Fish and some amphibians possess a unique sensory capability in the so-called lateral-line system. It allows them, in effect, to "touch" objects in their surroundings without direct physical contact or to "see" in the dark. Professor Leo van Hermmen and his team in the physics department of the Technische Universitaet Muenchen are exploring the fundamental basis for this sensory system. What they discover might one day, through biomimetic engineering, better equip robots to orient themselves in their environments.
With our senses we take in only a small fraction of the information that surrounds us. Infrared light, electromagnetic waves, and ultrasound are just a few examples of the external influences that we humans can grasp only with the help of technological measuring devices - whereas some other animals use special sense organs, their own biological equipment, for the purpose. One such system found in fish and some amphibians is under investigation by the research team of Professor Leo van Hemmen, chair of theoretical biophysics at TUM, the Technische Universitaet Muenchen.
Even in murky waters hardly penetrated by light, pike and pickerel can feel out their prey before making contact. The blind Mexican cave fish can perceive structures in its surroundings and can effortlessly avoid obstacles. Catfish on the hunt follow invisible tracks that lead directly to their prey. The organ that makes this possible is the lateral-line system, which registers changes in currents and even smaller disturbances, providing backup support for the sense of sight particularly in dark or muddy waters.
This remote sensing system, at first glance mysterious, rests on measurement of the pressure distribution and velocity field in the surrounding water. The lateral-line organs responsible for this are aligned along the left and right sides of the fish's body and also surround the eyes and mouth. They consist of gelatinous, flexible, flag-like units about a tenth of a millimeter long. These so-called neuromasts - which sit either directly on the animal's skin or just underneath, in channels that water can permeate through pores - are sensitive to the slightest motion of the water. Coupled to them are hair cells similar to the acoustic pressure sensors in the human inner ear. Nerves deliver signals from the hair cells for processing in the brain, which localizes and identifies possible sources of the changes detected in the water's motion.
These changes can arise from various sources: A fish swimming by produces vibrations or waves that are directly conveyed to the lateral-line organ. Schooling fishes can recognize a nearby attacker and synchronize their swimming motion so that they resemble a single large animal. The Mexican cave fish pushes a bow wave ahead of itself, which is reflected from obstacles. The catfish takes advantage of the fact that a swimming fish that beats its tail fin leaves a trail of eddies behind. This so-called "vortex street" persists for more than a minute and can betray the prey.
For the past five years, Leo van Hemmen and his team have been investigating the capabilities of the lateral-line system and assessing the potential to translate it into technology. How broad is the operating range of such a sense organ, and what details can it reveal about moving objects? Which stimuli does the lateral-line system receive from the eddy trail of another fish, and how are these stimuli processed? To get to the bottom of these questions, the scientists develop mathematical models and compare these with experimentally observed electrical nerve signals called action potentials. The biophysicists acquire the experimental data - measurements of lateral-line organ activity in clawed frogs and cave fish - through collaboration with biologists. "Biological systems follow their own laws," van Hemmen says, "but laws that are universally valid within biology and can be described mathematically - once you find the right biophysical or biological concepts, and the right formula."
The models yield surprisingly intuitive-sounding conclusions: Fish can reliably fix the positions of other fish in terms of a distance corresponding to their own body length. Each fish broadcasts definite and distinguishing information about itself into the field of currents. So if, for example, a prey fish discloses its size and form to a possible predator within the radius of its body length, the latter can decide if a pursuit is worth the effort. This is a key finding of van Hemmen's research team.
The TUM researchers have discovered another interesting formula. With this one, the angle between a fish's axis and a vortex street can be computed from the signals that a lateral-line system acquires. The peak capability of this computation matches the best that a fish's nervous system can do. The computed values for nerve signals from an animal's sensory organ agree astonishingly well with the actual measured electrical impulses from the discharge of nerve cells. "The lateral-line sense fascinated me from the start because it's fundamentally different from other senses such as vision or hearing, not just at first glance but also the second," van Hemmen says. "It's not just that it describes a different quality of reality, but also that in place of just two eyes or ears this sense is fed by many discrete lateral-line organs - from 180 in the clawed frog to several thousand in a fish, each of which in turn is composed of several neuromasts. The integration behind it is a tour de force."
The neuronal processing and integration of diverse sense impressions into a unified mapping of reality is a major focus for van Hemmen's group. They are pursuing this same fundamental investation through the study of desert snakes' infrared perception, vibration sensors in scorpions' feet, and barn owls' hearing.
"Technology has overtaken nature in some domains," van Hemmen says, "but lags far behind in the cognitive processing of received sense impressions. My dream is to endow robots with multiple sensory modalities. Instead of always building in more cameras, we should also along the way give them additional sensors for sound and touch." With a sense modeled on the lateral-line system, but which would function as well in air as under water, robots might for example move safely among crowds of people. But such a system also offers many promising applications in the water. Underwater robots could use it to orient themselves during the exploration of inaccessible cave systems and deep-sea volcanoes. Autonomous submarines could also locate obstacles in turbid water. Such an underwater vehicle is currently being developed within the framework of the EU project CILIA, in collaboration with the TUM chair for guidance and control technology.
Further research includes collaborations with the excellence cluster CoTeSys (Cognition for Technical Systems) and the newly created Leonardo da Vinci Center for Bionics at TUM, as well as with the chair for humanoid robots and the Bernstein Center for Computational Neuroscience.
