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Genetic diversity of the species significantly increased providing fresh hope for the future survival of this near-extinct species

Date:
August 13, 2015

Source:
Lincoln Park Zoo

Summary:
Black-footed ferrets, a critically endangered species native to North America, have renewed hope for future survival thanks to successful efforts by a coalition of conservationists, to reproduce genetically important offspring using frozen semen from a ferret who has been dead for approximately 20 years. The sire, ‘Scarface,’ as he is affectionately called, was one of the last 18 black-footed ferrets to exist in the world in the 1980s.

 

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Initially, scientists used fresh semen to artificially inseminate females who failed to naturally mate with males, resulting in 135 kits. With just a few founders to rebuild an entire species, early managers of the black-footed ferret recovery program knew that genetic diversity would be lost.
Credit: © flytoskyft11 / Fotolia

 

 

Black-footed ferrets, a critically endangered species native to North America, have renewed hope for future survival thanks to successful efforts by a coalition of conservationists, including scientists at Lincoln Park Zoo, to reproduce genetically important offspring using frozen semen from a ferret who has been dead for approximately 20 years. The sire, “Scarface,” as he is affectionately called by the team, was one of the last 18 black-footed ferrets to exist in the world in the 1980s. Eight kits, including offspring of Scarface, were born recently, significantly increasing the gene diversity of this endangered population that a dedicated team is working to recover in the wild.

Their work published Aug. 13 in the journal Animal Conservation “Recovery of Gene Diversity Using Long-Term Cryopreserved Spermatozoa and Artificial Insemination in the Endangered Black-Footed Ferret.”

Partners working to save black-footed ferrets from extinction, and recover a healthy population back to the wild include Lincoln Park Zoo, The Smithsonian Conservation Biology Institute (SCBI), U.S. Fish and Wildlife Service, Louisville Zoological Garden, Cheyenne Mountain Zoo, Phoenix Zoo and Toronto Zoo.

“Our study is the first to provide empirical evidence that artificial insemination with long-stored spermatozoa is not only possible but also beneficial to the genetic diversity of an endangered species,” said David Wildt, lead author, senior scientist and head of the Center for Species Survival at SCBI. “What we’ve done here with the black-footed ferret is an excellent example of how sperm preservation can benefit species recovery programs.”

The U.S. Fish and Wildlife Service developed and oversee the Black-Footed Ferret Recovery Program. The Association of Zoos and Aquariums’ Species Survival Plan manages the black-footed ferret breeding program at ex situ facilities, the breeding population in which is comprised of approximately 300 animals.

“The entire species survival depends on successful captive management to ensure healthy genetics over the next 100 years and to produce individuals for the reintroduction program,” explained Black-Footed Ferret Reproduction Advisor Rachel Santymire, PhD, director of the Davee Center for Endocrinology and Epidemiology at Lincoln Park Zoo. “To balance out these demands on the breeding program, we have to ensure that each individual ferret passes its genes on to the next generation.”

Over the past several years, the team has been developing assisted reproductive technology like artificial insemination and semen cryopreservation. For this study, all of the males were managed either at SCBI or at the USFWS National Black-Footed Ferret Conservation Center. Scientists collected semen samples from adult black-footed ferrets that ranged in age from one to six years old. All females were managed at SCBI.

Initially, scientists used fresh semen to artificially inseminate females who failed to naturally mate with males, resulting in 135 kits. With just a few founders to rebuild an entire species, early managers of the black-footed ferret recovery program knew that genetic diversity would be lost. Loss of genetic variation can lead to increased sperm malformation and lower success of pregnancy over time. Researchers, led by Santymire, routinely collected and preserved black-footed ferret semen for later use as part of standard operating procedures.

SCBI developed a successful laparoscopic artificial insemination technique for black-footed ferrets. Females are induced ovulators, which mean that mating itself causes the ovary to release its eggs. SCBI researchers developed a hormone treatment that artificially causes ovulation to occur. Scientists then deposited the male’s fresh or frozen-thawed sperm directly into the female’s uterus. Animal care staff closely monitored potentially pregnant females by taking weight measurements and remote monitoring of the nest boxes via closed-circuit cameras.

During the 2008 breeding season, SCBI scientists used semen samples from four male black-footed ferrets donors that had been frozen for 10 years. Black-footed ferret Population Advisor Colleen Lynch of Riverbanks Zoo and Garden conducted population genetic analysis to select pairings of deceased sperm donors with living females based on several genetic metrics including mean kinship of the parents and inbreeding coefficients of potential offspring to maximize the genetic benefit of successful pairings. In the years that followed, subsequent AIs incorporated semen that had been cryopreserved up to 20 years, also resulting in successful pregnancies.

“Our findings show how important it is to bank sperm and other biomaterials from rare and endangered animal species over time,” said Paul Marinari, senior curator at the Smithsonian Conservation Biology Institute. “These ‘snapshots’ of biodiversity could be invaluable to future animal conservation efforts, which is why we must make every effort to collect, store and study these materials now.”


Story Source:

The above post is reprinted from materials provided by Lincoln Park Zoo.Note: Materials may be edited for content and length.


Journal Reference:

  1. J. G. Howard, C. Lynch, R. M. Santymire, P. E. Marinari, D. E. Wildt.Recovery of gene diversity using long-term cryopreserved spermatozoa and artificial insemination in the endangered black-footed ferret. Animal Conservation, 2015; DOI: 10.1111/acv.12229

 

Source: Lincoln Park Zoo. “Critically endangered species successfully reproduced using frozen sperm from ferret dead for 20 years: Genetic diversity of the species significantly increased providing fresh hope for the future survival of this near-extinct species.” ScienceDaily. ScienceDaily, 13 August 2015. <www.sciencedaily.com/releases/2015/08/150813130242.htm>.

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How evolutionary biology in ants doesn’t play by the rules

Date:
August 11, 2015

Source:
Earlham College

Summary:
The evolutionary loss of the ‘altruistic’ worker caste in ants is not accompanied by a loss of genes, an international team of researchers has found. The results reported in this new research add to a growing body of literature suggesting that many traits may evolve by tweaks in the regulation of pre-existing genes and networks. Phenotype gain and loss may be facilitated by changes in the environment within and outside of the organism, not necessarily requiring changes to protein coding genes, just changes to when and how they are used.

