime repository for the energy locked within plant cell walls.
"Engineering E. coli to produce hemicellulases enables the microbes to produce fuels directly from the biomass of plants that are not used as food for humans or feed for animals," Steen says. "Currently, biochemical processing of cellulosic biomass requires costly enzymes for sugar liberation. By giving the E. coli the capacity to ferment both cellulose and hemicellulose without the addition of expensive enzymes, we can improve the economics of cellulosic biofuels."
The JBEI team is now working on maximizing the efficiency and the speed by which their engineered strain of E. coli can directly convert biomass into biodiesel. They are also looking into ways of maximizing the total amount of biodiesel that can be produced from a single fermentation.
"Productivity, titer and efficient conversion of feedstock into fuelare the three most important factors for engineering microbes that can produce biofuels on an industrial scale," Steen says. "There is still much more research to do before this process becomes commercially feasible."
This research was supported by funds from LS9, Inc., and the UC Discovery Grant program. LS9 is using synthetic biology techniques to develop patent-pending UltraClean™ fuels and sustainable chemicals. The UC Discovery Grant program is a three-way partnership between the University of California, private industry and the state of California that is aimed at strengthening and expanding California's economy through targeted fields of research.
(http://www.sciencedaily.com/releases/2010/01/100127144545.htm)
ScienceDaily (Jan. 31, 2010) — A collaboration led by researchers with the U.S. Department of Energy's Joint BioEnergy Institute (JBEI) has developed a microbe that can produce an advanced biofuel directly from biomass. Deploying the tools of synthetic biology, the JBEI researchers engineered a strain of Escherichia coli (E. coli) bacteria to produce biodiesel fuel and other important chemicals derived from fatty acids.
"The fact that our microbes can produce a diesel fuel directly from biomass with no additional chemical modifications is exciting and important," says Jay Keasling, the Chief Executive Officer for JBEI, and a leading scientific authority on synthetic biology. "Given that the costs of recovering biodiesel are nowhere near the costs required to distill ethanol, we believe our results can significantly contribute to the ultimate goal of producing scalable and cost effective advanced biofuels and renewable chemicals."
Keasling led the collaboration, which was was made up of a team from JBEI's Fuels Synthesis Division that included Eric Steen, Yisheng Kang and Gregory Bokinsky, and a team from LS9, a privately-held industrial biotechnology firm based in South San Francisco. The LS9 team was headed by Stephen del Cardayre and included Zhihao Hu, Andreas Schirmer and Amy McClure. The collaboration has published the results of their research in the January 28, 2010 edition of the journal Nature. The paper is titled, "Microbial Production of Fatty Acid-Derived Fuels and Chemicals from Plant Biomass."
A combination of ever-increasing energy costs and global warming concerns has created an international imperative for new transportation fuels that are renewable and can be produced in a sustainable fashion. Scientific studies have consistently shown that liquid fuels derived from plant biomass are one of the best alternatives if a cost-effective means of commercial production can be found. Major research efforts to this end are focused on fatty acids -- the energy-rich molecules in living cells that have been dubbed nature's petroleum.
Fuels and chemicals have been produced from the fatty acids in plant and animal oils for more than a century. These oils now serve as the raw materials not only for biodiesel fuel, but also for a wide range of important chemical products including surfactants, solvents and lubricants.
"The increased demand and limited supply of these oils has resulted in competition with food, higher prices, questionable land-use practices and environmental concerns associated with their production," Keasling says. "A more scalable, controllable, and economic alternative route to these fuels and chemicals would be through the microbial conversion of renewable feedstocks, such as biomass-derived carbohydrates."
E. coli isa well-studied microorganism whose natural ability to synthesize fatty acids and exceptional amenability to genetic manipulation make it an ideal target for biofuels research. The combination of E. coli with new biochemical reactions realized through synthetic biology, enabled Keasling, Steen and their colleagues to produce structurally tailored fatty esters (biodiesel), alcohols and waxes directly from simple sugars.
"Biosynthesis of microbial fatty acids produces fatty acids bound to a carrier protein, the accumulation of which inhibits the making of additional fatty acids," Steen says. "Normally E. coli doesn't waste energy making excess fat, but by cleaving fatty acids from their carrier proteins, we're able to unlock the natural regulation and make an abundance of fatty acids that can be converted into a number of valuable products. Further, we engineered our E. coli to no longer eat fatty acids or use them for energy."
After successfully diverting fatty acid metabolism toward the production of fuels and other chemicals from glucose, the JBEI researchers engineered their new strain of E. coli to produce hemicellulases -- enzymes that are able to ferment hemicellulose, the complex sugars that are a major constituent of cellulosic biomass and a prime repository for the energy locked within plant cell walls.
"Engineering E. coli to produce hemicellulases enables the microbes to produce fuels directly from the biomass of plants that are not used as food for humans or feed for animals," Steen says. "Currently, biochemical processing of cellulosic biomass requires costly enzymes for sugar liberation. By giving the E. coli the capacity to ferment both cellulose and hemicellulose without the addition of expensive enzymes, we can improve the economics of cellulosic biofuels."