Original papers:
"Hydrodynamic Object Recognition: When Multipoles Count," Andreas B. Sichert, Robert Bamler, and J. Leo van Hemmen, Physical Review Letters, 102, 058104 (2009)
Link: dx.doi/10.1103/PhysRevLett.102.058104
"Wake Tracking and the Detection of Vortex Rings by the Canal Lateral Line of Fish," Jan-Moritz P. Franosch, Hendrik J. A. Hagedorn, Julie Goulet, Jacob Engelmann, and J. Leo van Hemmen, Physical Review Letters 103, 078102 (2009)
Link: dx.doi/10.1103/PhysRevLett.103.078102
See also: "Following in the wake," Nature 460, 1061 (27 August 2009)
Link: dx.doi/10.1038/4601061a
Source:
Patrick Regan
Technische Universitaet Muenchen
понедельник, 6 июня 2011 г.
Phylonix Awarded National Science Foundation Phase II SBIR For Zebrafish Screening
Phylonix Pharmaceuticals, Inc. has announced it has received a $500,000 Phase II Small Business Innovation Grant (SBIR) from the National Science Foundation to assess potential toxic effects of chemicals on the development of human organs and tissues using a panel of assays performed in zebrafish.
"This award validates the importance of zebrafish as a predictive model for assessing toxic effects of environmental contaminants on mammalian development," commented Patricia McGrath, Phylonix President and Chief Executive Officer. "Our preliminary data show a striking correlation between results in zebrafish and results in mammals."
All essential components of vertebrate form and organ development are mimicked in the transparent zebrafish and their molecular basis is either identical or similar, underscoring the potential for use in research on human developmental toxicity. "Using our comprehensive ZETAXTM panel of assays, effects on morphology, organ development, neurons and cell death can easily be assessed in the transparent animal. Compounds are added directly to the fish water and results are assessed in 4 to 7 days. Endpoints can be quantitated using comparatively high through-put scanning image analysis or microplate formats," McGrath continued.
Currently, 85,000 industrial chemicals are manufactured each year in the United States and 2,000 to 3,000 new chemicals are registered for production. However, there is little or no toxicity data for more than 70% of these chemicals. The lack of efficient in vivo screening assays contributes to the lack of knowledge about short and long-term chemical effects on development. Pesticides are of particular concern, since they are designed to be toxic to insects and they can have deleterious effects on other species.
Historically, zebrafish have been used in a variety of applications to assess environmental toxicity, including directly monitoring water, soil and wastewater quality for ecotoxicity studies. However, a systematic analysis of effects in vivo in this model organism has not been performed.
About Phylonix
Phylonix Pharmaceuticals, Inc. (phylonix) is a Contract Research Organization developing and marketing novel in vivo zebrafish-based assays, eZ-ScreensTM, for assessing chemical and drug effects on developmental defects, cancers, central nervous system disorders, cardiovascular diseases, apoptosis, and organ toxicity. The company's business strategy is to leverage the speed and cost-effectiveness of the zebrafish model to provide services for industrial and biopharmaceutical companies.
Contact: Patricia McGrath
Phylonix
"This award validates the importance of zebrafish as a predictive model for assessing toxic effects of environmental contaminants on mammalian development," commented Patricia McGrath, Phylonix President and Chief Executive Officer. "Our preliminary data show a striking correlation between results in zebrafish and results in mammals."
All essential components of vertebrate form and organ development are mimicked in the transparent zebrafish and their molecular basis is either identical or similar, underscoring the potential for use in research on human developmental toxicity. "Using our comprehensive ZETAXTM panel of assays, effects on morphology, organ development, neurons and cell death can easily be assessed in the transparent animal. Compounds are added directly to the fish water and results are assessed in 4 to 7 days. Endpoints can be quantitated using comparatively high through-put scanning image analysis or microplate formats," McGrath continued.
Currently, 85,000 industrial chemicals are manufactured each year in the United States and 2,000 to 3,000 new chemicals are registered for production. However, there is little or no toxicity data for more than 70% of these chemicals. The lack of efficient in vivo screening assays contributes to the lack of knowledge about short and long-term chemical effects on development. Pesticides are of particular concern, since they are designed to be toxic to insects and they can have deleterious effects on other species.
Historically, zebrafish have been used in a variety of applications to assess environmental toxicity, including directly monitoring water, soil and wastewater quality for ecotoxicity studies. However, a systematic analysis of effects in vivo in this model organism has not been performed.
About Phylonix
Phylonix Pharmaceuticals, Inc. (phylonix) is a Contract Research Organization developing and marketing novel in vivo zebrafish-based assays, eZ-ScreensTM, for assessing chemical and drug effects on developmental defects, cancers, central nervous system disorders, cardiovascular diseases, apoptosis, and organ toxicity. The company's business strategy is to leverage the speed and cost-effectiveness of the zebrafish model to provide services for industrial and biopharmaceutical companies.
Contact: Patricia McGrath
Phylonix
In New Way To Manipulate Matter, Mechanics Meets Chemistry
The inventors of self-healing plastic have come up with another invention: a new way of doing chemistry.
Researchers at the University of Illinois at Urbana-Champaign have found a novel way to manipulate matter and drive chemical reactions along a desired direction. The new technique utilizes mechanical force to alter the course of chemical reactions and yield products not obtainable through conventional conditions.
Potential applications include materials that more readily repair themselves, or clearly indicate when they have been damaged.
"This is a fundamentally new way of doing chemistry," said Jeffrey Moore, a William H. and Janet Lycan Professor of Chemistry at Illinois and corresponding author of a paper that describes the technique in the March 22 issue of the journal Nature.