 

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This image shows workers of the rough harvester ant, Pogonomyrmex rugosus, one of the host species used by the social parasites, and one of the genomes sequenced as part of the study.
Credit: Chris R. Smith, used with permission

 

 

An international team of researchers found that the evolutionary loss of the “altruistic” worker caste in ants is not accompanied by a loss of genes.

Social insects, such as ants, are typically characterized by two distinct female castes: workers and queens. Previous research has found that workers and queens each express different sets of genes leading scientists to speculate that there are worker specific or “altruistic” genes that promote sociality.

Testing this “novel gene” hypothesis is difficult given that all ants are social. However, not all ants make workers. Some ants are “workerless social parasites” whose queens exploit the worker force of other species by invading and setting up shop in their colonies. The authors took advantage of the unusual biology of these ants that have lost their worker caste to determine if worker genes really exist.

The research team, led by Chris R. Smith (Earlham College) and Alexander (Sasha) Mikheyev (Okinawa Institute of Science and Technology), sequenced and compared the genomes of six ants (3 hosts and 3 workerless social parasites) and looked for evidence that genes that are typically over expressed in the worker caste would degenerate through time when workers are no longer produced. Instead of finding degeneration in “worker” genes, they found that there are no “worker” genes and the majority of the protein coding genome is maintained in species that stopped producing workers even after one million years. Their research is online early in the journalMolecular Biology and Evolution.

“This was a total surprise, we hypothesized the opposite — when you lose a trait then the genes for that trait should disappear over time,” said Smith. “This result has two interesting implications: first, there don’t seem to be any genes that are explicitly ‘worker’ and thus truly ‘altruistic’, and two, that the loss of an entire body plan is not accompanied by a loss of genes.”

This result suggests that any organism’s genome may harbor the potential to produce historic phenotypes that are no longer under selection (for ~1 million years) — one need only speculate about what ancient human traits may continue to lurk in our own genomes, waiting to be expressed in a different environmental context.

When looking across developmental stages in an ant (the red harvester ant,Pogonomyrmex barbatus), the researchers found that most genes are expressed in both queens and workers, but often at different points in development. For example, there are no uniquely “worker” or “queen” genes. They then looked at whether genes with a greater bias in workers were more likely to get lost in species that no longer produce workers (social parasites).

To do this the researchers sequenced the genomes of two host species and two of their social parasites. The answer was no, the entire protein coding genome was under selection to maintain the genes present in both hosts and workerless social parasites.

The researchers found their results so surprising that they sequenced the genomes of another host-social parasite pair in the genus Vollenhovia, which are evolutionarily independent. Once again, the result was the same. Again surprised, they tested whether they could even expect to see the deterioration of genes in the mere 700,000 to million years of divergence between worker and worker-less species. Indeed, models do predict gene loss, yet none was evident in their actual samples.

“Social parasitism is relatively widespread in social insects, and our results suggest why — most changes are regulatory, and don’t require complex genome-wide alterations,” Mikheyev said.

The results reported in this new research add to a growing body of literature suggesting that many traits (and whole body plans) may evolve by tweaks in the regulation of pre-existing genes and networks. Phenotype gain and loss may be facilitated by changes in the environment within and outside of the organism, not necessarily requiring changes to protein coding genes, just changes to when and how they are used).

“This research reminds us of the importance of studying organisms with unusual natural history in order to get insight into the processes that govern diversity more generally,” said Andrew Suarez from the University of Illinois and a co-author of the study.

While this work was on species far removed from the origin of sociality, it does suggest that sociality may have evolved from regulatory changes in a solitary ancestor rather than requiring novel altruism genes for social living and division of labor.


Story Source:

The above post is reprinted from materials provided by Earlham College.Note: Materials may be edited for content and length.


Journal Reference:

  1. Chris R. Smith, Sara Helms Cahan, Carsten Kemena, Seán G. Brady, Wei Yang, Erich Bornberg-Bauer, Ti Eriksson, Juergen Gadau, Martin Helmkampf, Dietrich Gotzek, Misato Okamoto Miyakawa, Andrew V. Suarez, Alexander Mikheyev. How do genomes create novel phenotypes? Insights from the loss of the worker caste in ant social parasites.. Molecular Biology and Evolution, 2015; msv165 DOI:10.1093/molbev/msv165

 

Source: Earlham College. “Loss of altruism (and a body plan) without a loss of genes: How evolutionary biology in ants doesn’t play by the rules.” ScienceDaily. ScienceDaily, 11 August 2015. <www.sciencedaily.com/releases/2015/08/150811103549.htm>.

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Date:
August 11, 2015

Source:
Ecole Polytechnique Fédérale de Lausanne

Summary:
Recent years have seen an upsurge of brain imaging, with renewed interest in techniques like electron microscopy, which allows us to observe and study the architecture of the brain in unprecedented detail. But at the same time, they have also revived old problems associated with how this delicate tissue is prepared before images can be collected. Using an innovative method, scientists now show that the brain is not as compact as we have thought all along.

 

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This image shows two models of brain tissue reconstructed from serial EM images. The purple one is cryo-fixed, the brown one chemically fixed.
Credit: Graham Knott/EPFL

 

 

Using an innovative method, EPFL scientists show that the brain is not as compact as we have thought all along.

To study the fine structure of the brain, including its connections between neurons, the synapses, scientists must use electron microscopes. However, the tissue must first be fixed to prepare it for this high magnification imaging method. This process causes the brain to shrink; as a result, microscope images can be distorted, e.g. showing neurons to be much closer than they actually are. EPFL scientists have now solved the problem by using a technique that rapidly freezes the brain, preserving its true structure. The work is published in eLife.

The shrinking brain

Recent years have seen an upsurge of brain imaging, with renewed interest in techniques like electron microscopy, which allows us to observe and study the architecture of the brain in unprecedented detail. But at the same time, they have also revived old problems associated with how this delicate tissue is prepared before images can be collected.

Typically, the brain is fixed with stabilizing agents, such as aldehydes, and then encased, or embedded, in a resin. However, it has been known since the mid-sixties that this preparation process causes the brain to shrink by at least 30 percent. This in turn, distorts our understanding of the brain’s anatomy, e.g. the actual proximity of neurons, the structures of blood vessels etc.