The JBEI team is now working on maximizing the efficiency and the speed by which their engineered strain of E. coli can directly convert biomass into biodiesel. They are also looking into ways of maximizing the total amount of biodiesel that can be produced from a single fermentation.
"Productivity, titer and efficient conversion of feedstock into fuelare the three most important factors for engineering microbes that can produce biofuels on an industrial scale," Steen says. "There is still much more research to do before this process becomes commercially feasible."
This research was supported by funds from LS9, Inc., and the UC Discovery Grant program. LS9 is using synthetic biology techniques to develop patent-pending UltraClean™ fuels and sustainable chemicals. The UC Discovery Grant program is a three-way partnership between the University of California, private industry and the state of California that is aimed at strengthening and expanding California's economy through targeted fields of research.
(http://www.sciencedaily.com/releases/2010/01/100127144545.htm)
Breakthrough Could Lead to New Treatment for Malaria
Site of the day: http://milw0rm.com/
ScienceDaily (Jan. 29, 2010) — Malaria causes more than two million deaths each year, but an expert multinational team battling the global spread of drug-resistant parasites has made a breakthrough in the search for better treatment. Better understanding of the make-up of these parasites and the way they reproduce has enabled an international team, led by John Dalton, a biochemist in McGill's Institute of Parasitology, to identify a plan of attack for the development of urgently needed new treatments.
Malaria parasites live inside our red blood cells and feed on proteins, breaking them down so that they can use the proceeds (amino acids) as building blocks for their own proteins. When they have reached a sufficient size they divide and burst out of the red cell and enter another, repeating the process until severe disease or death occurs. Dalton and his colleagues found that certain "digestive enzymes" in the parasites enable them to undertake this process. Importantly, the researchers have also now determined the three-dimensional structures of two enzymes and demonstrated how drugs can be designed to disable the enzymes.
"By blocking the action of these critical parasite enzymes, we have shown that the parasites can no longer survive within the human red blood cell," Dalton explains. The discovery will be published in the Proceedings of the National Academy of Sciences, and is the result of collaboration including Australia's Queensland Institute of Medical Research, Monash University and the University of Western Sydney, Wroclaw University of Technology in Poland and the University of Virginia in the U.S. The team is putting their findings into action immediately and is already pursuing anti-malarial drug development.
(http://www.sciencedaily.com/releases/2010/01/100128165850.htm)
ScienceDaily (Jan. 29, 2010) — Malaria causes more than two million deaths each year, but an expert multinational team battling the global spread of drug-resistant parasites has made a breakthrough in the search for better treatment. Better understanding of the make-up of these parasites and the way they reproduce has enabled an international team, led by John Dalton, a biochemist in McGill's Institute of Parasitology, to identify a plan of attack for the development of urgently needed new treatments.
Malaria parasites live inside our red blood cells and feed on proteins, breaking them down so that they can use the proceeds (amino acids) as building blocks for their own proteins. When they have reached a sufficient size they divide and burst out of the red cell and enter another, repeating the process until severe disease or death occurs. Dalton and his colleagues found that certain "digestive enzymes" in the parasites enable them to undertake this process. Importantly, the researchers have also now determined the three-dimensional structures of two enzymes and demonstrated how drugs can be designed to disable the enzymes.
"By blocking the action of these critical parasite enzymes, we have shown that the parasites can no longer survive within the human red blood cell," Dalton explains. The discovery will be published in the Proceedings of the National Academy of Sciences, and is the result of collaboration including Australia's Queensland Institute of Medical Research, Monash University and the University of Western Sydney, Wroclaw University of Technology in Poland and the University of Virginia in the U.S. The team is putting their findings into action immediately and is already pursuing anti-malarial drug development.
(http://www.sciencedaily.com/releases/2010/01/100128165850.htm)
Secrets of Immunologic Memory: New Understanding of CD44 Receptor's Role in Immune Cell Survival
Site of the day: http://milw0rm.com/
ScienceDaily (Jan. 28, 2010) — Investigators at Sanford-Burnham Medical Research Institute (Sanford-Burnham) have discovered a new way the cell surface protein, CD44, helps specific T helper (Th1) cells develop immunologic memory. Linda Bradley, Ph.D., Bas Baaten, Ph.D., and colleagues determined that without CD44, Th1 cells died off during their initial immune response and were unable to generate immunologic memory. This is the first time scientists have identified this unique CD44 function on Th1 cells, making the protein a potential target to treat a variety of diseases.
The study was published online on January 14 in the journal Immunity.
CD44, a protein found on many cell types throughout the body, binds to the glycan hyaluronic acid (HA) in the extracellular matrix. When T helper cells are activated by infection, they upregulate (increase the activity of) CD44. Though CD44 is a marker for these "experienced" cells, its function has remained elusive. T cells are important components in the body's defense against diseases and, as memory cells, provide immunity to subsequent infections.