"By harnessing mechanical energy, we can go into molecules and pull on specific bonds to drive desired reactions," said Moore, who also is a researcher at the Frederick Seitz Materials Laboratory on campus and at the university's Beckman Institute for Advanced Science and Technology. The directionally specific nature of mechanical force makes this approach to reaction control fundamentally different from the usual chemical and physical constraints. To demonstrate the technique, Moore and colleagues placed a mechanically active molecule - called a mechanophore - at the center of a long polymer chain. The polymer chain was then stretched in opposite directions by a flow field created by the collapse of cavitating bubbles produced by ultrasound, subjecting the mechanophore to a mechanical tug of war.
"We created a situation where a chemical reaction could go down one of two pathways," Moore said. "By applying force to the mechanophore, we could bias which of those pathways the reaction chose to follow."
One potential application of the technique is as a trigger to divert mechanical energy stored in stressed polymers into chemical pathways such as self-healing reactions.
In the original self-healing concept, microcapsules of healing agent are ruptured when a crack forms in the material. Capillary action then transports the healing agent to the crack, where it mixes with a chemical catalyst, and polymerization takes place.
With new mechanical triggers, however, mechanical energy would initiate the polymerization directly, thereby skipping many steps. The cross-linking of neighboring chains would prevent further propagation of a crack and avoid additional damage.
"We have demonstrated that it is now possible to use mechanical force to steer chemical reactions along pathways that are unattainable by conventional means," Moore said. "We look forward to developing additional mechanophores whose chemical reactivity will be activated by external force."
The other authors of the paper besides Moore are graduate student and lead author Charles Hickenboth, aerospace engineering professor Scott White, materials science and engineering professor Nancy Sottos, and research chemists Scott Wilson and Jerome Baudry. White, Sottos and Moore co-invented self-healing plastic.
The work was supported by the U.S. Air Force Office of Scientific Research and the Petroleum Research Fund.
Contact: James E. Kloeppel
University of Illinois at Urbana-Champaign
Researchers at the University of Illinois at Urbana-Champaign have found a novel way to manipulate matter and drive chemical reactions along a desired direction. The new technique utilizes mechanical force to alter the course of chemical reactions and yield products not obtainable through conventional conditions.
Potential applications include materials that more readily repair themselves, or clearly indicate when they have been damaged.
"This is a fundamentally new way of doing chemistry," said Jeffrey Moore, a William H. and Janet Lycan Professor of Chemistry at Illinois and corresponding author of a paper that describes the technique in the March 22 issue of the journal Nature.
"By harnessing mechanical energy, we can go into molecules and pull on specific bonds to drive desired reactions," said Moore, who also is a researcher at the Frederick Seitz Materials Laboratory on campus and at the university's Beckman Institute for Advanced Science and Technology. The directionally specific nature of mechanical force makes this approach to reaction control fundamentally different from the usual chemical and physical constraints. To demonstrate the technique, Moore and colleagues placed a mechanically active molecule - called a mechanophore - at the center of a long polymer chain. The polymer chain was then stretched in opposite directions by a flow field created by the collapse of cavitating bubbles produced by ultrasound, subjecting the mechanophore to a mechanical tug of war.
"We created a situation where a chemical reaction could go down one of two pathways," Moore said. "By applying force to the mechanophore, we could bias which of those pathways the reaction chose to follow."
One potential application of the technique is as a trigger to divert mechanical energy stored in stressed polymers into chemical pathways such as self-healing reactions.
In the original self-healing concept, microcapsules of healing agent are ruptured when a crack forms in the material. Capillary action then transports the healing agent to the crack, where it mixes with a chemical catalyst, and polymerization takes place.
With new mechanical triggers, however, mechanical energy would initiate the polymerization directly, thereby skipping many steps. The cross-linking of neighboring chains would prevent further propagation of a crack and avoid additional damage.
"We have demonstrated that it is now possible to use mechanical force to steer chemical reactions along pathways that are unattainable by conventional means," Moore said. "We look forward to developing additional mechanophores whose chemical reactivity will be activated by external force."
The other authors of the paper besides Moore are graduate student and lead author Charles Hickenboth, aerospace engineering professor Scott White, materials science and engineering professor Nancy Sottos, and research chemists Scott Wilson and Jerome Baudry. White, Sottos and Moore co-invented self-healing plastic.
The work was supported by the U.S. Air Force Office of Scientific Research and the Petroleum Research Fund.
Contact: James E. Kloeppel
University of Illinois at Urbana-Champaign
Similar Influence Found Of Sex And Handedness On Brain In Capuchin Monkeys And Humans
Capuchin monkeys are playful, inquisitive primates known for their manual dexterity, complex social behavior, and cognitive abilities. New research now shows that just like humans, they display a fundamental sex difference in the organization of the brain, specifically in the corpus callosum, the region that connects the two cerebral lobes.
A recently published paper by Associate Professor of Psychology and Biology Kimberley A. Phillips (Hiram College), Chet C. Sherwood (George Washington University) and Alayna L. Lilak (Hiram College), reports finding both sex and handedness influences on the relative size of the corpus callosum. The researchers' contribution appears in PLoS ONE, the online, open-access journal of the Public Library of Science. The paper can be read at: plosone/doi/pone.0000792.
In the study, thirteen adult capuchins underwent magnetic resonance imaging of the brain to determine the size of their corpus callosum, which is the major white matter tract connecting the left and right cerebral hemispheres. The monkeys were later given a task to determine hand preference. The authors' results led them to conclude that, as in humans, male capuchins have a smaller relative size of the corpus callosum than females, and right-handed individuals have a smaller relative size of the corpus callosum than left-handed individuals.