The freezing brain

A study by Graham Knott at EPFL, led by Natalya Korogod and working with Carl Petersen, has successfully used an innovative method, called “cryofixation,” to prevent brain shrinkage during the preparation for electron microscopy. The method, whose roots go back to 1965, uses jets of liquid nitrogen to “snap-freeze” brain tissue down to -90oC, within milliseconds. The brain tissue here was mouse cerebral cortex.

The rapid freezing method is able to prevent the water in the tissue from forming crystals, as it would do in a regular freezer, by also applying very high pressures. Water crystals can severely damage the tissue by rupturing its cells. But in this high-pressure freezing method, the water turns into a kind of glass, preserving the original structures and architecture of the tissue.

The next step is to embed the frozen tissue in resin. This requires removing the glass-water and replacing it first with acetone, which is still a liquid at the low temperatures of cryofixation, and then, over a period of days, with resin; allowing it to slowly and gently push out the glassified water from the brain.

The real brain

After the brain was cryofixed and embedded, it was observed and photographed in using 3D electron microscopy. The researchers then compared the cryofixed brain images to those taken from a brain fixed with an “only chemical” method.

The analysis showed that the chemically fixed brain was much smaller in volume, showing a significant loss of extracellular space — the space around neurons. In addition, supporting brain cells called “astrocytes,” seemed to be less connected with neurons and even blood vessels in the brain. And finally, the connections between neurons, the synapses, seemed significantly weaker in the chemically-fixed brain compared to the cryofixed one.

The researchers then compared their measurements of the brain to those calculated in functional studies — studies that measure the time it takes for a molecule to travel across that brain region. To the researchers’ surprise, the data matched, adding even more evidence that cryofixation preserves the real anatomy of the brain.

“All this shows us that high-pressure cryofixation is a very attractive method for brain imaging,” says Graham Knott. “At the same time, it challenges previous imaging efforts, which we might have to re-examine in light of new evidence.” His team is now aiming to use cryofixation on other parts of the brain and even other types of tissue.


Story Source:

The above post is reprinted from materials provided by Ecole Polytechnique Fédérale de Lausanne. Note: Materials may be edited for content and length.


Journal Reference:

  1. Natalya Korogod, Carl CH Petersen, Graham W Knott. Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation. eLife, 2015; 4 DOI: 10.7554/eLife.05793

 

Source: Ecole Polytechnique Fédérale de Lausanne. “The brain is not as cramped as we thought.” ScienceDaily. ScienceDaily, 11 August 2015. <www.sciencedaily.com/releases/2015/08/150811091751.htm>.

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Date:
August 10, 2015

Source:
University of Adelaide

Summary:
A world-first underwater study of fish in their natural environment has shown how predicted ocean acidification from climate change will devastate temperate marine habitats and biodiversity.

 

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Healthy kelp forest in the present-day carbon dioxide levels.
Credit: Ivan Nagelkerken, University of Adelaide

 

 

A world-first underwater study of fish in their natural environment by University of Adelaide marine ecologists has shown how predicted ocean acidification from climate change will devastate temperate marine habitats and biodiversity.

Published in the journal Nature Climate Change, the researchers used natural CO2 underwater seeps to study how entire ecosystems have been impacted by the resulting acidification of the water.

They compared ecosystems in the high-CO2 levels found at volcanic vents in temperate waters in both the Northern and Southern hemispheres with adjacent ecosystems with present-day levels of CO2. These underwater vents have specific sites that release CO2 into the water at concentrations predicted for the end of the century.

“Human greenhouse gas emissions are rapidly acidifying our oceans,” says project leader Associate Professor Ivan Nagelkerken, Australian Researcher Council (ARC) Future Fellow with the University’s Environment Institute. “Using these CO2 seeps, we’ve been able to get a unique preview of what the future ocean will look like under current projections for the end of the century — and it’s not good.

“Previous studies have largely looked at how single fish species are affected by acidification in laboratory experiments. But we used these ‘natural laboratories’ to see the effects on whole ecosystems, as well as how acidification affects the behaviour and physiology of individual species.”

The study confirmed previous laboratory research which showed acidification of the water affects fish behaviour, for example, by reducing the escape response from predators.

But there were some surprising results. When the fish were close to shelter in their natural environment, this negative effect of acidification disappeared.

“We also found that some species were more abundant in the acidified waters. But these were common or generalist species such as gobie and triplefin fishes which doubled or even tripled in number to the detriment of other species,” Associate Professor Nagelkerken says.

The most dramatic finding was the marked habitat shift found in the high-CO2, acidified waters.

“As you swim from one area to the other you see a dramatic difference,” says co-author Professor Sean Connell. “One minute you’re in a kelp forest with one metre high kelp and lots of different fish. Then you move into the vent area where everything is barren with short turf algae, just a few centimetres high and devoid of the life and colour of the other areas.

“Ecosystems represent complex interactions between different species, and between species and their environment. Our research has given us a greater understanding of increasing CO2 emissions as a driver of ecological change and what this might mean for future marine biodiversity and fisheries production.”


Story Source:

The above post is reprinted from materials provided by University of Adelaide. Note: Materials may be edited for content and length.


Journal Reference:

  1. Ivan Nagelkerken, Bayden D. Russell, Bronwyn M. Gillanders, Sean D. Connell. Ocean acidification alters fish populations indirectly through habitat modification. Nature Climate Change, 2015; DOI:10.1038/nclimate2757

 

Source: University of Adelaide. “Volcanic vents preview future ocean habitats.” ScienceDaily. ScienceDaily, 10 August 2015. <www.sciencedaily.com/releases/2015/08/150810111227.htm>.

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Date:
August 3, 2015

Source:
Princeton University

Summary:
For the first time, researchers have directly calculated the rate at which water crystallizes into ice in a realistic computer model of water molecules. Understanding ice formation adds to our knowledge of how cold temperatures affect both living and non-living systems, including how living cells respond to cold and how ice forms in clouds at high altitudes.