"In various infections and autoimmune conditions, Th1 cells are often the bad guys," said Dr. Bradley. "They can contribute to disease by overproducing cytokines and are often responsible for the disease pathology. Our findings reveal an opportunity to harness CD44 to control this pathogenesis."
The Bradley laboratory used T cells lacking CD44 that recognized a protein fragment in the influenza virus. Noting that the T cells did not survive and were unable to generate immunologic memory, the laboratory determined that CD44 protected the cells from programmed cell death initiated by the Fas receptor. This protective effect was specific to a subset of T cells, the Th1 cells, and mediated by the PI 3 kinase pathway. The researchers also demonstrated that survival of the cells could be controlled by antibodies capable of modulating CD44 signaling.
(http://www.sciencedaily.com/releases/2010/01/100128142141.htm)
ScienceDaily (Jan. 28, 2010) — Investigators at Sanford-Burnham Medical Research Institute (Sanford-Burnham) have discovered a new way the cell surface protein, CD44, helps specific T helper (Th1) cells develop immunologic memory. Linda Bradley, Ph.D., Bas Baaten, Ph.D., and colleagues determined that without CD44, Th1 cells died off during their initial immune response and were unable to generate immunologic memory. This is the first time scientists have identified this unique CD44 function on Th1 cells, making the protein a potential target to treat a variety of diseases.
The study was published online on January 14 in the journal Immunity.
CD44, a protein found on many cell types throughout the body, binds to the glycan hyaluronic acid (HA) in the extracellular matrix. When T helper cells are activated by infection, they upregulate (increase the activity of) CD44. Though CD44 is a marker for these "experienced" cells, its function has remained elusive. T cells are important components in the body's defense against diseases and, as memory cells, provide immunity to subsequent infections.
"In various infections and autoimmune conditions, Th1 cells are often the bad guys," said Dr. Bradley. "They can contribute to disease by overproducing cytokines and are often responsible for the disease pathology. Our findings reveal an opportunity to harness CD44 to control this pathogenesis."
The Bradley laboratory used T cells lacking CD44 that recognized a protein fragment in the influenza virus. Noting that the T cells did not survive and were unable to generate immunologic memory, the laboratory determined that CD44 protected the cells from programmed cell death initiated by the Fas receptor. This protective effect was specific to a subset of T cells, the Th1 cells, and mediated by the PI 3 kinase pathway. The researchers also demonstrated that survival of the cells could be controlled by antibodies capable of modulating CD44 signaling.
(http://www.sciencedaily.com/releases/2010/01/100128142141.htm)
Lack of Cellular Enzyme Triggers Switch in Glucose Processing
Site of the day: http://milw0rm.com/
ScienceDaily (Jan. 27, 2010) — A study investigating how a cellular enzyme affects blood glucose levels in mice provides clues to pathways that may be involved in processes including the regulation of longevity and the proliferation of tumor cells. In their report in the January 22 issue of Cell, a Massachusetts General Hospital (MGH)-based team of researchers describes the mechanism by which absence of the enzyme SIRT6 induces a fatal drop in blood sugar in mice by triggering a switch between two critical cellular processes.
"We found that SIRT6 functions as a master regulator of glucose levels by maintaining the normal processes by which cells convert glucose into energy," says Raul Mostoslavsky, MD, PhD, of the MGH Cancer Center, who led the study. "Learning more about how this protein controls the way cells handle glucose could lead to new approaches to treating type 2 diabetes and even cancer."
SIRT6 belongs to a family of proteins called sirtuins, which regulate important biological pathways in organisms from bacteria to humans. Originally discovered in yeast, sirtuins in mammals have been shown to have important roles in metabolic regulation, programmed cell death and adaptation to stress. SIRT6 is one of seven mammalian sirtuins, and Mostoslavsky's team previously showed that mice lacking the protein die in the first month of life from acute hypoglycemia. The current study was designed to investigate exactly how lack of SIRT6 causes this radical drop in blood sugar.
Normally cells convert glucose into energy through a two-step process. The first stage called glycolysis takes place in the cytoplasm, where glucose is broken down into an acid called pyruvate and a few molecules of ATP, the enzyme that provides the energy to power most biological processes. Pyruvate is taken into cellular structures called mitochondria, where it is further processed to release much greater amounts of ATP through a process called cellular respiration.
In a series of experiments in mouse cells, the researchers showed that SIRT6-deficiency hypoglycemia is caused by increased cellular uptake of glucose and not by elevated insulin levels or defects in the absorption of glucose from food. They then found increased levels of glycolysis and reduced mitochondrial respiration in SIRT6-knockout cells, something usually seen when cells are starved for oxygen or glucose, and showed that activation of the switch from cellular respiration to glycolysis is controlled through SIRT6's regulation of a protein called HIF1alpha. Normally, SIRT6 represses glycolytic genes through its role as a compactor of chromatin -- the tightly wound combination of DNA and a protein backbone that makes up chromosomes. In the absence of SIRT6, this structure is opened, causing activation of these glycolytic genes. The investigators' finding increased expression of glycolytic genes in living SIRT6-knockout mice -- which also had elevated levels of lactic acid, characteristic of a switch to glycolytic glucose processing -- supported their cellular findings.