As the two hemispheres show greater independence of function, the relative size of the corpus callosum is expected to be smaller. This has been documented in humans, and same pattern was found in capuchins. Phillips and her co-authors hypothesize their results are related to hemispheric specialization for complex foraging tasks that require the integration of motor actions and visuospatial information. In the wild, capuchin monkeys utilize both arboreal and terrestrial substrates and are also noted for being very adept at capturing small rapid prey, such as birds, lizards, and squirrels.
While such research frequently is associated with large research universities, Phillips says scientists at small liberal arts colleges such as Hiram often do not receive enough credit and, especially, for involving undergraduates, such as Lilak, in their work.
"It is not where you are," Phillips says. "It is the quality of the science, and scientists at small liberal arts colleges can and do conduct high-quality research. Undergraduates are an integral part of my research team - they participate in lab meetings, brainstorming, sharing ideas. They are colleagues in my lab. They just need a little more mentoring."
Disclaimer
The following press release refers to an upcoming article in PLoS ONE. The release has been provided by the article authors and/or their institutions. Any opinions expressed in this are the personal views of the contributors, and do not necessarily represent the views or policies of PLoS. PLoS expressly disclaims any and all warranties and liability in connection with the information found in the release and article and your use of such information.
At Hiram College, Phillips typically has six to eight students working in her laboratory. Alayna Lilak, who received her degree in psychology in May, has recently begun a job as a research technician in a Stanford University lab.
Citation: Phillips KA, Sherwood CC, Lilak AL (2007) Corpus Callosum Morphology in Capuchin Monkeys Is Influenced by Sex and Handedness. PLoS ONE 2(8): e792.doi:10.1371/journal.pone.0000792
Click here for a link to the published article.
Source: Steve Love
Public Library of Science
A recently published paper by Associate Professor of Psychology and Biology Kimberley A. Phillips (Hiram College), Chet C. Sherwood (George Washington University) and Alayna L. Lilak (Hiram College), reports finding both sex and handedness influences on the relative size of the corpus callosum. The researchers' contribution appears in PLoS ONE, the online, open-access journal of the Public Library of Science. The paper can be read at: plosone/doi/pone.0000792.
In the study, thirteen adult capuchins underwent magnetic resonance imaging of the brain to determine the size of their corpus callosum, which is the major white matter tract connecting the left and right cerebral hemispheres. The monkeys were later given a task to determine hand preference. The authors' results led them to conclude that, as in humans, male capuchins have a smaller relative size of the corpus callosum than females, and right-handed individuals have a smaller relative size of the corpus callosum than left-handed individuals.
As the two hemispheres show greater independence of function, the relative size of the corpus callosum is expected to be smaller. This has been documented in humans, and same pattern was found in capuchins. Phillips and her co-authors hypothesize their results are related to hemispheric specialization for complex foraging tasks that require the integration of motor actions and visuospatial information. In the wild, capuchin monkeys utilize both arboreal and terrestrial substrates and are also noted for being very adept at capturing small rapid prey, such as birds, lizards, and squirrels.
While such research frequently is associated with large research universities, Phillips says scientists at small liberal arts colleges such as Hiram often do not receive enough credit and, especially, for involving undergraduates, such as Lilak, in their work.
"It is not where you are," Phillips says. "It is the quality of the science, and scientists at small liberal arts colleges can and do conduct high-quality research. Undergraduates are an integral part of my research team - they participate in lab meetings, brainstorming, sharing ideas. They are colleagues in my lab. They just need a little more mentoring."
Disclaimer
The following press release refers to an upcoming article in PLoS ONE. The release has been provided by the article authors and/or their institutions. Any opinions expressed in this are the personal views of the contributors, and do not necessarily represent the views or policies of PLoS. PLoS expressly disclaims any and all warranties and liability in connection with the information found in the release and article and your use of such information.
At Hiram College, Phillips typically has six to eight students working in her laboratory. Alayna Lilak, who received her degree in psychology in May, has recently begun a job as a research technician in a Stanford University lab.
Citation: Phillips KA, Sherwood CC, Lilak AL (2007) Corpus Callosum Morphology in Capuchin Monkeys Is Influenced by Sex and Handedness. PLoS ONE 2(8): e792.doi:10.1371/journal.pone.0000792
Click here for a link to the published article.
Source: Steve Love
Public Library of Science
Identification Of The Molecule That Helps The Sleep-Deprived To Mentally Rebound
Sleep experts know that the mental clarity lost because of a few sleepless nights can often be restored with a good night's rest. Now, UT Southwestern Medical Center researchers have identified a key molecular mechanism that regulates the brain's ability to mentally compensate for sleep deprivation.
Working with mice, they found that a molecule called an adenosine receptor is necessary for sleep-restricted animals to attain adequate levels of slow-wave activity in the brain once normal sleep resumes. It is this increase in slow-wave activity, or SWA, during rebound sleep that helps restore normal working memory and attention skills to the sleep-deprived, the scientists report in the Feb. 4 issue of the Journal of Neuroscience.
"Normal society pushes people to burn candles at both ends - going to bed late, getting up early, and somehow performing mentally with lack of adequate sleep," said senior author Dr. Robert Greene, professor of psychiatry at UT Southwestern. "We need to have our adenosine receptors intact to do that."
Adenosine receptors on nerve cells, including brain cells, are akin to docking points for the molecule adenosine. Adenosine levels increase in the brain with each hour of waking activity, and "docking" of the molecule with its receptor is shown in this study to help promote the slow-wave activity of sleep. Scientists have known that recovery from sleep deprivation involves not only an increase in sleep time, or rebound sleep, but also an elevation in this slow-wave activity.
