Baik I.,Kookmin University |
Cho N.H.,Ajou University |
Kim S.H.,Korea University |
Han B.-G.,National Institutes of Health |
Shin C.,Korea University
American Journal of Clinical Nutrition | Year: 2011
Background: Genome-wide association (GWA) studies regarding the quantitative trait of alcohol consumption are limited. Objective: The objective of the study was to explore genetic loci associated with the amount of alcohol consumed. Design: We conducted a GWA study with discovery data on single nucleotide polymorphisms (SNPs) for 1721 Korean male drinkers aged 40-69 y who were included in an urban population-based cohort. Another sample that comprised 1113 male drinkers who were from an independent cohort enrolled in a rural area served as a resource for replication. At baseline (18 June 2001 through 29 January 2003), members of both cohorts provided information on average daily alcohol consumptions, and their DNA samples were collected for genotyping. Results: We tested 315,914 SNPs of discovery data by using multivariate linear regression analysis adjusted for age and smoking, and 12 SNPs on chromosome 12q24 had genome-wide significant associations with alcohol consumption; adjusted P values by using Bonferroni correction were 1.6 × 10 -5 through 5.8 × 10-46. We observed most SNPs in intronic regions and showed that the genes that harbor SNPs were C12orf51, CCDC63, MYL2, OAS3, CUX2, and RPH3A. In particular, signals in or near C12orf51, CCDC63, and MYL2 were successfully replicated in the test for 317,951 SNPs; rs2074356 in C12orf51 was in high linkage disequilibrium with SNPs in ALDH2, but other SNPs were not. Conclusions: In a GWA study, we identified loci and alleles highly associated with alcohol consumption. The findings suggest the need for further investigations on the genetic propensity for drinking excessive amounts of alcohol. © 2011 American Society for Nutrition.
Tu T.-W.,National Institutes of Health
Journal of Neuropathology and Experimental Neurology | Year: 2014
ABSTRACT: Wistar rats are widely used in biomedical research and commonly serve as a model organism in neuroscience studies. In most cases when noninvasive imaging is not used, studies assume a consistent baseline condition in rats that lack visible differences. While performing a series of traumatic brain injury studies, we discovered mild spontaneous ventriculomegaly in 70 (43.2%) of 162 Wistar rats that had been obtained from 2 different vendors. Advanced magnetic resonance (MR) imaging techniques, including MR angiography and diffusion tensor imaging, were used to evaluate the rats. Multiple neuropathologic abnormalities, including presumed arteriovenous malformations, aneurysms, cysts, white matter lesions, and astrogliosis were found in association with ventriculomegaly. Postmortem microcomputed tomography and immunohistochemical staining confirmed the presence of aneurysms and arteriovenous malformations. Diffusion tensor imaging showed significant decreases in fractional anisotropy and increases in mean diffusivity, axial diffusivity, and radial diffusivity in multiple white matter tracts (p < 0.05). These results could impact the interpretation, for example, of a pseudo-increase of axon integrity and a pseudo-decrease of myelin integrity, based on characteristics intrinsic to rats with ventriculomegaly. We suggest the use of baseline imaging to prevent the inadvertent introduction of a high degree of variability in preclinical studies of neurologic disease or injury in Wistar rats. © 2014 by American Association of Neuropathologists, Inc.