Studies in yeast, worms and flies have suggested a role for sirtuins in aging and longevity, and while much of the enzymes' activity in mammals is unclear, SIRT6's control of critical glucose-metabolic pathways could signify a contribution to lifespan regulation. Elevated glycolysis also is commonly found in tumor cells, suggesting that a lack of SIRT6 could contribute to tumor growth. Conversely, since knocking out SIRT6 causes blood sugar to drop, limited SIRT6 inhibition could be a novel strategy for treating type 2 diabetes.
"There's a lot we still don't know about SIRT6," adds Mostoslavsky, who is an assistant professor of Medicine at Harvard Medical School. "We need to identify the factors that interact with SIRT6 and determine how it is regulated; investigate whether it acts as a tumor suppressor and how it might help lower glucose levels in diabetes; and determine its target organs in living animals, all of which we are investigating."
Lei Zhong of the MGH Cancer Center is lead author of the Cell report. Co-authors are Agustina D'Urso, Debra Toiber, Carlos Sebastian, Douangsone Vadysirisack, Othon Iliopoulos, and Leif Ellisen, MGH Cancer Center; Alexander Guimaraes, Brett Marinelli, and Ralph Weissleder, MGH Center for Systems Biology; Ryan Henry and Joaquin Espinosa, Howard Hughes Medical Institute; Jakob Wikstrom and Orian Shirihai, Boston University School of Medicine; Tomer Nir and Yuval Dor, Hebrew University-Hadassah Medical School; Clary Clish, Broad Institute; and Bhavapriya Vaitheesvaran, Albert Einstein College of Medicine. The study was supported by grants from the V Foundation, the Sidney Kimmel Cancer Research Foundation, the American Federation for Aging Research, Massachusetts Life Sciences Center, Joslin Diabetes Center and the Boston Area Diabetes Endocrinology Research Center.
(http://www.sciencedaily.com/releases/2010/01/100121140332.htm)
ScienceDaily (Jan. 27, 2010) — A study investigating how a cellular enzyme affects blood glucose levels in mice provides clues to pathways that may be involved in processes including the regulation of longevity and the proliferation of tumor cells. In their report in the January 22 issue of Cell, a Massachusetts General Hospital (MGH)-based team of researchers describes the mechanism by which absence of the enzyme SIRT6 induces a fatal drop in blood sugar in mice by triggering a switch between two critical cellular processes.
"We found that SIRT6 functions as a master regulator of glucose levels by maintaining the normal processes by which cells convert glucose into energy," says Raul Mostoslavsky, MD, PhD, of the MGH Cancer Center, who led the study. "Learning more about how this protein controls the way cells handle glucose could lead to new approaches to treating type 2 diabetes and even cancer."
SIRT6 belongs to a family of proteins called sirtuins, which regulate important biological pathways in organisms from bacteria to humans. Originally discovered in yeast, sirtuins in mammals have been shown to have important roles in metabolic regulation, programmed cell death and adaptation to stress. SIRT6 is one of seven mammalian sirtuins, and Mostoslavsky's team previously showed that mice lacking the protein die in the first month of life from acute hypoglycemia. The current study was designed to investigate exactly how lack of SIRT6 causes this radical drop in blood sugar.
Normally cells convert glucose into energy through a two-step process. The first stage called glycolysis takes place in the cytoplasm, where glucose is broken down into an acid called pyruvate and a few molecules of ATP, the enzyme that provides the energy to power most biological processes. Pyruvate is taken into cellular structures called mitochondria, where it is further processed to release much greater amounts of ATP through a process called cellular respiration.
In a series of experiments in mouse cells, the researchers showed that SIRT6-deficiency hypoglycemia is caused by increased cellular uptake of glucose and not by elevated insulin levels or defects in the absorption of glucose from food. They then found increased levels of glycolysis and reduced mitochondrial respiration in SIRT6-knockout cells, something usually seen when cells are starved for oxygen or glucose, and showed that activation of the switch from cellular respiration to glycolysis is controlled through SIRT6's regulation of a protein called HIF1alpha. Normally, SIRT6 represses glycolytic genes through its role as a compactor of chromatin -- the tightly wound combination of DNA and a protein backbone that makes up chromosomes. In the absence of SIRT6, this structure is opened, causing activation of these glycolytic genes. The investigators' finding increased expression of glycolytic genes in living SIRT6-knockout mice -- which also had elevated levels of lactic acid, characteristic of a switch to glycolytic glucose processing -- supported their cellular findings.
Studies in yeast, worms and flies have suggested a role for sirtuins in aging and longevity, and while much of the enzymes' activity in mammals is unclear, SIRT6's control of critical glucose-metabolic pathways could signify a contribution to lifespan regulation. Elevated glycolysis also is commonly found in tumor cells, suggesting that a lack of SIRT6 could contribute to tumor growth. Conversely, since knocking out SIRT6 causes blood sugar to drop, limited SIRT6 inhibition could be a novel strategy for treating type 2 diabetes.