To investigate how adenosine receptors and SWA might be linked, Dr. Greene and his team engineered mice that lacked a receptor to pair up with adenosine.
Sleep-restricted mice were kept awake by being placed on a moving treadmill. Researchers then electronically monitored sleep and waking activity of both normal and genetically engineered mice, including monitoring electronically the brain waves of the animals. The mice also traveled a maze with eight paths, each with a piece of chocolate at the end of it.
Electronic measurements showed that, unlike normal mice, the mice lacking the adenosine receptor could not increase the intensity of their slow-wave activity in response to the sleep deprivation. Under normal sleep conditions both the normal and mutant mice were almost error-free on the maze test. However, when sleep-deprived, the engineered mice made significantly more errors on the maze test than their normal counterparts. This type of skills test represents the human equivalent of the attention and working memory needed to multitask or build on tasks already done, such as being given a phone number, reaching for a pen to write it down and recalling the number, said Dr. Greene.
Linking the lack of functioning adenosine receptors to depressed normal SWA rebound response might aid in developing treatments for people with sleep-related cognitive deficits, he said.
The research also further explains the effects of caffeine, which also "docks" to adenosine receptors, preventing the docking of adenosine and keeping the caffeine-drinker awake. Dr. Greene compared the study mice's behavior response on the maze test to how a person drinking a "permanent cup of coffee" might behave.
"They probably won't get the regular amount of slow-wave activity or deep sleep as they normally would," Dr. Greene said. "This is not to say that coffee is bad, but drinking it all the time or in the evening could affect your mental performance the next day."
The researchers next will investigate the relationship between sleep, adenosine and energy metabolism, a biological process in which adenosine plays a key role.
Other researchers from UT Southwestern involved in the study were lead author Dr. Theresa Bjorness, postdoctoral research fellow in psychiatry, and Virginia Poffenberger, research technician in psychiatry.
The study was funded by the U.S. Department of Veterans Affairs and the National Institutes of Health.
Visit utsouthwestern/neurosciences to learn more about UT Southwestern's clinical services in the neurosciences, including psychiatry.
Source: LaKisha Ladson
UT Southwestern Medical Center
Working with mice, they found that a molecule called an adenosine receptor is necessary for sleep-restricted animals to attain adequate levels of slow-wave activity in the brain once normal sleep resumes. It is this increase in slow-wave activity, or SWA, during rebound sleep that helps restore normal working memory and attention skills to the sleep-deprived, the scientists report in the Feb. 4 issue of the Journal of Neuroscience.
"Normal society pushes people to burn candles at both ends - going to bed late, getting up early, and somehow performing mentally with lack of adequate sleep," said senior author Dr. Robert Greene, professor of psychiatry at UT Southwestern. "We need to have our adenosine receptors intact to do that."
Adenosine receptors on nerve cells, including brain cells, are akin to docking points for the molecule adenosine. Adenosine levels increase in the brain with each hour of waking activity, and "docking" of the molecule with its receptor is shown in this study to help promote the slow-wave activity of sleep. Scientists have known that recovery from sleep deprivation involves not only an increase in sleep time, or rebound sleep, but also an elevation in this slow-wave activity.
To investigate how adenosine receptors and SWA might be linked, Dr. Greene and his team engineered mice that lacked a receptor to pair up with adenosine.
Sleep-restricted mice were kept awake by being placed on a moving treadmill. Researchers then electronically monitored sleep and waking activity of both normal and genetically engineered mice, including monitoring electronically the brain waves of the animals. The mice also traveled a maze with eight paths, each with a piece of chocolate at the end of it.
Electronic measurements showed that, unlike normal mice, the mice lacking the adenosine receptor could not increase the intensity of their slow-wave activity in response to the sleep deprivation. Under normal sleep conditions both the normal and mutant mice were almost error-free on the maze test. However, when sleep-deprived, the engineered mice made significantly more errors on the maze test than their normal counterparts. This type of skills test represents the human equivalent of the attention and working memory needed to multitask or build on tasks already done, such as being given a phone number, reaching for a pen to write it down and recalling the number, said Dr. Greene.
Linking the lack of functioning adenosine receptors to depressed normal SWA rebound response might aid in developing treatments for people with sleep-related cognitive deficits, he said.
The research also further explains the effects of caffeine, which also "docks" to adenosine receptors, preventing the docking of adenosine and keeping the caffeine-drinker awake. Dr. Greene compared the study mice's behavior response on the maze test to how a person drinking a "permanent cup of coffee" might behave.
"They probably won't get the regular amount of slow-wave activity or deep sleep as they normally would," Dr. Greene said. "This is not to say that coffee is bad, but drinking it all the time or in the evening could affect your mental performance the next day."
The researchers next will investigate the relationship between sleep, adenosine and energy metabolism, a biological process in which adenosine plays a key role.
Other researchers from UT Southwestern involved in the study were lead author Dr. Theresa Bjorness, postdoctoral research fellow in psychiatry, and Virginia Poffenberger, research technician in psychiatry.
The study was funded by the U.S. Department of Veterans Affairs and the National Institutes of Health.
Visit utsouthwestern/neurosciences to learn more about UT Southwestern's clinical services in the neurosciences, including psychiatry.