 

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Using a computer model to explore how water molecules connect and nucleate into ice crystals, the researchers found that two types of ice compete for dominance during nucleation: cubic ice (blue) which is less stable, and hexagonal ice (red), which is stable and forms the majority of ice on Earth. Nucleation occurs when water molecules come together to form blobs (pictured above), which grow over time (left to right). Eventually hexagonal ice wins out (not shown). The researchers found that adding new cubic features onto an existing crystalline blob gives rise to nuclei that are more spherical, and hence more stable. In contrast, adding hexagonal features tends to give rise to chains of hexagonal cages that make the nucleus less spherical, and hence less stable.
Credit: Images courtesy of Amir Haji-Akbari, Princeton University.

 

 

Researchers at Princeton University have for the first time directly calculated the rate at which water crystallizes into ice in a realistic computer model of water molecules. The simulations, which were carried out on supercomputers, provide insight into the mechanism by which water transitions from a liquid to a crystalline solid.

Understanding ice formation adds to our knowledge of how cold temperatures affect both living and non-living systems, including how living cells respond to cold and how ice forms in clouds at high altitudes. A more precise knowledge of the initial steps of freezing could eventually help improve weather forecasts and climate models, as well as inform the development of better materials for seeding clouds to increase rainfall.

The researchers looked at the process by which, as the temperature drops, water molecules begin to cling to each other to form a blob of solid ice within the surrounding liquid. These blobs tend to disappear quickly after their formation. Occasionally, a large enough blob, known as a critical nucleus, emerges and is stable enough to grow rather than to melt. The process of forming such a critical nucleus is known as nucleation.

To study nucleation, the researchers used a computerized model of water that mimics the two atoms of hydrogen and one atom of oxygen found in real water. Through the computer simulations, the researchers calculated the average amount of time it takes for the first critical nucleus to form at a temperature of about 230 degrees Kelvin or minus 43 degrees Celsius, which is representative of conditions in high-altitude clouds.

They found that, for a cubic meter of pure water, the amount of time it takes for a critical nucleus to form is about one-millionth of a second. The study, conducted by Amir Haji-Akbari, a postdoctoral research associate, and Pablo Debenedetti, a professor of chemical and biological engineering, was published online this week in the journal Proceedings of the National Academy of Sciences.

“The main significance of this work is to show that it is possible to calculate the nucleation rate for relatively accurate models of water,” said Haji-Akbari.

In addition to calculating the nucleation rate, the researchers explored the origin of the two different crystalline shapes that ice can take at ambient pressure. The ice that we encounter in daily life is known as hexagonal ice. A second form, cubic ice, is less stable and can be found in high-altitude clouds. Both ices are made up of hexagonal rings, with an oxygen atom on each vertex, but the relative arrangement of the rings differs in the two structures.

“When water nucleates to form ice there is usually a combination of the cubic and hexagonal forms, but it was not well-understood why this would be the case,” said Haji-Akbari. “We were able to look at how the shapes of ice blobs change during the nucleation process, and one of the main findings of our work is to explain how a less stable form of ice is favored over the more stable hexagonal ice during the initial stages of the nucleation process.”

Debenedetti added, “What we found in our simulations is that before we go to hexagonal ice we tend to form cubic ice, and that was very satisfying because this has been reported in experiments.” One of the strengths of the study, Debenedetti said, was the innovative method developed by Haji-Akbari to identify cubic and hexagonal forms in the computer simulation.

Computer models come in handy for studies of nucleation because conducting experiments at the precise temperatures and atmospheric conditions when water molecules nucleate is very difficult, said Debenedetti, who is Princeton’s Class of 1950 Professor in Engineering and Applied Science and Dean for Research. But these calculations take huge amounts of computer time.

Haji-Akbari found a way to complete the calculation, whereas previous attempts failed to do so. The technique for modeling ice formation involves looking at computer-simulated blobs of ice, known as crystallites, as they form. Normally the technique involves looking at the crystallites after every step in the simulation, but Haji-Akbari modified the procedure such that longer intervals of time could be examined, enabling the algorithm to converge to a solution and obtain a sequence of crystallites that eventually led to the formation of a critical nucleus.

Even with the modifications, the technique took roughly 21 million computer processing unit (CPU) hours to track the behavior of 4,096 virtual water molecules in the model, which is known as TIP4P/Ice and is considered one of the most accurate molecular models of water. The calculations were carried out on several supercomputers, namely the Della and Tiger supercomputers at the Princeton Institute for Computational Science and Engineering; the Stampede supercomputer at the Texas Advanced Computing Center; the Gordon supercomputer at the San Diego Supercomputer Center; and the Blue Gene/Q supercomputer at the Rensselaer Polytechnic Institute.

Debenedetti noted that the rate of ice formation obtained in their calculations is much lower than what had been found by experiment. However, the computer calculations are extremely sensitive, meaning that small changes in certain parameters of the water model have very large effects on the calculated rate. The researchers were able to trace the discrepancy, which is 10 orders of magnitude, to aspects of the water model rather than to their method. As the modeling of water molecules improves, the researchers may be able to refine their calculations of the rate.


Story Source:

The above post is reprinted from materials provided by Princeton University. The original item was written by Catherine Zandonella. Note: Materials may be edited for content and length.


Journal Reference:

  1. Amir Haji-Akbari, Pablo G. Debenedetti. Direct calculation of ice homogeneous nucleation rate for a molecular model of water.Proceedings of the National Academy of Sciences, 2015; 201509267 DOI: 10.1073/pnas.1509267112

 

Source: Princeton University. “Study calculates the speed of ice formation.” ScienceDaily. ScienceDaily, 3 August 2015. <www.sciencedaily.com/releases/2015/08/150803155318.htm>.

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Date:
August 6, 2015

Source:
California Institute of Technology

Summary:
An international team of scientists has pieced together the first complete account of what physically happened during the Gorkha earthquake — a picture that explains how the large temblor wound up leaving the majority of low-story buildings in Kathmandu unscathed while devastating some treasured taller structures.

 

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John Galetzka, then of Caltech, and Sudhir Rajaure, of the Department of Mines and Geology in Kathmandu, install a high-rate GPS station in the Himalaya.
Credit: John Galetzka

 

 

For more than 20 years, Caltech geologist Jean-Philippe Avouac has collaborated with the Department of Mines and Geology of Nepal to study the Himalayas–the most active, above-water mountain range on Earth–to learn more about the processes that build mountains and trigger earthquakes. Over that period, he and his colleagues have installed a network of GPS stations in Nepal that allows them to monitor the way Earth’s crust moves during and in between earthquakes. So when he heard on April 25 that a magnitude 7.8 earthquake had struck near Gorkha, Nepal, not far from Kathmandu, he thought he knew what to expect–utter devastation throughout Kathmandu and a death toll in the hundreds of thousands.

