Washington, DC, United States
Washington, DC, United States

Time filter

Source Type

News Article | April 11, 2016
Site: www.nrl.navy.mil

The U.S. Naval Research Laboratory (NRL) was in the news a lot in 2014. Such public interest in NRL is a testimony to our people and their creativity when it comes to answering the nation's research needs. Below are the 10 most-viewed stories on our website in 2014, ordered by publication date. NRL Restores World War II-Era Equipment for Today's Research Needs (Jan 7) NRL has taken a 96,000-pound piece of equipment that was used in the 1940s and is refurbishing it for use in research today. Solar Power When It's Raining: NRL Builds Space Satellite Module to Try (Mar 12) Dr. Paul Jaffe, a spacecraft engineer at NRL, has built and tested a module to capture and transmit solar power; including a 'step' variation, which is in the patent process. Assembled in satellite array, modules could beam power to an on-Earth receiver, providing sustainable, base-load power for a city or military missions. NRL Autonomy Lab Hosts Shipboard Fire Robotics Consortium (Mar 24) Robotics research teams from Virginia Tech and the University of Pennsylvania demonstrated the most current developments in advanced autonomous systems to assist in discovery, control, and damage control of shipboard fires using humanoid robots. Scale Model WWII Craft Takes Flight With Fuel From the Sea Concept (Apr 7) Navy researchers demonstrate proof-of-concept in first flight of an internal combustion-powered model aircraft fueled by a novel gas-to-liquid process that uses seawater as carbon feedstock. Clothes That Self-Decontaminate; NRL Material May Also Purify Biofuel (Apr 17) Dr. Brandy White, in the NRL Center for Biomolecular Science and Engineering, is making materials that capture entire classes of contaminants, then break them down into something harmless. Her technology is stable and can be used for clothing, air filters, or even coated on windows and vehicles. NRL Researchers Develop Harder Ceramic for Armor Windows (Apr 29) NRL scientists have developed a method to fabricate nanocrystalline spinel that is 50% harder than the current spinel armor materials used in military vehicles. This harder spinel offers the potential for better armor windows in military vehicles, which would provide improved protection and other benefits for personnel and equipment. NRL Simulates IED-Like Blast Waves Against Army Helmet Prototypes (Jul 17) The U.S. Army's looking at helmet prototypes with optional parts to protect the face and jaw from various threats, including blast waves. But, as Dr. David Mott—an aerospace engineer at the NRL—says, more parts lead to more surprises. He and colleagues Ted Young and Doug Schwer have published their findings with the American Institute of Aeronautics and Astronautics. New York City Tracks Firefighters to Scene with NRL Radio Tags, Automated Display (Aug 26) On 15 of its vehicles, Fire Department New York (FDNY) can now automatically see which firefighters are nearby from the onboard computer and relay that information to the city's Operations Center. The system was invented by David DeRieux of NRL Space Systems, along with Michael Manning of Manning RF and in close partnership with FDNY. NRL Invents CubeSat Release Mechanism: To Deploy Solar Panels, Tethers (Sep 3) When a satellite is launched into space, there's sometimes room on the rocket for a few mini satellites to hitch a ride, too. Adam Thurn, an Aerospace Engineer at NRL, has invented a nichrome burn wire mechanism for these CubeSats, as they're called, to deploy something once in orbit. "This is developed as a low-cost, simple mechanism that would do different deployables on a satellite like that," he says. With SpinSat Mission, NRL Will Spin Small Satellite in Space with New Thruster Technology (Sep 18) On September 20, NRL will launch a small, spherical satellite called SpinSat. "It's a multifold mission," says Andy Nicholas, the Primary Investigator, "but the primary mission is demonstration of a new thruster technology." SpinSat will also be used to test the space surveillance network and monitor the effects of atmospheric drag. About the U.S. Naval Research Laboratory The U.S. Naval Research Laboratory provides the advanced scientific capabilities required to bolster our country's position of global naval leadership. The Laboratory, with a total complement of approximately 2,500 personnel, is located in southwest Washington, D.C., with other major sites at the Stennis Space Center, Miss., and Monterey, Calif. NRL has served the Navy and the nation for over 90 years and continues to advance research further than you can imagine. For more information, visit the NRL website or join the conversation on Twitter, Facebook, and YouTube.