Abstract: Bacteria are the most abundant form of life on Earth, and they are capable of living in diverse habitats ranging from the surface of rocks to the insides of our intestines. Over millennia, these adaptable little organisms have evolved a variety of specialized mechanisms to move themselves through their particular environments. In two recent Caltech studies, researchers used a state-of-the-art imaging technique to capture, for the first time, three-dimensional views of this tiny complicated machinery in bacteria. Credit: Science/AAAS "Bacteria are widely considered to be 'simple' cells; however, this assumption is a reflection of our limitations, not theirs," says Grant Jensen, a professor of biophysics and biology at Caltech and an investigator with the Howard Hughes Medical Institute (HHMI). "In the past, we simply didn't have technology that could reveal the full glory of the nanomachines--huge complexes comprising many copies of a dozen or more unique proteins--that carry out sophisticated functions." Jensen and his colleagues used a technique called electron cryotomography to study the complexity of these cell motility nanomachines. The technique allows them to capture 3-D images of intact cells at macromolecular resolution--specifically, with a resolution that ranges from 2 to 5 nanometers (for comparison, a whole cell can be several thousand nanometers in diameter). First, the cells are instantaneously frozen so that water molecules do not have time to rearrange to form ice crystals; this locks the cells in place without damaging their structure. Then, using a transmission electron microscope, the researchers image the cells from different angles, producing a series of 2-D images that--like a computed tomography, or CT, scan--can be digitally reconstructed into a 3-D picture of the cell's structures. Jensen's laboratory is one of only a few in the entire world that can do this type of imaging. In a paper published in the March 11 issue of the journal Science, the Caltech team used this technique to analyze the cell motility machinery that involves a structure called the type IVa pilus machine (T4PM). This mechanism allows a bacterium to move through its environment in much the same way that Spider-Man travels between skyscrapers; the T4PM assembles a long fiber (the pilus) that attaches to a surface like a grappling hook and subsequently retracts, thus pulling the cell forward. Although this method of movement is used by many types of bacteria, including several human pathogens, Jensen and his team used electron cryotomography to visualize this cell motility mechanism in intact Myxococcus xanthus--a type of soil bacterium. The researchers found that the structure is made up of several parts, including a pore on the outer membrane of the cell, four interconnected ring structures, and a stemlike structure. By systematically imaging mutants, each of which lacked one of the 10 T4PM core components, and comparing these mutants with normal M. xanthus cells, they mapped the locations of all 10 T4PM core components, providing insights into pilus assembly, structure, and function. "In this study, we revealed the beautiful complexity of this machine that may be the strongest motor known in nature. The machine lets M. xanthus, a predatory bacterium, move across a field to form a 'wolf pack' with other M. xanthus cells, and hunt together for other bacteria on which to prey," Jensen says. Another way that bacteria move about their environment is by employing a flagellum--a long whiplike structure that extends outward from the cell. The flagellum is spun by cellular machinery, creating a sort of propeller that motors the bacterium through a substrate. However, cells that must push through the thick mucus of the intestine, for example, need more powerful versions of these motors, compared to cells that only need enough propeller power to travel through a pool of water. In a second paper, published in the online early edition of the Proceedings of the National Academy of Sciences (PNAS) on March 14, Jensen and his colleagues again used electron cryotomography to study the differences between these heavy-duty and light-duty versions of the bacterial propeller. The 3-D images they captured showed that the varying levels of propeller power among several different species of bacteria can be explained by structural differences in these tiny motors. In order for the flagellum to act as a propeller, structures in the cell's motor must apply torque--the force needed to cause an object to rotate--to the flagellum. The researchers found that the high-power motors have additional torque-generating protein complexes that are found at a relatively wide radius from the flagellum. This extra distance provides greater leverage to rotate the flagellum, thus generating greater torque. The strength of the cell's motor was directly correlated with the number of these torque-generating complexes in the cell. "These two studies establish a technique for solving the complete structures of large macromolecular complexes in situ, or inside intact cells," Jensen says. "Other structure determination methods, such as X-ray crystallography, require complexes to be purified out of cells, resulting in loss of components and possible contamination. On the other hand, traditional 2-D imaging alone doesn't let you see where individual protein pieces fit in the complete structure. Our electron cryotomography technique is a good solution because it can be used to look at the whole cell, providing a complete picture of the architecture and location of these structures." ### The work involving the type IVa pilus machinery was published in a Science paper titled "Architecture of the type IVa pilus machine." First author Yi-Wei Chang is a research scientist at Caltech; additional coauthors include collaborators from the Max Planck Institute for Terrestrial Microbiology, in Marburg, Germany, and from the University of Utah. The study was funded by the National Institutes of Health (NIH), HHMI, the Max Planck Society, and the Deutsche Forschungsgemeinschaft. Work involving the flagellum machinery was published in a PNAS paper titled "Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold." Additional coauthors include collaborators from Imperial College London; the University of Texas Southwestern Medical Center; and the University of Wisconsin-Madison. The study was supported by funding from the UK's Biotechnology and Biological Sciences Research Council and from HHMI and NIH. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.