"There's a lot we still don't know about SIRT6," adds Mostoslavsky, who is an assistant professor of Medicine at Harvard Medical School. "We need to identify the factors that interact with SIRT6 and determine how it is regulated; investigate whether it acts as a tumor suppressor and how it might help lower glucose levels in diabetes; and determine its target organs in living animals, all of which we are investigating."
Lei Zhong of the MGH Cancer Center is lead author of the Cell report. Co-authors are Agustina D'Urso, Debra Toiber, Carlos Sebastian, Douangsone Vadysirisack, Othon Iliopoulos, and Leif Ellisen, MGH Cancer Center; Alexander Guimaraes, Brett Marinelli, and Ralph Weissleder, MGH Center for Systems Biology; Ryan Henry and Joaquin Espinosa, Howard Hughes Medical Institute; Jakob Wikstrom and Orian Shirihai, Boston University School of Medicine; Tomer Nir and Yuval Dor, Hebrew University-Hadassah Medical School; Clary Clish, Broad Institute; and Bhavapriya Vaitheesvaran, Albert Einstein College of Medicine. The study was supported by grants from the V Foundation, the Sidney Kimmel Cancer Research Foundation, the American Federation for Aging Research, Massachusetts Life Sciences Center, Joslin Diabetes Center and the Boston Area Diabetes Endocrinology Research Center.
(http://www.sciencedaily.com/releases/2010/01/100121140332.htm)
Unwanted Guests: How Herpes Simplex Virus Gets Rid of the Cell's Security Guards
Site of the day: http://milw0rm.com/
ScienceDaily (Jan. 26, 2010) — A viral infection is like an uninvited, tenacious houseguest in the cell, using a range of tricks to prevent its eviction. Researchers at the Salk Institute for Biological Studies have identified one of the key proteins allowing herpes simplex virus (HSV) DNA to fly under the radar of their hosts' involuntary hospitality.
Their findings, to be published in a forthcoming issue of The EMBO Journal, reveal one of the tactics that HSV employs in order to overcome its hosts' defenses and may suggest a common mechanism by which viruses can successfully infect host cells.
HSV, like all viruses, requires a living host in order to multiply. But before it can hijack the cellular machinery to produce scores of copies of itself, it needs to evade the cell's security system. "We found that detection of the viral DNA by the host cell is an important barrier that the virus must overcome in order to achieve its goal," says Matthew Weitzman, Ph.D., associate professor in the Laboratory of Genetics, who led the study. "For this purpose, it brings along a protein that shuts down the normal cellular responses that would otherwise recognize and silence it."
To the host cell, invading viral DNA looks just like the product of DNA damage, which must be repaired or removed in order for the cell to stay healthy. As a result, DNA "security guards" continuously patrol our cells looking for unusual bits of DNA. "We reasoned that viral DNA would be recognized by the cell's DNA repair machinery and that the virus must somehow manipulate the cell's response to this foreign DNA," explains Weitzman.
To test this hypothesis, Weitzman and his team looked at what happens in a virus- infected cell when its DNA is damaged. In a normal cell, DNA damage sensor proteins rush to the site of damage. In cells infected with HSV, however, the cells' emergency repair teams don't respond correctly. "The virus effectively overrides the cell's DNA damage response in order to prevent its own DNA from being recognized," says Weitzman.
The team went on to identify a single viral protein that is to blame for knocking out the cell's security system, a protein called ICP0. They discovered that it flags for destruction two important DNA "security guards," the proteins called RNF8 and RNF168, thereby taking out the DNA damage response in human cells in one big swipe.
ICP0 attaches so-called ubiquitin marks, which instruct the cell to get rid of the very proteins that protect it. With RNF8 and RNF168 safely out of the way, the virus can begin to take over.
Delving deeper, the team looked at the role of these DNA "security guards" that are singled out by ICP0. Surprisingly, RNF8 and RNF168 also leave ubiquitin tags, but in this case, they mark regions of damage. They tag a protein called histone H2A, which directs DNA damage response proteins to accumulate at the sites of damage. The Salk team discovered that by removing RNF8 and RNF168, the viral ICP0 protein results in a decrease to the tag on the cellular H2A protein.
"We found that HSV targets the mark that is required to keep DNA damage sensors at damage sites," says postdoctoral researcher and first author Caroline Lilley, Ph.D. "We now think that HSV deliberately removes this mark so that the virus can infect cells without any trouble from its new host."
The findings highlight the importance of these histone marks in DNA damage. "By identifying how HSV dismantles the host's defense systems, we are shown the key steps, not only in viral infections, but also in the human DNA damage response," Weitzman explains.
HSV may have evolved this weapon because our cells use histone ubiquitination to try to silence gene expression from the viral DNA. "Ubiquitination would be a great way for the cell to silence the viral genome, and ICP0 provides the counterattack by the virus, so the virus and the cell are battling it out at that point," says Mira Chaurushiya, a graduate student in the lab and contributor to the study.