News Article | September 7, 2016
Site: www.nature.com

Misha Angrist is not worried about strangers discovering his personal genetic information, even though it was made public in 2007 and has his name attached. Angrist was the fourth person to submit his genetic sequence to the Personal Genome Project, an effort led by George Church, a geneticist at Harvard Medical School in Boston, Massachusetts, to advance medicine by publicly sharing genomic and health data. “It was kind of a political statement,” says Angrist, a geneticist who studies bioethics and science policy at Duke University's Social Science Research Institute in Durham, North Carolina. He had become frustrated that privacy considerations prohibited scientists involved in genetic studies from interacting with the people those genes belonged to. “We were not allowed to talk to the people we studied, and that always struck me as silly and wrong-headed,” he says. The restrictions prevented researchers from gathering additional information, such as recent medical histories or health-related habits, that might give them more insight into disease risk — and stopped them developing a trusting relationship with the DNA donors. The Personal Genome Project aims to share DNA sequences, medical histories and other personal information with researchers looking to link gene variants, environment and lifestyle habits to disease risk. The project explicitly does not promise anonymity, and warns that the data will be shared publicly. Each participant is put through an online, questionnaire-based screening process to ensure that they understand both the benefits and the risks of making such information available. The US Precision Medicine Initiative, meanwhile, is seeking to collect the genomic information and medical records of 1 million participants, and the UK 100,000 Genomes Project is gathering similar data through the National Health Service, raising concerns among privacy advocates that too much personal information could become public. Both projects promise to remove information that identifies participants from the data, and store the data on secure servers that are accessible only to authorized personnel, and they prohibit people from re-identifying the sequences. They concede, however, that anonymity cannot be absolutely guaranteed, and computer scientists have shown that at least some participants can be re-identified fairly easily. Scientists and policymakers are trying to work out exactly what the harm of such disclosures could be, and how they can reduce the risks, but any solutions are more likely to be policy-based than technological. Anonymous data are not as unidentifiable as the term suggests. Not all participants in the Personal Genome Project are identified by name like Angrist, but the project does not guarantee anonymity. In 2013, Latanya Sweeney, a computer scientist who heads Harvard's Data Privacy Lab, was able to put names to many of the profiles simply by comparing them with available public records. More than half of the nameless profiles available at the time contained the person's date of birth, gender and postal zip code. By cross-checking against public records such as voter registrations, she was able to attach a name and address to 241 of the 579 profiles. Staff at the Personal Genome Project confirmed that she was correct in all but 7 cases. The Personal Genome Project is not the only database that is vulnerable to re-identification. Yaniv Erlich, a computer scientist at Columbia University in New York City looked at repeating patterns of nucleotides, known as short tandem repeats (STRs), on the Y chromosomes of men whose DNA had been made publicly available by the international 1000 Genomes Project. He then compared them with data found on two public genealogy databases. The project had not collected names or other identifying information, such as birth date or social security number, and because it stored more samples than were used, there was no way to tell if a given sample was even part of the database. As the project's consent form reassuringly put it: “Because of these measures, it will be very hard for anyone who looks at any of the scientific databases to know which information came from you, or even that any information in the scientific databases came from you.” Despite that promise, however, Erlich was able to put names to nearly 50 people who had donated their DNA. Because the Y chromosome is inherited only by males, it is often linked to family surnames. This means that even if participants in the genome study had not also given their DNA to a genealogy website, people with matching STRs were probably relatives, allowing the researchers to infer more surnames. When his study was published in 2013, Erlich estimated that 12% of US males were vulnerable to this kind of breach. Three years later, with genome databases growing and algorithms for comparing data improving, that figure could be as high as 20%. “It definitely gets easier and easier,” he says. “With some knowledge and some dedicated effort, you can identify people from genomic data.” Even those who agree to make their data public may have some information that they would rather keep from other people — or even from themselves. One participant in the Public Genome Project was James Watson, co-discoverer of the double helix structure of DNA. Watson asked that information about his apolipoprotein E gene be redacted — a variant of that gene can indicate a heightened risk for developing Alzheimer's disease, and he did not want to know his risk. But researchers from the Queensland Institute of Medical Research in Australia and the University of Washington School of Medicine pointed out that merely removing the gene from the database would not hide the information. Other changes to the genome, some in fairly distant parts of the DNA, are correlated with the higher-risk mutation. Watson responded by deleting an even larger swathe of his genome from the database. But that could be a losing battle, the researchers warned. As our understanding of the genome improves, it will be easier to estimate risks for various diseases from different points along the genome. If privacy cannot be guaranteed, the next question is whether this is a problem. Some risks seem relatively minor, such as the potential