“At first when I saw the news trickling in from Kathmandu, I thought there was a problem of communication, that we weren’t hearing the full extent of the damage,” says Avouac, Caltech’s Earle C. Anthony Professor of Geology. “As it turns out, there was little damage to the regular dwellings, and thankfully, as a result, there were far fewer deaths than I originally anticipated.”

Using data from the GPS stations, an accelerometer that measures ground motion in Kathmandu, data from seismological stations around the world, and radar images collected by orbiting satellites, an international team of scientists led by Caltech has pieced together the first complete account of what physically happened during the Gorkha earthquake–a picture that explains how the large earthquake wound up leaving the majority of low-story buildings unscathed while devastating some treasured taller structures.

The findings are described in two papers that now appear online. The first, in the journal Nature Geoscience, is based on an analysis of seismological records collected more than 1,000 kilometers from the epicenter and places the event in the context of what scientists knew of the seismic setting near Gorkha before the earthquake. The second paper, appearing in Science Express, goes into finer detail about the rupture process during the April 25 earthquake and how it shook the ground in Kathmandu.

In the first study, the researchers show that the earthquake occurred on the Main Himalayan Thrust (MHT), the main megathrust fault along which northern India is pushing beneath Eurasia at a rate of about two centimeters per year, driving the Himalayas upward. Based on GPS measurements, scientists know that a large portion of this fault is “locked.” Large earthquakes typically release stress on such locked faults–as the lower tectonic plate (here, the Indian plate) pulls the upper plate (here, the Eurasian plate) downward, strain builds in these locked sections until the upper plate breaks free, releasing strain and producing an earthquake. There are areas along the fault in western Nepal that are known to be locked and have not experienced a major earthquake since a big one (larger than magnitude 8.5) in 1505. But the Gorkha earthquake ruptured only a small fraction of the locked zone, so there is still the potential for the locked portion to produce a large earthquake.

“The Gorkha earthquake didn’t do the job of transferring deformation all the way to the front of the Himalaya,” says Avouac. “So the Himalaya could certainly generate larger earthquakes in the future, but we have no idea when.”

The epicenter of the April 25 event was located in the Gorkha District of Nepal, 75 kilometers to the west-northwest of Kathmandu, and propagated eastward at a rate of about 2.8 kilometers per second, causing slip in the north-south direction–a progression that the researchers describe as “unzipping” a section of the locked fault.

“With the geological context in Nepal, this is a place where we expect big earthquakes. We also knew, based on GPS measurements of the way the plates have moved over the last two decades, how ‘stuck’ this particular fault was, so this earthquake was not a surprise,” says Jean Paul Ampuero, assistant professor of seismology at Caltech and coauthor on the Nature Geoscience paper. “But with every earthquake there are always surprises.”

In this case, one of the surprises was that the quake did not rupture all the way to the surface. Records of past earthquakes on the same fault–including a powerful one (possibly as strong as magnitude 8.4) that shook Kathmandu in 1934–indicate that ruptures have previously reached the surface. But Avouac, Ampuero, and their colleagues used satellite Synthetic Aperture Radar data and a technique called back projection that takes advantage of the dense arrays of seismic stations in the United States, Europe, and Australia to track the progression of the earthquake, and found that it was quite contained at depth. The high-frequency waves that were largely produced in the lower section of the rupture occurred at a depth of about 15 kilometers.

“That was good news for Kathmandu,” says Ampuero. “If the earthquake had broken all the way to the surface, it could have been much, much worse.”

The researchers note, however, that the Gorkha earthquake did increase the stress on the adjacent portion of the fault that remains locked, closer to Kathmandu. It is unclear whether this additional stress will eventually trigger another earthquake or if that portion of the fault will “creep,” a process that allows the two plates to move slowly past one another, dissipating stress. The researchers are building computer models and monitoring post-earthquake deformation of the crust to try to determine which scenario is more likely.

Another surprise from the earthquake, one that explains why many of the homes and other buildings in Kathmandu were spared, is described in theScience Express paper. Avouac and his colleagues found that for such a large-magnitude earthquake, high-frequency shaking in Kathmandu was actually relatively mild. And it is high-frequency waves, with short periods of vibration of less than one second, that tend to affect low-story buildings. TheNature Geoscience paper showed that the high-frequency waves that the quake produced came from the deeper edge of the rupture, on the northern end away from Kathmandu.

The GPS records described in the Science Express paper show that within the zone that experienced the greatest amount of slip during the earthquake–a region south of the sources of high-frequency waves and closer to Kathmandu–the onset of slip on the fault was actually very smooth. It took nearly two seconds for the slip rate to reach its maximum value of one meter per second. In general, the more abrupt the onset of slip during an earthquake, the more energetic the radiated high-frequency seismic waves. So the relatively gradual onset of slip in the Gorkha event explains why this patch, which experienced a large amount of slip, did not generate many high-frequency waves.

“It would be good news if the smooth onset of slip, and hence the limited induced shaking, were a systematic property of the Himalayan megathrust fault, or of megathrust faults in general.” says Avouac. “Based on observations from this and other megathrust earthquakes, this is a possibility.”

In contrast to what they saw with high-frequency waves, the researchers found that the earthquake produced an unexpectedly large amount of low-frequency waves with longer periods of about five seconds. This longer-period shaking was responsible for the collapse of taller structures in Kathmandu, such as the Dharahara Tower, a 60-meter-high tower that survived larger earthquakes in 1833 and 1934 but collapsed completely during the Gorkha quake.

To understand this, consider plucking the strings of a guitar. Each string resonates at a certain natural frequency, or pitch, depending on the length, composition, and tension of the string. Likewise, buildings and other structures have a natural pitch or frequency of shaking at which they resonate; in general, the taller the building, the longer the period at which it resonates. If a strong earthquake causes the ground to shake with a frequency that matches a building’s pitch, the shaking will be amplified within the building, and the structure will likely collapse.