Source: LaKisha Ladson
UT Southwestern Medical Center
Environmental Problems Could Be Reduced By More Recycling On The Farm
Growing environmental problems resulting from farming argue for a shift toward practices that use lower inputs of pesticides and energy and more recycling of energy and materials, according to an article published in the May 2007 issue of BioScience. The author, Craig J. Pearson of the University of Guelph, documents how semiclosed agricultural systems -- which he terms "regenerative" -- could enhance global sustainability of biological resources, curtail greenhouse gas emissions and groundwater contamination, and reduce farming's reliance on oil imports and water.
A switch to regenerative agriculture would involve a variety of changes, including reduced use of inorganic fertilizers and more on-farm energy generation from wind and fermentation of biosolids. It would also reduce overcropping and leakage from manure storage that contaminates groundwater. Yet despite similarities, Pearson's concept of regenerative agriculture is distinct from organic farming; for example, regenerative agriculture could use some chemically treated fertilizer and would exploit robotic systems.
The approach would entail more use of human labor, which is costly, and may reduce output per unit area farmed. Pearson summarizes studies of organic farming suggesting, however, that price premiums could overcome this disadvantage, and points out that social benefits could be expected. Pearson argues that existing funding programs for farmers could be modified to encourage more regenerative agriculture, and suggests that philanthropists and professional bodies could stimulate its uptake.
BioScience, which is published by the American Institute of Biological Sciences (AIBS), publishes commentary and peer-reviewed articles covering a wide range of biological fields, with a focus on "organisms from molecules to the environment." The journal has been published since 1964. AIBS is an umbrella organization for professional scientific societies and organizations that are involved with biology. It represents some 200 member societies and organizations with a combined membership of about 250,000.
Contact: Samantha Katz
American Institute of Biological Sciences
A switch to regenerative agriculture would involve a variety of changes, including reduced use of inorganic fertilizers and more on-farm energy generation from wind and fermentation of biosolids. It would also reduce overcropping and leakage from manure storage that contaminates groundwater. Yet despite similarities, Pearson's concept of regenerative agriculture is distinct from organic farming; for example, regenerative agriculture could use some chemically treated fertilizer and would exploit robotic systems.
The approach would entail more use of human labor, which is costly, and may reduce output per unit area farmed. Pearson summarizes studies of organic farming suggesting, however, that price premiums could overcome this disadvantage, and points out that social benefits could be expected. Pearson argues that existing funding programs for farmers could be modified to encourage more regenerative agriculture, and suggests that philanthropists and professional bodies could stimulate its uptake.
BioScience, which is published by the American Institute of Biological Sciences (AIBS), publishes commentary and peer-reviewed articles covering a wide range of biological fields, with a focus on "organisms from molecules to the environment." The journal has been published since 1964. AIBS is an umbrella organization for professional scientific societies and organizations that are involved with biology. It represents some 200 member societies and organizations with a combined membership of about 250,000.
Contact: Samantha Katz
American Institute of Biological Sciences
Pacific Rim researchers to collaborate on distributed bioinformatics analysis of avian flu
Researchers at the University of California, San Diego and the University of Hawaii will use bioinformatics, grid computing and networking infrastructure, as well as collaborative ties to Asian institutions to learn more about avian flu, in hopes of helping to head off a much-feared pandemic in the region of the world where the disease has already cost human lives.
"We will use modern high-throughput biology to annotate the biological structures of different subtypes of the avian influenza virus, at the same time as we study their variations," said principal investigator Peter Arzberger, director of Life Science Initiatives at UC San Diego. "We will also construct a grid infrastructure to support avian flu research - an infrastructure that could one day handle research on other infectious diseases as well."
Added Arzberger: "Fighting a pandemic will also be easier if we put in place the infrastructure to replicate data, support medical informatics, and even assist in remote diagnosis."
UC San Diego will lead the one-year project, with more than $350,000 in funding from the Telemedicine and Advanced Technology Research Center (TATRC), part of the U.S. Army Medical Research and Material Command (USAMRMC). TATRC invests in telemedicine and advanced medical technologies in order to deliver world-class health care to military personnel. The increasing frequency of biological events relevant to national security, and current disease surveillance systems in the United States (U.S.) require an integrated computational environment to support easy access to a set of universal tools, novel algorithmic approaches and tracking mechanisms for reproducibility at a global level.
Having Asian researchers involved in the TATRC-funded project lends an added dimension of urgency and depth to the U.S. research program. "Avian flu is very important to sites worldwide, but especially in Asia, where most of the known cases have occurred," said Wilfred Li, executive director of the UC San Diego-based National Biomedical Computation Resource (NBCR). "This partnership will give U.S. researchers enhanced access to new genomic information as it becomes available in the region. It will also promote global cooperation in case of a flu pandemic." Institutions in three Asian nations will leverage TATRC's investment by funding their own researchers to work with their counterparts in California and Hawaii, as part of their ongoing collaboration in the National Science Foundation-funded Pacific Rim Applications and Grid Middleware Assembly (PRAGMA).
"We could not be successful in this project without the substantial prior investment in partnerships with our friends and colleagues across the Pacific," said Arzberger, who directs the five-year-old PRAGMA initiative. "We will be able to hit the ground running thanks to the shared expertise, interconnected cyberinfrastructure, grid-enabled software tools and student exchange programs that have emerged out of PRAGMA."
Pacific Rim institutions collaborate in PRAGMA to develop grid-enabled applications and coordinate deployment of the needed infrastructure throughout the Pacific region to allow data, computing, and other resource sharing. The announcement of the TATRC award coincided with PRAGMA 12, which ran March 20-22 in Bangkok, Thailand. The meeting was hosted by Thailand's National Electronics and Computer Technology Center (NECTEC), and the Thai National Grid Center (TGNC).