embarrassment of having people find out that you participated in a particular study. But some adoptees have used genetic data to find birth parents who had not expected their identity to be revealed. Others might discover that someone they thought to be a parent or grandparent is not actually related to them. Include someone's medical history and the potential for awkward revelations grows. If a name can be attached to a genome, and the genome is attached to medical records, then treatments for sexually transmitted diseases, alcoholism or mental illness could be revealed. Some people worry that they may face job discrimination — or health-insurance discrimination in the United States — if a risk of debilitating and expensive diseases is made public. Some privacy advocates worry that despite the general guidelines developed for the Precision Medicine Initiative, the project lacks legal protections. The World Privacy Forum, a non-profit organization based in San Diego, California, says that data collected by the project are not covered by the main US health-privacy law, the Health Insurance Portability and Accountability Act of 1996. It also fears that courts may decide that when participants volunteer information to researchers, they give away their right to doctor–patient confidentiality. Courts have, after all, previously ruled that police do not need a warrant to collect mobile-phone location data because callers have already shared that information with telephone companies. “People are still worried about discrimination in health insurance and jobs,” says Robert Cook-Deegan, a biologist who studies genomics policy at Duke University's Sanford School of Public Policy. In the United States, the Genetic Information Nondiscrimination Act of 2008 is supposed to prohibit that, but it does not cover long-term care or disability insurance, so people who discover that they may need extensive care for a late-onset disease such as Alzheimer's could still face ruinous expenses. The Canadian government recently debated a similar law, and the European Union has a general mandate against genetic discrimination. There is no specific UK law against it, however, although the Association of British Insurers agreed to a moratorium until 2019 on using predictive genetic tests to inform insurance policies. Some of the concerns are speculative, such as the possibility that someone's DNA could be planted at a crime scene. Indeed, the trouble with figuring out how to handle privacy, Erlich says, is that “we really don't understand the concept of harm due to privacy loss.” If anything, the risk of personal information being revealed is probably no greater than that from other sources where people willingly provide information, Erlich says. He points to a 2013 study by researchers at the University of Cambridge, UK, and Microsoft Research that identified people's sexual orientation, political affiliation and race with high degrees of accuracy just by examining their 'likes' on Facebook. That is much more information than you could glean from a genome at present. “There is not a single genetic marker in the genome that can predict homosexuality,” Erlich says. Privacy may not even be the right focus, argues Jenny Reardon, a sociologist at the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, who in May chaired a conference focusing on the fraught issue of personal data in the age of precision medicine. “Privacy doesn't get us to what is more fundamental: what as a society should we be doing with this data,” she says. She would like to see more focus on how these large data sets can improve people's lives. But “no one wants to discuss this”, she says. Whatever the problem with privacy, the solution is unlikely to be technological, Erlich says. Techniques to encrypt data or disguise it with statistical noise are of limited value, he explains, because the more they protect privacy, the less useful they make the data. He thinks that a better approach is to rethink how privacy and consent are handled, and to treat the people who hand over their DNA with respect and honesty. In an example of this approach, Erlich and colleagues at the New York Genome Center, in collaboration with the National Breast Cancer Coalition in Washington DC, have created a project called DNALand to study the genetic risks of breast cancer. People donate the genetic information that they get from DNA-testing companies such as 23andMe, Family Tree DNA and Ancestry.com. In return, DNALand offers users free information about their genome and the possibility of identifying relatives based on genetic matches, as well as the chance to contribute to improving medical knowledge. The consent form spells out the risks and benefits of participating and allows people to withdraw at any time. It also promises to seek further consent before sharing data with a third party. One problem in obtaining consent is that, once collected, genomic data can be stored indefinitely and used in ways that the original researchers did not foresee. “That's the whole idea of research. You don't know what you're going to find,” Cook-Deegan says. The people who set up databases need to take a long view when making promises and asking for consent as they collect the data, he says. The Precision Medicine Initiative has a set of general guidelines about transparency and respect for participants' wishes, and these will be used to inform the future development of more concrete privacy protocols. “The problem we're going to have is to make sure we have a system that respects the rights and interests that were set up at the front end,” Cook-Deegan says. Not being clear about how participation in a study could lead to privacy breaches creates the risk that any problems that arise may make potential donors less willing to have their DNA sequenced. “We can't do research on human beings and look people in the eye and promise them that nothing bad will ever happen,” Angrist says. “If we reassure people and something bad happens, then it's that much worse.” Instead, he argues, engaging with donors and spelling out the risks and benefits can change the privacy equation. “If you talk to people who have children with undiagnosed diseases, they would tell you: 'We would gladly forgo privacy in the interest of accelerated research'.”