Turning to the GPS records from two of Avouac’s stations in the Kathmandu Valley, the researchers found that the effect of the low-frequency waves was amplified by the geological context of the Kathmandu basin. The basin is an ancient lakebed that is now filled with relatively soft sediment. For about 40 seconds after the earthquake, seismic waves from the quake were trapped within the basin and continued to reverberate, ringing like a bell with a frequency of five seconds.

“That’s just the right frequency to damage tall buildings like the Dharahara Tower because it’s close to their natural period,” Avouac explains.

In follow-up work, Domniki Asimaki, professor of mechanical and civil engineering at Caltech, is examining the details of the shaking experienced throughout the basin. On a recent trip to Kathmandu, she documented very little damage to low-story buildings throughout much of the city but identified a pattern of intense shaking experienced at the edges of the basin, on hilltops or in the foothills where sediment meets the mountains. This was largely due to the resonance of seismic waves within the basin.

Asimaki notes that Los Angeles is also built atop sedimentary deposits and is surrounded by hills and mountain ranges that would also be prone to this type of increased shaking intensity during a major earthquake.

“In fact,” she says, “the buildings in downtown Los Angeles are much taller than those in Kathmandu and therefore resonate with a much lower frequency. So if the same shaking had happened in L.A., a lot of the really tall buildings would have been challenged.”

That points to one of the reasons it is important to understand how the land responded to the Gorkha earthquake, Avouac says. “Such studies of the site effects in Nepal provide an important opportunity to validate the codes and methods we use to predict the kind of shaking and damage that would be expected as a result of earthquakes elsewhere, such as in the Los Angeles Basin.”


Story Source:

The above post is reprinted from materials provided by California Institute of Technology. The original item was written by Kimm Fesenmaier. Note: Materials may be edited for content and length.


Journal References:

  1. Jean-Paul Ampuero et al. Lower edge of locked Main Himalayan Thrust unzipped by the 2015 Gorkha earthquake. Nature Geoscience, August 2015 DOI: 10.1038/ngeo2518
  2. N. Maharjan et al. Slip pulse and resonance of Kathmandu basin during the 2015 Mw 7.8 Gorkha earthquake, Nepal imaged with geodesy. Science Express, August 2015 DOI: 10.1126/science.aac6383

 

Source: California Institute of Technology. “April 2015 earthquake in Nepal reviewed in detail.” ScienceDaily. ScienceDaily, 6 August 2015. <www.sciencedaily.com/releases/2015/08/150806144555.htm>.

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Date:
August 5, 2015

Source:
Cell Press

Summary:
A challenging morning meeting or an interaction with an upset client at work may affect whether we go for that extra chocolate bar at lunch. In a study, researchers placed human volunteers in a similar food choice scenario to explore how stress can alter the brain to impair self-control when we’re confronted with a choice.

 

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Participants’ brains in this study exhibited altered patterns of connectivity between regions including the amygdala, striatum, and the dorsolateral and ventromedial prefrontal cortex, essentially reducing individuals’ ability to exercise self-control over food choices.
Credit: © alexandrum01 / Fotolia

 

 

A challenging morning meeting or an interaction with an upset client at work may affect whether we go for that extra chocolate bar at lunch. In a study appearing August 5 in Neuron, researchers placed human volunteers in a similar food choice scenario to explore how stress can alter the brain to impair self-control when we’re confronted with a choice.

“Our findings provide an important step towards understanding the interactions between stress and self-control in the human brain, with the effects of stress operating through multiple neural pathways,” says lead author Silvia Maier, of the University of Zurich’s Laboratory for Social and Neural Systems Research. “Self-control abilities are sensitive to perturbations at several points within this network, and optimal self-control requires a precise balance of input from multiple brain regions rather than a simple on/off switch.” She emphasized that much work still remains, however, to fully understand the mechanisms involved.

In the study, 29 participants underwent a treatment known to induce moderate stress in the laboratory before they were asked to choose between two food options. An additional 22 participants did not undergo the treatment, which involved being observed and evaluated by the experimenter while immersing a hand in an ice water bath for 3 minutes, before choosing between the food options.

All of the participants who were selected for the study were making an effort to maintain a healthy lifestyle, so the study presented them with a conflict between eating a very tasty but unhealthy item and one that is healthy but less tasty.

The scientists found that when individuals chose between different food options after having experienced the stressful ice bath treatment, they overweighed food taste attributes and were more likely to choose an unhealthy food compared with people who were not stressed.

The effects of stress were also visible in the brain. Stressed participants’ brains exhibited altered patterns of connectivity between regions including the amygdala, striatum, and the dorsolateral and ventromedial prefrontal cortex, essentially reducing individuals’ ability to exercise self-control over food choices. Only some of these changes were associated with cortisol, a hormone commonly linked to stress.

The investigators say that their study indicates that even moderate levels of stress can impair self-control. “This is important because moderate stressors are more common than extreme events and will thus influence self-control choices more frequently and for a larger portion of the population,” says senior author Todd Hare. “One interesting avenue for future research will be to determine whether some of the factors shown to protect against structural brain changes following severe stress–such as exercise and social support–can also buffer the effects of moderate stress on decision making,” he adds.

There was also a good deal of variation in the degree to which stress affected individuals in the study, so it will be important to investigate why some people are more resilient than others.


Story Source:

The above post is reprinted from materials provided by Cell Press. Note: Materials may be edited for content and length.


Journal Reference:

  1. Silvia U. Maier, Aidan B. Makwana, Todd A. Hare. Acute Stress Impairs Self-Control in Goal-Directed Choice by Altering Multiple Functional Connections within the Brain’s Decision Circuits. Neuron, 2015; 87 (3): 621 DOI: 10.1016/j.neuron.2015.07.005

 

Source: Cell Press. “How stress can tweak the brain to sabotage self-control.” ScienceDaily. ScienceDaily, 5 August 2015. <www.sciencedaily.com/releases/2015/08/150805140245.htm>.

 

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Date:
August 4, 2015

Source:
Imperial College London

Summary:
Scientists have discovered how earthworms can digest plant material, such as fallen leaves, that would defeat most other herbivores. Earthworms are responsible for returning the carbon locked inside dead plant material back into the ground. They drag fallen leaves and other plant material down from the surface and eat them, enriching the soil, and they do this in spite of toxic chemicals produced by plants to deter herbivores.