Five non-U.S. partners have pledged to fund collaboration on the avian flu virus project: Japan's National Institute for Advanced Industrial Science and Technology (AIST); China's Jilin University (JLU) and Computer Network Information Center (CNIC); as well as the Korea Institute for Science and Technology Information (KISTI) and Konkuk University (KU). Significantly, Malaysia's Universiti Sains Malaysia (USM) has pledged new funding for the collaborative project at the PRAGMA 12 workshop.
Flu vaccines are usually developed using attenuated viruses, but the new focus is on the use of reverse genetics techniques to combat emerging bird flu pandemic threats. To that end, researchers intend to:
* Characterize the function of the influenza viruses using a structure-based approach;
* Develop simulations of the molecular dynamics involving interactions among major factors that may determine the virulence of a virus; and
* Test whether the multinational collaboration can establish a successful, large-scale, distributed computational data grid.
Scientists at UC San Diego, the California Institute for Telecommunications and Information Technology (Calit2) and San Diego Supercomputer Center (SDSC) will use bioinformatics software, including the integrated Genome Analysis Pipeline (iGAP), to analyze avian flu genomes. (The iGAP suite of bioinformatics applications are designed specifically for protein structural homology recognition and functional annotation.) The San Diego-based researchers will also develop a robust production environment for routine computational analysis, using PRAGMA member-developed tools, including Grid Datafarm (Gfarm) and Community Scheduler Framework (CSF4), while making any new software publicly available through open-source licenses.
The funding to the University of Hawaii will allow it to become a node in the computational grid - allowing it to access data for molecular-dynamics simulations using high-performance computing. "We need a better way to gain insight into the interactions among factors determining how virulent a particular type of flu might be, and this will require a lot of raw computing power," said Maqsudul Alam, director at the Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii. "This will allow us to analyze the biosynthetic pathways of viruses as well as the signal transduction pathways for clues to understanding how avian flu interferes with human metabolism."
The Asian institutions - all members of PRAGMA - will host some U.S. students and researchers, while taking responsibility for specific tasks:
* JLU will support the scheduling of multiple clusters (CSF4) to distribute jobs transparently at multiple sites around the region;
* AIST will support the deployment of Gfarm in conjunction with researchers at the University of Tsukuba;
* KISTI in conjunction with researchers at KU in Korea will create an integrated portal environment for the computational pipeline using results of Korea National e-Science Project by the Korean Ministry of Science and Technology (MOST); and
* CNIC will develop a transparent web service layer for data access.
* USM will contribute its natural compound database for use in virtual screening for new inhibitors and drug discovery.
CNIC will also become the central repository for the project's research data. The database will be distributed through the computational data grid, and accessible through web portals mirrored at partner sites. "The availability of a central repository that is built upon distributed information and data storage not only allows one to collect information more effectively, but also makes the data immediately available to researchers worldwide," said Kai Nan, director of CNIC's Network Technology and Applications Research Laboratory. "The end result is a dynamic research community response network that can meet the needs of a global response to a global threat such as the avian flu."
Much of the nitty-gritty work on the avian flu project will be done by students, at both the graduate and undergraduate level. "We'll be engaging students from the above institutions as an international research team," said NBCR's Li. "We will also send U.S. students and graduate researchers to work in the labs of our partners around Asia - giving those students an experience that will equip them to do ongoing research in this field." This activity also leverages NSF's investment in the Pacific Rim undergraduate Education (PRIME) project, an undergraduate research abroad program awarded to UCSD.
"The next step for PRAGMA is a pragmatic one - to demonstrate that international team science can address pressing challenges in a way that might not be possible in one institution or just one country," said Arzberger. "We expect that this project will engage other researchers, both in other PRAGMA sites, e.g., at USM in Malaysia, and also at the National Biomedical Computation Resource, through the complementary, ongoing Avian flu Drug Discovery project led by professors J. Andrew McCammon and Art Olson of NBCR, by sharing expertise and resources."
Related Links
TATRC tatrc
PRAGMA pragma-grid/
PRAGMA 12 pragma12.thai-research/pragma12/index.php/Main_Page
NECTEC nectec.or.th/
TGNC thaigrid.or.th/index.php
NBCR nbcr
PRIME prime.ucsd
Calit2 calit2
SDSC sdsc
UCSD ucsd
Contact: Doug Ramsey
University of California - San Diego
"We will use modern high-throughput biology to annotate the biological structures of different subtypes of the avian influenza virus, at the same time as we study their variations," said principal investigator Peter Arzberger, director of Life Science Initiatives at UC San Diego. "We will also construct a grid infrastructure to support avian flu research - an infrastructure that could one day handle research on other infectious diseases as well."
Added Arzberger: "Fighting a pandemic will also be easier if we put in place the infrastructure to replicate data, support medical informatics, and even assist in remote diagnosis."
UC San Diego will lead the one-year project, with more than $350,000 in funding from the Telemedicine and Advanced Technology Research Center (TATRC), part of the U.S. Army Medical Research and Material Command (USAMRMC). TATRC invests in telemedicine and advanced medical technologies in order to deliver world-class health care to military personnel. The increasing frequency of biological events relevant to national security, and current disease surveillance systems in the United States (U.S.) require an integrated computational environment to support easy access to a set of universal tools, novel algorithmic approaches and tracking mechanisms for reproducibility at a global level.