The research, which is featured in the April 1 issue of the Journal of Cell Science, is the first to show how the function of neurons is impaired by specific genetic defects that have been proven to cause HSP, a group of inherited neurological disorders that affect about 20,000 people in the United States. Those with HSP suffer from numbness and weakness in the legs and feet due to progressive deterioration of the neurons that carry signals from the brain to the spinal column, and Rice researchers hope that a better understanding of the root causes of HSP could lead to improved treatments. The new study is the latest to stem from a groundbreaking series of discoveries about HSP that have come from the laboratory of Rice biochemist James McNew since 2009. The new research was done in collaboration with the lab of fellow Rice biochemist Michael Stern and involved thousands of painstaking experiments by graduate students Jimmy Summerville, from Stern's group, and Joseph Faust, from McNew's. Summerville and Faust, co-lead authors of the new study, created dozens of mutant strains of the fruit fly Drosophila melanogaster, which has analogous genes to two human genes—atlastin and reticulon—that are known to cause HSP. By selectively mutating genes in the flies, Summerville and Faust manipulated the amount of the proteins atlastin and reticulon made in the flies' nerve cells. Both proteins are known to play roles in building and maintaining the structural framework of the endoplasmic reticulum (ER). The ER is an interconnected network of tubules and sheets that provide a cell with numerous critical functions. The research highlights the functional importance of the overall architecture and structure of the ER network. "This work is foundational in the sense that we now understand, at a mechanistic level, how ER structure influences the ability of a neuron to send a signal," McNew said. "That was unknown before. The ER is an essential organelle. Our cells need it to function correctly, and this study shows how a couple of specific changes to the ER can dramatically influence the ways that neurons 'talk' to muscles." HSP can be caused by defects in more than 70 genes, but defects to the atlastin gene have been linked to as many as 10 percent of HSP cases. Reticulon defects also can cause HSP, but the exact mechanisms by which these genes cause neurological problems are unclear. McNew began studying atlastin almost a decade ago, and in 2009 he and Italian scientist Andrea Daga of the Eugenio Medea Scientific Institute discovered that atlastin was a fusion protein that helped join together ER membranes. At the time, scientists knew that atlastin was associated with HSP, but its role as a membrane fusion protein was wholly unexpected because membrane fusion proteins were relatively rare and were all thought to operate in the same way. Scientists had never encountered a protein like atlastin, which is an enzyme that uses chemical energy to drive fusion. "Atlastin was completely different than any other membrane fusion protein, so we really had to start from scratch to determine how it worked," McNew said. Based on its role as a membrane fusion protein, McNew and colleagues hypothesized that atlastin was a key player in helping to form and maintain a healthy ER network in cells. Prior to the 2009 discovery, McNew's lab had used yeast as a model organism to study other fusion proteins. To study atlastin, he needed to adopt a new model organism, the fruit fly. As luck would have it, McNew's office in Rice's BioScience Research Collaborative was next door to Stern's, the leader of one of Rice's best-known groups for fruit fly research. The two researchers and their graduate students began collaborating, and McNew won a grant from the National Institutes of Health in 2011 to fund the experiments that Summerville and Faust carried out to study how atlastin influenced behavior at the cellular level. Stern said reticulon was thrown into the mix because it's also known to affect ER shape and structure, and because it sometimes counteracts atlastin. "One does one thing, and the other does another," he said. "They sort of work in opposition." Summerville and Faust first created three mutant strains of Drosophila: one that lacked the atlastin gene, another that lacked the reticulon gene and a third that lacked both genes. They then created dozens of subcategories of each type by adding back genes that would express one or more of the missing proteins in specific amounts and in specific tissues. They also created a new method for expressing a fluorescent tag in the ER so they could examine the resulting ER structure in Drosophila neuronal cells. In particular, they concentrated on the longest neurons in the flies' bodies, cells that stretched about 2 millimeters from end to end. These neurons are analogous to the human neurons that connect the spinal cord to the lower legs, which are immediately downstream of the corticospinal neurons that are known to misfunction in HSP patients. "These neurons are the longest cells in the human body," McNew said. "They can be up to a meter or more in length, and the hypothesis has long been that because these neurons are so long, they are somehow more susceptible to whatever ER defects result from the loss of atlastin or reticulon. "In fact, that is exactly what we found. Faust's imaging of the ER structure in the synapse found that the shape and look of the ER changed dramatically when atlastin was knocked out. Under