 

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Earthworms, however, are able to digest fallen leaves and other plant material, thanks to the ability of drilodefensins to counteract polyphenols. Dr Bundy and his team found that the more polyphenols present in the earthworm diet, the more drilodefensins they produce in their guts.
Credit: © Kokhanchikov / Fotolia

 

 

Scientists have discovered how earthworms can digest plant material, such as fallen leaves, that would defeat most other herbivores.

Earthworms are responsible for returning the carbon locked inside dead plant material back into the ground. They drag fallen leaves and other plant material down from the surface and eat them, enriching the soil, and they do this in spite of toxic chemicals produced by plants to deter herbivores.

The scientists, led by Dr Jake Bundy and Dr Manuel Liebeke from Imperial College London, have identified molecules in the earthworm gut that counteract the plant’s natural defences and enable digestion. Their work is published in Nature Communications and includes support from the Centre for Ecology and Hydrology, the University of Oxford, and Cardiff University.

The molecules, which have been named drilodefensins, are so abundant that Dr Liebeke estimates that for every person on earth there is at least 1kg of drilodefensins present within the earthworms that populate the world’s soils. Their abundance is not, however, an excess — drilodefensins are so precious that earthworms recycle the molecules in order to harness their effects again.

A world without drilodefensins would be a very different world, according to the researchers. Dr Bundy, from the Department of Surgery and Cancer at Imperial, said: “Without drilodefensins, fallen leaves would remain on the surface of the ground for a very long time, building up to a thick layer. Our countryside would be unrecognisable, and the whole system of carbon cycling would be disrupted.”

Plants make polyphenols, which act as antioxidants and give the plants their colour; they also inhibit the digestion of many herbivores. Earthworms, however, are able to digest fallen leaves and other plant material, thanks to the ability of drilodefensins to counteract polyphenols. Dr Bundy and his team found that the more polyphenols present in the earthworm diet, the more drilodefensins they produce in their guts.

The finding that the molecules are abundant in the gut of earthworms was made possible by using modern visualization techniques based on mass spectrometry (MALDI imaging). Dr Liebeke , formerly of the Department of Surgery and Cancer at Imperial, and now working at the Max Planck Institute for Marine Microbiology, in Germany, said: “Using these molecular microscopes is changing how we understand complex biochemistry of living beings; we are now able to locate every molecule in, for example, an earthworm to a specific location. Knowing the location of a molecule can help us to figure out what it actually does.”

The first record of a molecule that would now be considered a drilodefensin was in 1988 when a patent was filed for a molecule that was thought to dilate blood vessels. In traditional Chinese medicine, this molecule was ingested in the form of dried earthworm products. But Dr Bundy cautioned that the drying process would almost certainly render drilodefensins inactive.

Dr Dave Spurgeon of the Centre for Ecology and Hydrology is a co-author on the paper. He said: “We’ve established that earthworms, referred to as ‘nature’s ploughs’ by Charles Darwin, have a metabolic coping mechanism to deal with a range of leaf litter diets. In this role, drilodefensin support the role of earthworm as key “ecosystem engineers” within the carbon cycle.”


Story Source:

The above post is reprinted from materials provided by Imperial College London. The original item was written by Nancy Wavell Mendoza. Note: Materials may be edited for content and length.


Journal Reference:

  1. Manuel Liebeke, Nicole Strittmatter, Sarah Fearn, A. John Morgan, Peter Kille, Jens Fuchser, David Wallis, Vitalii Palchykov, Jeremy Robertson, Elma Lahive, David J. Spurgeon, David McPhail, Zoltán Takáts, Jacob G. Bundy. Unique metabolites protect earthworms against plant polyphenols. Nature Communications, 2015; 6: 7869 DOI:10.1038/ncomms8869

 

Source: Imperial College London. “Mystery behind earthworm digestion solved.” ScienceDaily. ScienceDaily, 4 August 2015. <www.sciencedaily.com/releases/2015/08/150804142947.htm>.

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Date:
August 3, 2015

Source:
American Geophysical Union

Summary:
Shifting winds, ocean currents doubled endangered Galápagos penguin population, new research shows. The Galápagos Islands, a chain of islands 1,000 kilometers (600 miles) west of mainland Ecuador, are home to the only penguins in the Northern Hemisphere. The 48-centimeter (19-inch) tall black and white Galápagos penguins landed on the endangered species list in 2000 after the population plummeted to only a few hundred individuals and are now considered the rarest penguins in the world.

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Galápagos penguin (stock image). The Galápagos Islands are home to the only penguins in the Northern Hemisphere. The 48-centimeter (19-inch) tall black and white Galápagos penguins landed on the endangered species list in 2000 after the population plummeted to only a few hundred individuals and are now considered the rarest penguins in the world.
Credit: © Roger Schmid / Fotolia

 

 

Shifts in trade winds and ocean currents powered a resurgence of endangered Galápagos penguins over the past 30 years, according to a new study. These changes enlarged a cold pool of water the penguins rely on for food and breeding — an expansion that could continue as the climate changes over the coming decades, the study’s authors said.

The Galápagos Islands, a chain of islands 1,000 kilometers (600 miles) west of mainland Ecuador, are home to the only penguins in the Northern Hemisphere. The 48-centimeter (19-inch) tall black and white Galápagos penguins landed on the endangered species list in 2000 after the population plummeted to only a few hundred individuals and are now considered the rarest penguins in the world.

Most of the penguins live on the archipelago’s westernmost islands, Isabela and Fernandina, where they feed on fish that live in a cold pool of water on the islands’ southwestern coasts. The cold pool is fed by an ocean current, the Equatorial Undercurrent, which flows toward the islands from the west. When the current runs into Isabela and Fernandina, water surges upward, bringing cold, nutrient-rich water to the surface.

New research suggests shifts in wind currents over the past three decades, possibly due to climate change and natural variability, have nudged the Equatorial Undercurrent north. The changing current expanded the nutrient-rich, cold water farther north along the coasts of the two islands, likely bolstering algae and fish numbers in the cold pool. This allowed the penguin population to double over the past 30 years, swelling to more than 1,000 birds by 2014, according to the new study.

Climate change could further shift wind patterns and ocean currents, expanding cold water further north along the coasts of Isabela and Fernandina and driving fish populations higher, according to the new study.