Paz I.,Technion - Israel Institute of Technology | Kosti I.,Technion - Israel Institute of Technology | Ares Jr. M.,Cellular and Developmental Biology | Cline M.,Center for Biomolecular Science and Engineering | Mandel-Gutfreund Y.,Technion - Israel Institute of Technology
Nucleic Acids Research | Year: 2014

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. © 2014 The Author(s).


News Article | November 17, 2015
Site: www.cemag.us

Research biologists, chemists, and theoreticians at the U.S. Naval Research Laboratory (NRL) are on pace to develop the next generation of functional materials that could enable the mapping of the complex neural connections in the brain. The ultimate goal is to better understand how the billions of neurons in the brain communicate with one another during normal brain function or dysfunction as result of injury or disease. "There is tremendous interest in mapping all the neuron connections in the human brain," says Dr. James Delehanty, research biologist, Center for Biomolecular Science and Engineering. "To do that we need new tools or materials that allow us to see how large groups of neurons communicate with one another while, at the same time, being able to focus in on a single neuron's activity. Our most recent work potentially opens the integration of voltage-sensitive nanomaterials into live cells and tissues in a variety of configurations to achieve real-time imaging capabilities not currently possible." The basis of neuron communication is the time-dependent modulation of the strength of the electric field that is maintained across the cell's plasma membrane. This is called an action potential. Among the nanomaterials under consideration for application in neuronal action potential imaging are quantum dots (QDs) — crystalline semiconductor nanomaterials possessing a number of advantageous photophysical attributes. "QDs are very bright and photostable so you can look at them for long times and they allow for tissue imaging configurations that are not compatible with current materials, for example, organic dyes," Delehanty adds. "Equally important, we've shown here that QD brightness tracks, with very high fidelity, the time-resolved electric field strength changes that occur when a neuron undergoes an action potential. Their nanoscale size make them ideal nanoscale voltage sensing materials for interfacing with neurons and other electrically active cells for voltage sensing." QDs are small, bright, photo-stable materials that possess nanosecond fluorescence lifetimes. They can be localized within or on cellular plasma membranes and have low cytotoxicity when interfaced with experimental brain systems. Additionally, QDs possess two-photon action cross-section orders of magnitude larger than organic dyes or fluorescent proteins. Two-photon imaging is the preferred imaging modality for imaging deep (millimeters) into the brain and other tissues of the body. In their most recent work, the NRL researchers showed that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect — the shifting and splitting of spectral lines of atoms and molecules due to presence of an external electric field. "The inherent superior photostability properties of QDs coupled with their voltage sensitivity could prove advantageous to long-term imaging capabilities that are not currently attainable using traditional organic voltage sensitive dyes," Delehanty says. "We anticipate that continued research will facilitate the rational design and synthesis of voltage-sensitive QD probes that can be integrated in a variety of imaging configurations for the robust functional imaging and sensing of electrically active cells." Additional contributors to this study included the Optical Sciences Division, and the Materials Science and Technology Division at NRL, Washington, D.C. A full report of the team's findings, entitled "Electric Field Modulation of Semiconductor Quantum Dot Photoluminescence: Insights Into the Design of Robust Voltage-Sensitive Cellular Imaging Probes," was published Sept. 28, 2015 in the American Chemical Society publication, NANO Letters. This groundbreaking work was funded by the NRL Nanoscience Institute.