This work may point to a general mechanism viruses use to overcome the cell's defense. "DNA damage signaling and ubiquitination may be part of an anti-viral defense mechanism," explains Lilley. "Part of the cell's defense is to try to silence viral genomes, and viral proteins have to prevent this in order to achieve infection."
Along with Weitzman, Lilley and Chaurushiya, other contributors to this work were Sebastien Landry and Junghae Suh from the Salk Institute's Laboratory of Genetics (J.S. is now at Rice University, Houston); Stephanie Panier and Daniel Durocher from the Samuel Lunenfeld Research Institute, Mount Sinai Hospital in Toronto, Canada; Chris Boutell and Roger D. Everett at the University of Glasgow, UK; and Grant S. Stewart at Birmingham University, UK.
(http://www.sciencedaily.com/releases/2010/01/100121101126.htm)
ScienceDaily (Jan. 26, 2010) — A viral infection is like an uninvited, tenacious houseguest in the cell, using a range of tricks to prevent its eviction. Researchers at the Salk Institute for Biological Studies have identified one of the key proteins allowing herpes simplex virus (HSV) DNA to fly under the radar of their hosts' involuntary hospitality.
Their findings, to be published in a forthcoming issue of The EMBO Journal, reveal one of the tactics that HSV employs in order to overcome its hosts' defenses and may suggest a common mechanism by which viruses can successfully infect host cells.
HSV, like all viruses, requires a living host in order to multiply. But before it can hijack the cellular machinery to produce scores of copies of itself, it needs to evade the cell's security system. "We found that detection of the viral DNA by the host cell is an important barrier that the virus must overcome in order to achieve its goal," says Matthew Weitzman, Ph.D., associate professor in the Laboratory of Genetics, who led the study. "For this purpose, it brings along a protein that shuts down the normal cellular responses that would otherwise recognize and silence it."
To the host cell, invading viral DNA looks just like the product of DNA damage, which must be repaired or removed in order for the cell to stay healthy. As a result, DNA "security guards" continuously patrol our cells looking for unusual bits of DNA. "We reasoned that viral DNA would be recognized by the cell's DNA repair machinery and that the virus must somehow manipulate the cell's response to this foreign DNA," explains Weitzman.
To test this hypothesis, Weitzman and his team looked at what happens in a virus- infected cell when its DNA is damaged. In a normal cell, DNA damage sensor proteins rush to the site of damage. In cells infected with HSV, however, the cells' emergency repair teams don't respond correctly. "The virus effectively overrides the cell's DNA damage response in order to prevent its own DNA from being recognized," says Weitzman.
The team went on to identify a single viral protein that is to blame for knocking out the cell's security system, a protein called ICP0. They discovered that it flags for destruction two important DNA "security guards," the proteins called RNF8 and RNF168, thereby taking out the DNA damage response in human cells in one big swipe.
ICP0 attaches so-called ubiquitin marks, which instruct the cell to get rid of the very proteins that protect it. With RNF8 and RNF168 safely out of the way, the virus can begin to take over.
Delving deeper, the team looked at the role of these DNA "security guards" that are singled out by ICP0. Surprisingly, RNF8 and RNF168 also leave ubiquitin tags, but in this case, they mark regions of damage. They tag a protein called histone H2A, which directs DNA damage response proteins to accumulate at the sites of damage. The Salk team discovered that by removing RNF8 and RNF168, the viral ICP0 protein results in a decrease to the tag on the cellular H2A protein.
"We found that HSV targets the mark that is required to keep DNA damage sensors at damage sites," says postdoctoral researcher and first author Caroline Lilley, Ph.D. "We now think that HSV deliberately removes this mark so that the virus can infect cells without any trouble from its new host."
The findings highlight the importance of these histone marks in DNA damage. "By identifying how HSV dismantles the host's defense systems, we are shown the key steps, not only in viral infections, but also in the human DNA damage response," Weitzman explains.
HSV may have evolved this weapon because our cells use histone ubiquitination to try to silence gene expression from the viral DNA. "Ubiquitination would be a great way for the cell to silence the viral genome, and ICP0 provides the counterattack by the virus, so the virus and the cell are battling it out at that point," says Mira Chaurushiya, a graduate student in the lab and contributor to the study.
This work may point to a general mechanism viruses use to overcome the cell's defense. "DNA damage signaling and ubiquitination may be part of an anti-viral defense mechanism," explains Lilley. "Part of the cell's defense is to try to silence viral genomes, and viral proteins have to prevent this in order to achieve infection."
Along with Weitzman, Lilley and Chaurushiya, other contributors to this work were Sebastien Landry and Junghae Suh from the Salk Institute's Laboratory of Genetics (J.S. is now at Rice University, Houston); Stephanie Panier and Daniel Durocher from the Samuel Lunenfeld Research Institute, Mount Sinai Hospital in Toronto, Canada; Chris Boutell and Roger D. Everett at the University of Glasgow, UK; and Grant S. Stewart at Birmingham University, UK.