Penguins, as well as other animals like fur seals and marine iguanas that feed and reproduce near the cold waters, may increase in numbers as the northwestern coasts of the islands become more habitable, said the study’s authors. They noted that wind and ocean currents could also return to earlier conditions, leading to a decline in penguin populations.

“The penguins are the innocent bystanders experiencing feast or famine depending on what the Equatorial Undercurrent is doing from year to year,” said Kristopher Karnauskas, a climate scientist who performed the research while at Woods Hole Oceanographic Institution in Cape Cod, Massachusetts, and lead author of the new study recently accepted in Geophysical Research Letters, an American Geophysical Union journal.

The new findings could help inform conservation efforts to save the endangered penguins, said the study’s authors. Increasing efforts on the northern coasts of the islands and expanding marine-protected areas north to where the penguins are now feeding and breeding could support population growth, the study’s authors said.

Karnauskas notes that the vast majority of marine organisms will be negatively affected by the rise in ocean temperatures and acidification that are expected to occur across the globe as a result of climate change.

“With climate change, there are a lot of new and increasing stresses on ecosystems, but biology sometimes surprises us,” said Karnauskas. “There might be places–little outposts–where ecosystems might thrive just by coincidence.”

Penguin population changes

The Galápagos penguin population tenuously hangs onto the islands that so enthralled Charles Darwin during his visit in 1835. The penguins once numbered around 2,000 individuals, but in the early 1980s a strong El Niño — a time when sea surface temperatures in the tropical Pacific are unusually warm — brought their numbers down to less than 500 birds. Dogs, cats and rats introduced to the islands also stymied the penguin population by attacking the birds, disturbing their nests, and introducing new diseases, according to previous research.

Despite these setbacks, the penguins gradually increased in number in the following decades, according to local bird counts. Researchers, interested by the increase in penguins, noted that the birds remained near the coldest stretches of water. Nearly all of the Galápagos penguins live on the western coasts of Isabela and Fernandina, and two-thirds of them huddled near the coldest waters at the southern tips of the islands, according to previous research.

The study’s authors wanted to know whether the growing numbers of penguins were related to local changes in ocean temperature. They combined previously-collected penguin population data from 1982 to 2014 with sea surface temperature data from satellites, ships and buoys for the same time period.

They found that the cold pool, where sea surface temperatures are below 22 degrees Celsius (71 degrees Fahrenheit), expanded 35 kilometers (22 miles) farther north than where it was located at the beginning of the study period. In the 1980s the cold water pocket reached only the southern halves of the western coasts of Isabela and Fernandina. By 2014, the cold water pocket extended across the entire western coasts of the islands.

Varying trade winds, ocean currents

A shift in trade winds and underwater ocean currents likely caused the Galápagos cold pool expansion, propose the authors.

Trade winds blow surface ocean waters from the southern side of the equator to the northern side of the equator. As surface waters pile up in the north, the water at the bottom of the pile is squished south, nudging the Equatorial Undercurrent — a cold current that flows roughly 50 meters (160 feet) under the ocean surface — south of the equator.

Likely due to a combination of natural variation and human-caused climate change, trade winds west of the Galápagos slackened during the study period, lessening the pressure pushing the Equatorial Undercurrent south, according to the new study. Consequently, the ocean current gradually shifted north, increasing the amount of cold water coming to the Galápagos Islands, according to the study’s authors.

Satellite images showed that this expanded pool of cold water likely encouraged the growth of phytoplankton, according to the new study. This increase in ocean algae attracted fish to the area — the main entrée for Galápagos penguins, suggest the authors. The largest pulses of cold water reached the islands from July through December, coinciding with the penguins’ breeding season. The bountiful fish helped the birds successfully reproduce and feed their young, according to the new study.

Models indicate trade winds will continue to abate in the future as the climate warms, Karnauskas said. This could cause the undercurrent to continue to move north, expanding the Galápagos cold pool and possibly further raising penguin populations, he said. Other animal populations like the endangered Galápagos fur seal and the marine iguana also may profit from the prolific amount of food in the Galápagos cold pool, according to the study’s authors.

Wind and ocean currents could also possibly return to where they were in the 1980s, compressing the cold pool and possibly leading to a decline in penguins, Karnauskas added.

The new study shows how large-scale changes in the climate can act locally, said Michelle L’Heureux, a climate scientist with the National Oceanic and Atmospheric Administration’s Climate Prediction Center in College Park, Maryland, and not an author on the new paper.

“While it is important that we focus on the big picture with climate change, it’s really the small scale that matters to the animals and plants that are impacted,” she said.


Story Source:

The above post is reprinted from materials provided by American Geophysical Union. Note: Materials may be edited for content and length.


Journal Reference:

  1. K. B. Karnauskas, S. Jenouvrier, C. W. Brown, R. Murtugudde. Strong sea surface cooling in the eastern equatorial Pacific and implications for Galápagos Penguin conservation. Geophysical Research Letters, 2015; DOI: 10.1002/2015GL064456

 

Source: American Geophysical Union. “Shifting winds, ocean currents doubled endangered Galápagos penguin population.” ScienceDaily. ScienceDaily, 3 August 2015. <www.sciencedaily.com/releases/2015/08/150803155108.htm>.

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On Target is Going on Vacation – “See you in September“

 

While Target Health continues full speed ahead getting products to the market, ON TARGET, one of the most popular non-commercial newsletters in the industry, is taking a break to recharge its batteries.

 

More Mountain Goats From Colorado

 

Two weeks ago we featured a Mountain Goat from Colorado. In response to that photo, our son Daniel, who lives in Colorado, sent us the photo below and said “the goats are great. I see them all the time. The kids are really cute.“

 

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©Target Health Inc. 2015

 

ON TARGET is the newsletter of Target Health Inc., a NYC-based, full-service, contract research organization (eCRO), providing strategic planning, regulatory affairs, clinical research, data management, biostatistics, medical writing and software services to the pharmaceutical and device industries, including the paperless clinical trial.

 

For more information about Target Health contact Warren Pearlson (212-681-2100 ext. 104). For additional information about software tools for paperless clinical trials, please also feel free to contact Dr. Jules T. Mitchel or Ms. Joyce Hays. The Target Health software tools are designed to partner with both CROs and Sponsors. Please visit the Target Health Website.

 

Joyce Hays, Founder and Editor in Chief of On Target

Jules Mitchel, Editor

 

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