News Article | November 20, 2015
Site: www.nanotech-now.com

Abstract: Research biologists, chemists and theoreticians at the U.S. Naval Research Laboratory (NRL), are on pace to develop the next generation of functional materials that could enable the mapping of the complex neural connections in the brain. The ultimate goal is to better understand how the billions of neurons in the brain communicate with one another during normal brain function, or dysfunction, as result of injury or disease. "There is tremendous interest in mapping all the neuron connections in the human brain," said Dr. James Delehanty, research biologist, Center for Biomolecular Science and Engineering. "To do that we need new tools or materials that allow us to see how large groups of neurons communicate with one another while, at the same time, being able to focus in on a single neuron's activity. Our most recent work potentially opens the integration of voltage-sensitive nanomaterials into live cells and tissues in a variety of configurations to achieve real-time imaging capabilities not currently possible." The basis of neuron communication is the time-dependent modulation of the strength of the electric field that is maintained across the cell's plasma membrane. This is called an action potential. Among the nanomaterials under consideration for application in neuronal action potential imaging are quantum dots (QDs) -- crystalline semiconductor nanomaterials possessing a number of advantageous photophysical attributes. "QDs are very bright and photostable so you can look at them for long times and they allow for tissue imaging configurations that are not compatible with current materials, for example, organic dyes," Delehanty added. "Equally important, we've shown here that QD brightness tracks, with very high fidelity, the time-resolved electric field strength changes that occur when a neuron undergoes an action potential. Their nanoscale size make them ideal nanoscale voltage sensing materials for interfacing with neurons and other electrically active cells for voltage sensing." QDs are small, bright, photo-stable materials that possess nanosecond fluorescence lifetimes. They can be localized within or on cellular plasma membranes and have low cytotoxicity when interfaced with experimental brain systems. Additionally, QDs possess two-photon action cross-section orders of magnitude larger than organic dyes or fluorescent proteins. Two-photon imaging is the preferred imaging modality for imaging deep (millimeters) into the brain and other tissues of the body. In their most recent work, the NRL researchers showed that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect -- the shifting and splitting of spectral lines of atoms and molecules due to presence of an external electric field. "The inherent superior photostability properties of QDs coupled with their voltage sensitivity could prove advantageous to long-term imaging capabilities that are not currently attainable using traditional organic voltage sensitive dyes," Delehanty said. "We anticipate that continued research will facilitate the rational design and synthesis of voltage-sensitive QD probes that can be integrated in a variety of imaging configurations for the robust functional imaging and sensing of electrically active cells." ### Additional contributors to this study included the Optical Sciences Division, and the Materials Science and Technology Division at NRL, Washington, D.C. A full report of the team's findings, entitled "Electric Field Modulation of Semiconductor Quantum Dot Photoluminescence: Insights Into the Design of Robust Voltage-Sensitive Cellular Imaging Probes", was published September 28, 2015 in the American Chemical Society publication, NANO Letters. This groundbreaking work was funded by the NRL Nanoscience Institute. 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.


News Article | April 11, 2016
Site: www.nrl.navy.mil

Research biologists, chemists, and theoreticians at the U.S. Naval Research Laboratory (NRL) are on pace to develop the next generation of functional materials that could enable the mapping of the complex neural connections in the brain. The ultimate goal is to better understand how the billions of neurons in the brain communicate with one another during normal brain function or dysfunction as result of injury or disease. "There is tremendous interest in mapping all the neuron connections in the human brain," said Dr. James Delehanty, research biologist, Center for Biomolecular Science and Engineering. "To do that we need new tools or materials that allow us to see how large groups of neurons communicate with one another while, at the same time, being able to focus in on a single neuron's activity. Our most recent work potentially opens the integration of voltage-sensitive nanomaterials into live cells and tissues in a variety of configurations to achieve real-time imaging capabilities not currently possible." The basis of neuron communication is the time-dependent modulation of the strength of the electric field that is maintained across the cell's plasma membrane. This is called an action potential. Among the nanomaterials under consideration for application in neuronal action potential imaging are quantum dots (QDs) — crystalline semiconductor nanomaterials possessing a number of advantageous photophysical attributes. "QDs are very bright and photostable so you can look at them for long times and they allow for tissue imaging configurations that are not compatible with current materials, for example, organic dyes," Delehanty added. "Equally important, we've shown here that QD brightness tracks, with very high fidelity, the time-resolved electric field strength changes that occur when a neuron undergoes an action potential. Their nanoscale size make them ideal nanoscale voltage sensing materials for interfacing with neurons and other electrically active cells for voltage sensing." QDs are small, bright, photo-stable materials that possess nanosecond fluorescence lifetimes. They can be localized within or on cellular plasma membranes and have low cytotoxicity when interfaced with experimental brain systems. Additionally, QDs possess two-photon action cross-section orders of magnitude larger than organic dyes or fluorescent proteins. Two-photon imaging is the preferred imaging modality for imaging deep (millimeters) into the brain and other tissues of the body. In their most recent work, the NRL researchers showed that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect — the shifting and splitting of spectral lines of atoms and molecules due to presence of an external electric field. "The inherent superior photostability properties of QDs coupled with their voltage sensitivity could prove advantageous to long-term imaging capabilities that are not currently attainable using traditional organic voltage sensitive dyes," Delehanty said. "We anticipate that continued research will facilitate the rational design and synthesis of voltage-sensitive QD probes that can be integrated in a variety of imaging configurations for the robust functional imaging and sensing of electrically active cells." Additional contributors to this study included the Optical Sciences Division, and the Materials Science and Technology Division at NRL, Washington, D.C. A full report of the team's findings, entitled "Electric Field Modulation of Semiconductor Quantum Dot Photoluminescence: Insights Into the Design of Robust Voltage-Sensitive Cellular Imaging Probes", was published September 28, 2015 in the American Chemical Society publication, NANO Letters. This groundbreaking work was funded by the NRL Nanoscience Institute. About the U.S. Naval Research Laboratory The U.S. Naval Research Laboratory provides the advanced scientific capabilities required to bolster our country's position of global naval leadership. The Laboratory, with a total complement of approximately 2,500 personnel, is located in southwest Washington, D.C., with other major sites at the Stennis Space Center, Miss., and Monterey, Calif. NRL has served the Navy and the nation for over 90 years and continues to advance research further than you can imagine. For more information, visit the NRL website or join the conversation on Twitter, Facebook, and YouTube.