(http://www.sciencedaily.com/releases/2010/01/100121101126.htm)
Saturday, February 6, 2010
New Insight Into Reprogramming of Cell Fate
Site of the day: http://www.shoemoney.com/
ScienceDaily (Feb. 1, 2010) — A discovery by Babraham scientists brings new insight into how cells are reprogrammed and a greater understanding of how the environment, or factors like nutritional signals, can interact with our genes to affect health. As an embryo develops, cells acquire a particular fate, for example becoming a nerve or skin cell. The findings, reported online in the journal Nature, pinpoint a protein called AID as being important for complete cellular reprogramming in mammals. In addition, these findings may advance the field of regenerative medicine, by potentially enhancing our ability to guide the reversal of cell fate, and pave the way for novel therapeutics.
Cell fate is governed not only by the genome, but also by chemical changes to DNA and its associated proteins, a research field called epigenetics. Modifying DNA by methylation for example, alters the DNA structure but not its sequence. These 'epigenetic' tags are one of the ways that genes get switched on or off in different places at different times, enabling different tissues and organs to arise from a single fertilised egg. When epigenetic processes go awry, diseases may occur. Epigenetics is therefore emerging as an important research area with relevance to understanding many adult conditions like heart disease, diabetes, obesity, cancer and autoimmune disorders.
Professor Wolf Reik, Associate Director at the Babraham Institute and Professor of Epigenetics at the University of Cambridge who led the research said, "With numerous human, animal and plant genomes now sequenced a key question is how genomes are regulated in normal development, health and disease. Altered regulation of the epigenome is likely to underlie many human diseases so unlocking the principles of reprogramming can be harnessed to benefit regenerative medicine and stem cell therapy."
This research at Babraham, an institute of the Biotechnology and Biological Sciences Research Council (BBSRC), reveals that AID plays an intriguing role in erasing the chemical marks that appear on the genome as an embryo develops and determine what a cell's identity will be. AID appears to be involved in removing the epigenetic tags from DNA by a process called demethylation, which has long been known to be a critical component of cellular reprogramming. A study published recently in Nature from Helen Blau's lab in Stanford backs up the findings that AID is important for reprogramming.
While it has been known that epigenetic modifications to the genome get erased and re-established in the early embryo, precisely how and the extent to which this occurs had remained elusive. This collaboration between scientists at Babraham, the Howard Hughes Medical Institute and University of California at Los Angeles (UCLA) reveals for the first time the massive extent to which erasure of epigenetic tags occurs in mammals, erasing the epigenome between generations.
They discovered that methylation levels drop from 80% to a staggering 7% before being re-established again. This defines the level of epigenetic inheritance of DNA methylation patterns between generations and is identifying parts of the genome apparently more resistant to reprogramming than others. Reik explained, "Whole epigenomes can now be unravelled and understood thanks to Next Generation Sequencing technology which we used in collaboration with the UCLA team, and which we also have at the Babraham, a partner in the East Anglia Sequencing and Informatics Hub."
The Aid gene is normally switched on early as the embryo develops, however, the Babraham team found that if the AID protein is missing in cells, the methylation patterns are not thoroughly wiped clean and an epigenetic 'memory' is inherited. Commenting on the discovery Reik said, "Clear mechanisms for DNA demethylation have been elusive for some time. The body of evidence is now pointing to indirect demethylation through the action of key enzymes such as AID."
Environmental factors can also affect the genome, producing epigenetic changes that influence cell behaviour. Reik added, "It is now well established that epigenetics is the 'integrator' between the environment and the genome and that external factors like nutritional signals may have consequences later in life or on future generations. There is also the possibility that epigenetic information could be inherited across generations, providing a shorter term and flexible type of inheritance in response to environmental signals. The ability to unravel whole epigenomes during normal development and healthy ageing, and to understand how epigenomes are modified by the environment is extremely exciting."
It is known that removing epigenetic information from the genome can induce adult cells to regain stem-cell like properties (induced pluripotent stem cells, iPS cells). Inducing 'pluripotency' is of direct relevance to regenerative medicine as it enables specific cell populations and tissues to be generated from and for patients. Currently reprogramming is inefficient because of the memory imparted by DNA methylation tags. These new findings pinpointing how DNA demethylation can be driven, may overcome a significant barrier in producing iPS cells.
The identification of proteins like AID, that drive epigenetic signalling, is an important advance in basic biomedical research, which may help define new targets and therapeutics for diseases including cancer. The Babraham team are pursuing commercial applications in collaboration with the company CellCentric.
"Epigenetics is a growing area of academic research and commercial development. By understanding what proteins cause cell fate change, new tools and methods can be designed for both regenerative medicine and the treatment of intractable diseases. Specifically, the identification of AID and its activity may offer the ability to test the importance of gene-specifc demethylation, as well as the potential to overcome a pivotal epigenetic barrier in reprogramming cells for induced pluripotent cell production," explained Dr Will West, CEO of CellCentric.