normal conditions, the ER in the synapse forms a basket-like shape, and without atlastin, that structure is completely missing, and you just have diffuse ER material that is devoid of structure," McNew said. Stern said, "Even just seeing that there was a complex structure of ER within the nerve terminals was completely unknown before." Summerville's measurements of electrophysiological function also showed that neurons with these misshapen synapses released fewer neurotransmitters needed to activate attached muscles. The reticulon tests weren't as conclusive. While clear decreases in neuron function were observed when reticulon was absent, the team could not discern a visual difference in the ER structure when the protein was absent. Stern said the structural changes are so minute that they might only show up under a stronger microscope. Stern credited the success of the project to Summerville and Faust's determination and persistence. He said they had to improvise, in part because atlastin proved finicky to manipulate. "Normally, in a knockout study like this, you examine what happens in the negative case, where none of the protein is present, and then you make genetic manipulations to add back protein in specific tissues. This often leads to overexpression, where you have two or three or five times more protein than normal," Stern said. But this approach did not work for atlastin. Summerville found that even the slightest alterations in atlastin levels often caused the flies to die before they could be tested. "I think that's interesting scientifically," Stern said. "That says something about atlastin. But it also made Jimmy's life very difficult because it denied him the use of many of the tools that scientists take for granted when they do this type of study." While the new paper revealed some aspects of neuronal structure that had not yet been seen, Stern and McNew said they expect their follow-up study, which is already under way, to provide even more compelling results in terms of the mechanism by which HSP operates. "I view this paper as an introductory paper," Stern said. "We did the characterization that you need to do to get the foundation of what's going on. That turns this into science, and it sets the stage for the experiments that we're doing now, which are aimed at answering the question of what this protein is doing, not only in nervous system function, but also in terms of how it might be affecting the patients with this disease." Explore further: Little-known protein found to be key player More information: J. Summerville et al. The effects of ER morphology on synaptic structure and function in Drosophila melanogaster, Journal of Cell Science (2016). DOI: 10.1242/jcs.184929
A $1.8-million National Institutes of Health grant to the Pittsburgh Supercomputing Center (PSC) will make a next-generation Anton 2 supercomputer developed by D. E. Shaw Research (DESRES) available to the biomedical research community. A specialized system for modeling the function and dynamics of biomolecules, the Anton 2 machine at PSC will be the only one of its kind publicly available to U.S. scientists. The grant also extends the operation of the Anton 1 supercomputer currently at PSC until the new Anton 2 is deployed, expected in the Fall of 2016. “Many life processes important to understanding the molecular basis of cellular events occur over timescales exceeding a millisecond in length,” says Phil Blood, principal investigator of the new grant and senior computational scientist at PSC. “Anton 2’s performance for molecular simulation will exceed that of current general-purpose supercomputing systems by orders of magnitude, enabling the study of biological processes not otherwise possible and offering new possibilities in drug discovery and development.” Molecular dynamics simulations can provide insights into the behavior of proteins, cell membranes, nucleic acids and other molecules at the atomic scale. But even the most advanced general-purpose supercomputers struggle to simulate beyond the microsecond level — a thousand times shorter than the millisecond level — without taking months of computational time. Anton has changed this, giving researchers practical access to simulations at far longer timescales. The Anton 1 supercomputer that has been in use at PSC since 2010 has been a great success and has so far enabled 277 simulation projects by 127 different PIs across the US and resulted in more than 120 peer-reviewed research papers. Three of these studies appeared in the scientific journal Nature, one of the international scientific community’s premier publications. The new 128-node Anton 2 will expand on the power and capabilities of the Anton 1 currently at PSC, increasing simulation speed approximately four-fold and enabling the simulation of biomolecular systems with around five times as many atoms as was possible using the previous machine. These capabilities will allow researchers to study larger biomolecules on timescales that weren’t previously accessible to molecular dynamics modeling. As with Anton 1, DESRES will provide the Anton 2 system without cost for non-commercial use by U.S. researchers. Time on the machine is expected to be allotted on the basis of research proposals submitted to an independent expert committee convened by the National Research Council at the National Academy of Sciences. More information on the Anton project at PSC can be found at https://www.psc.edu/index.php/computing-resources/anton