Having Asian researchers involved in the TATRC-funded project lends an added dimension of urgency and depth to the U.S. research program. "Avian flu is very important to sites worldwide, but especially in Asia, where most of the known cases have occurred," said Wilfred Li, executive director of the UC San Diego-based National Biomedical Computation Resource (NBCR). "This partnership will give U.S. researchers enhanced access to new genomic information as it becomes available in the region. It will also promote global cooperation in case of a flu pandemic." Institutions in three Asian nations will leverage TATRC's investment by funding their own researchers to work with their counterparts in California and Hawaii, as part of their ongoing collaboration in the National Science Foundation-funded Pacific Rim Applications and Grid Middleware Assembly (PRAGMA).
"We could not be successful in this project without the substantial prior investment in partnerships with our friends and colleagues across the Pacific," said Arzberger, who directs the five-year-old PRAGMA initiative. "We will be able to hit the ground running thanks to the shared expertise, interconnected cyberinfrastructure, grid-enabled software tools and student exchange programs that have emerged out of PRAGMA."
Pacific Rim institutions collaborate in PRAGMA to develop grid-enabled applications and coordinate deployment of the needed infrastructure throughout the Pacific region to allow data, computing, and other resource sharing. The announcement of the TATRC award coincided with PRAGMA 12, which ran March 20-22 in Bangkok, Thailand. The meeting was hosted by Thailand's National Electronics and Computer Technology Center (NECTEC), and the Thai National Grid Center (TGNC).
Five non-U.S. partners have pledged to fund collaboration on the avian flu virus project: Japan's National Institute for Advanced Industrial Science and Technology (AIST); China's Jilin University (JLU) and Computer Network Information Center (CNIC); as well as the Korea Institute for Science and Technology Information (KISTI) and Konkuk University (KU). Significantly, Malaysia's Universiti Sains Malaysia (USM) has pledged new funding for the collaborative project at the PRAGMA 12 workshop.
Flu vaccines are usually developed using attenuated viruses, but the new focus is on the use of reverse genetics techniques to combat emerging bird flu pandemic threats. To that end, researchers intend to:
* Characterize the function of the influenza viruses using a structure-based approach;
* Develop simulations of the molecular dynamics involving interactions among major factors that may determine the virulence of a virus; and
* Test whether the multinational collaboration can establish a successful, large-scale, distributed computational data grid.
Scientists at UC San Diego, the California Institute for Telecommunications and Information Technology (Calit2) and San Diego Supercomputer Center (SDSC) will use bioinformatics software, including the integrated Genome Analysis Pipeline (iGAP), to analyze avian flu genomes. (The iGAP suite of bioinformatics applications are designed specifically for protein structural homology recognition and functional annotation.) The San Diego-based researchers will also develop a robust production environment for routine computational analysis, using PRAGMA member-developed tools, including Grid Datafarm (Gfarm) and Community Scheduler Framework (CSF4), while making any new software publicly available through open-source licenses.
The funding to the University of Hawaii will allow it to become a node in the computational grid - allowing it to access data for molecular-dynamics simulations using high-performance computing. "We need a better way to gain insight into the interactions among factors determining how virulent a particular type of flu might be, and this will require a lot of raw computing power," said Maqsudul Alam, director at the Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii. "This will allow us to analyze the biosynthetic pathways of viruses as well as the signal transduction pathways for clues to understanding how avian flu interferes with human metabolism."
The Asian institutions - all members of PRAGMA - will host some U.S. students and researchers, while taking responsibility for specific tasks:
* JLU will support the scheduling of multiple clusters (CSF4) to distribute jobs transparently at multiple sites around the region;
* AIST will support the deployment of Gfarm in conjunction with researchers at the University of Tsukuba;
* KISTI in conjunction with researchers at KU in Korea will create an integrated portal environment for the computational pipeline using results of Korea National e-Science Project by the Korean Ministry of Science and Technology (MOST); and
* CNIC will develop a transparent web service layer for data access.
* USM will contribute its natural compound database for use in virtual screening for new inhibitors and drug discovery.
CNIC will also become the central repository for the project's research data. The database will be distributed through the computational data grid, and accessible through web portals mirrored at partner sites. "The availability of a central repository that is built upon distributed information and data storage not only allows one to collect information more effectively, but also makes the data immediately available to researchers worldwide," said Kai Nan, director of CNIC's Network Technology and Applications Research Laboratory. "The end result is a dynamic research community response network that can meet the needs of a global response to a global threat such as the avian flu."
Much of the nitty-gritty work on the avian flu project will be done by students, at both the graduate and undergraduate level. "We'll be engaging students from the above institutions as an international research team," said NBCR's Li. "We will also send U.S. students and graduate researchers to work in the labs of our partners around Asia - giving those students an experience that will equip them to do ongoing research in this field." This activity also leverages NSF's investment in the Pacific Rim undergraduate Education (PRIME) project, an undergraduate research abroad program awarded to UCSD.
"The next step for PRAGMA is a pragmatic one - to demonstrate that international team science can address pressing challenges in a way that might not be possible in one institution or just one country," said Arzberger. "We expect that this project will engage other researchers, both in other PRAGMA sites, e.g., at USM in Malaysia, and also at the National Biomedical Computation Resource, through the complementary, ongoing Avian flu Drug Discovery project led by professors J. Andrew McCammon and Art Olson of NBCR, by sharing expertise and resources."
Related Links
TATRC tatrc
PRAGMA pragma-grid/
PRAGMA 12 pragma12.thai-research/pragma12/index.php/Main_Page
NECTEC nectec.or.th/
TGNC thaigrid.or.th/index.php
NBCR nbcr
PRIME prime.ucsd
Calit2 calit2
SDSC sdsc
UCSD ucsd
Contact: Doug Ramsey
University of California - San Diego
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