Journal Reference:
Popp et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature, 2010; DOI: 10.1038/nature08829
(http://www.sciencedaily.com/releases/2010/01/100127111105.htm)
ScienceDaily (Feb. 1, 2010) — A discovery by Babraham scientists brings new insight into how cells are reprogrammed and a greater understanding of how the environment, or factors like nutritional signals, can interact with our genes to affect health. As an embryo develops, cells acquire a particular fate, for example becoming a nerve or skin cell. The findings, reported online in the journal Nature, pinpoint a protein called AID as being important for complete cellular reprogramming in mammals. In addition, these findings may advance the field of regenerative medicine, by potentially enhancing our ability to guide the reversal of cell fate, and pave the way for novel therapeutics.
Cell fate is governed not only by the genome, but also by chemical changes to DNA and its associated proteins, a research field called epigenetics. Modifying DNA by methylation for example, alters the DNA structure but not its sequence. These 'epigenetic' tags are one of the ways that genes get switched on or off in different places at different times, enabling different tissues and organs to arise from a single fertilised egg. When epigenetic processes go awry, diseases may occur. Epigenetics is therefore emerging as an important research area with relevance to understanding many adult conditions like heart disease, diabetes, obesity, cancer and autoimmune disorders.
Professor Wolf Reik, Associate Director at the Babraham Institute and Professor of Epigenetics at the University of Cambridge who led the research said, "With numerous human, animal and plant genomes now sequenced a key question is how genomes are regulated in normal development, health and disease. Altered regulation of the epigenome is likely to underlie many human diseases so unlocking the principles of reprogramming can be harnessed to benefit regenerative medicine and stem cell therapy."
This research at Babraham, an institute of the Biotechnology and Biological Sciences Research Council (BBSRC), reveals that AID plays an intriguing role in erasing the chemical marks that appear on the genome as an embryo develops and determine what a cell's identity will be. AID appears to be involved in removing the epigenetic tags from DNA by a process called demethylation, which has long been known to be a critical component of cellular reprogramming. A study published recently in Nature from Helen Blau's lab in Stanford backs up the findings that AID is important for reprogramming.
While it has been known that epigenetic modifications to the genome get erased and re-established in the early embryo, precisely how and the extent to which this occurs had remained elusive. This collaboration between scientists at Babraham, the Howard Hughes Medical Institute and University of California at Los Angeles (UCLA) reveals for the first time the massive extent to which erasure of epigenetic tags occurs in mammals, erasing the epigenome between generations.
They discovered that methylation levels drop from 80% to a staggering 7% before being re-established again. This defines the level of epigenetic inheritance of DNA methylation patterns between generations and is identifying parts of the genome apparently more resistant to reprogramming than others. Reik explained, "Whole epigenomes can now be unravelled and understood thanks to Next Generation Sequencing technology which we used in collaboration with the UCLA team, and which we also have at the Babraham, a partner in the East Anglia Sequencing and Informatics Hub."
The Aid gene is normally switched on early as the embryo develops, however, the Babraham team found that if the AID protein is missing in cells, the methylation patterns are not thoroughly wiped clean and an epigenetic 'memory' is inherited. Commenting on the discovery Reik said, "Clear mechanisms for DNA demethylation have been elusive for some time. The body of evidence is now pointing to indirect demethylation through the action of key enzymes such as AID."
Environmental factors can also affect the genome, producing epigenetic changes that influence cell behaviour. Reik added, "It is now well established that epigenetics is the 'integrator' between the environment and the genome and that external factors like nutritional signals may have consequences later in life or on future generations. There is also the possibility that epigenetic information could be inherited across generations, providing a shorter term and flexible type of inheritance in response to environmental signals. The ability to unravel whole epigenomes during normal development and healthy ageing, and to understand how epigenomes are modified by the environment is extremely exciting."
It is known that removing epigenetic information from the genome can induce adult cells to regain stem-cell like properties (induced pluripotent stem cells, iPS cells). Inducing 'pluripotency' is of direct relevance to regenerative medicine as it enables specific cell populations and tissues to be generated from and for patients. Currently reprogramming is inefficient because of the memory imparted by DNA methylation tags. These new findings pinpointing how DNA demethylation can be driven, may overcome a significant barrier in producing iPS cells.
The identification of proteins like AID, that drive epigenetic signalling, is an important advance in basic biomedical research, which may help define new targets and therapeutics for diseases including cancer. The Babraham team are pursuing commercial applications in collaboration with the company CellCentric.
"Epigenetics is a growing area of academic research and commercial development. By understanding what proteins cause cell fate change, new tools and methods can be designed for both regenerative medicine and the treatment of intractable diseases. Specifically, the identification of AID and its activity may offer the ability to test the importance of gene-specifc demethylation, as well as the potential to overcome a pivotal epigenetic barrier in reprogramming cells for induced pluripotent cell production," explained Dr Will West, CEO of CellCentric.
Journal Reference:
Popp et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature, 2010; DOI: 10.1038/nature08829
(http://www.sciencedaily.com/releases/2010/01/100127111105.htm)
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