Franks A.E.,University of Massachusetts Amherst | Nevin K.P.,University of Massachusetts Amherst | Glaven R.H.,University of Massachusetts Amherst | Glaven R.H.,Center for Biomolecular Science and Engineering | Lovley D.R.,University of Massachusetts Amherst
ISME Journal | Year: 2010

Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. Cells throughout anode biofilms of Geobacter sulfurreducens reduced the metabolic stains: 5-cyano-2,3-ditolyl tetrazolium chloride and Redox Green, suggesting metabolic activity throughout the biofilm. To compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, anode biofilms were encased in resin and sectioned into inner (0-20 m from anode surface) and outer (30-60 m) fractions. Transcriptional analysis revealed that, at a twofold threshold, 146 genes had significant (P>0.05) differences in transcript abundance between the inner and outer biofilm sections. Only 1 gene, GSU0093, a hypothetical ATP-binding cassette transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting lower metabolic rates. However, differences in transcript abundance were relatively low (>threefold) and the expression of genes for the tricarboxylic acid cycle enzymes was not significantly lower. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of this study suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms. © 2010 International Society for Microbial Ecology. All Rights Reserved.


Edwankar C.R.,University of Wisconsin - Milwaukee | Edwankar R.V.,University of Wisconsin - Milwaukee | Deschamps J.R.,Center for Biomolecular Science and Engineering | Cook J.M.,University of Wisconsin - Milwaukee
Angewandte Chemie - International Edition | Year: 2012

All five: The first total synthesis of the C2-symmetric indole alkaloid 1 involved a late-stage thallium(III) acetate-mediated intermolecular oxidative coupling to construct the C9-C9' bond with complete regio- and stereocontrol. The formation of a single atropodiastereomer in this critical step arises from internal asymmetric induction. The first total synthesis of four other monomeric sarpagine indole alkaloids is also described. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Deschamps J.R.,Center for Biomolecular Science and Engineering
Powder Diffraction | Year: 2013

Chitin is a natural polysaccharide found in many diverse phyla and almost always occurs in association with protein. In this study the chitin polymer is characterized by X-ray diffraction from its naturally occurring unprocessed state through various steps used in the purification procedure. In addition, the effect of different treatments on the final product is examined. These studies show that native chitin has a characteristic diffraction pattern that is not altered by the mild treatments used to isolate relatively pure chitin. Chitins prepared from different sources exhibit the same characteristic diffraction pattern. In addition, chitin films prepared using non-degrading solvents retain most of the characteristic patterns. De-acylation of chitin to produce chitosan results in large changes to the diffraction pattern. To a very limited extent features present in the diffraction pattern of native chitin can be recovered by re-acylation of chitosan. © 2013 International Centre for Diffraction Data.


Zerbino D.R.,Center for Biomolecular Science and Engineering
Current Protocols in Bioinformatics | Year: 2010

The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short-read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data. Copyright © 2010 John Wiley & Sons, Inc.

Loading Center for Biomolecular Science and Engineering collaborators
Loading Center for Biomolecular Science and Engineering collaborators