July 13, 2010, 7:17 AM CT

Breaking biomass better

One of the challenges in making cellulosic biofuels commercially viable is to cost-effectively deconstruct plant material to liberate fermentable energy-rich sugars. The U.S. Department of Energy (DOE) is funding several projects focused on identifying enzymes in organisms that optimally degrade cellulosic feedstocks. One such source are fungi, which break down dead wood and leaf litter in forests; in fact, some pest management companies consider wood rot more destructive for homes than termites.

The DOE Joint Genome Institute (JGI) previously sequenced and published the genomes of two wood-decaying fungi. Now a team of scientists led by researchers from the DOE JGI and the University of Utrecht announce the analysis of a third such genome as per a research findings published online July 11 in Nature Biotechnology (http://bit.ly/cjkaxO). All told, DOE JGI has sequenced and annotated 40 fungal genomes, and 40 more are currently in the works.

"When we go into a forest we don't see layers of dead branches because wood decay fungi take care of them," said Igor Grigoriev, head of the DOE JGI's Fungal Genomics Program and a senior author on the study. "So when we think about bioenergy and degrading biomass and converting that into biofuel, we would like to learn the most efficient ways of doing that from fungi, which have invented a number of ways of doing that in nature. Schizophyllum commune is the second white rot fungus and third wood degrader we've sequenced. The DOE JGI sequenced the first white rot fungal genome Phanerochaete chrysosporium in 2004. Then last year we sequenced the first brown rot fungal genome Postia placenta." Postia was found to utilize a unique arsenal of small oxidizing agents that blast through plant cell walls to decompose cellulose into simple sugars......... Posted by: Erica      Read more         Source

July 12, 2010, 7:17 AM CT

New virus may pose risk to wild salmon

Farmed fish are an increasingly important food source, with a global harvest now at 110 million tons and growing at more than 8 percent a year. But epidemics of infectious disease threaten this vital industry, including one of its most popular products: farmed Atlantic salmon. Perhaps even more worrisome: these infections can spread to wild fish coming in close proximity to marine pens and fish escaping from them.

Heart and skeletal muscle inflammation (HSMI), an often fatal disease, was first detected in salmon on a farm in Norway in 1999, and has now been reported in 417 fish farms in Norway as well as in the United Kingdom. The disease destroys heart and muscle tissue and kills up to 20 percent of infected fish. Eventhough studies have indicated an infectious basis, recent efforts to identify the pathogen causing the disease have been unsuccessful. Now, using cutting-edge molecular techniques, an international team led by W. Ian Lipkin, MD, the John Snow Professor of Epidemiology and director of the Center for Infection and Immunity at Columbia University's Mailman School of Public Health, has found evidence that the disease appears to be caused by a previously unknown virus. The newly identified virus is related but distinct from previously known reoviruses, which are double-stranded RNA viruses that infect a wide range of vertebrates......... Posted by: Kelly      Read more         Source

July 12, 2010, 7:10 AM CT

Mexican salamander and mysteries of stem cells

Dr Andrew Johnson is speaking today (12 July) at the UK National Stem Cell Network annual conference. He and his team from the University of Nottingham have been using a Mexican aquatic salamander called an axolotl to study the evolution and genetics of stem cells - research that supports the development of regenerative medicine to treat the consequences of disease and injury using stem cell therapies. This team has observed that there are extraordinary similarities in the development of axolotls and mammals that provide unique opportunities to study the properties of embryonic stem cells and germ cells. These findings are underpinned by a novel theory of evolution that unifies the diversity of mechanisms in animal developmental into a single conceptual framework.

Dr Johnson said "We've produced evidence that pluripotency the ability of an embryonic stem cell to become absolutely any kind of cell is actually very ancient in evolutionary terms. Even though received wisdom is that it evolved with mammals, our research suggests that it was there all along, just not in a number of of the species that people use in the lab. In fact, pluripotent cells probably exist in the embryos of the simple animals from which amphibians evolved.

"Axolotls, unlike a number of of the frogs, fish, flies and worms that are used in the lab, have pluripotent cells in their embryos that are the equivalent to those found in embryos from mammals, in that they can produce germ cells, in addition to somatic cells, a property known as ground-state pluripotency. And from a practical perspective, axolotl embryos will provide a very useful tool for understanding how to manipulate embryonic stem cells for modern regenerative medicine"......... Posted by: Kelly      Read more         Source

July 9, 2010, 7:26 AM CT

Refuting conventional thinking on evolution

Long before TV's campy Fantasy Island, the isolation of island communities has touched an exotic and magical core in us. Darwin's fascination with the Galapagos island chain and the evolution of its plant and animal life is just one example.

Think of the extensive lore surrounding island-bred creatures like Komodo dragons, dwarf elephants, and Hobbit-sized humans. Conventional wisdom has it that they - and a horde of monster-sized insects - are all products of island evolution.

But are they?

Dr. Shai Meiri of Tel Aviv University's Department of Zoology says "yes," they are a product of evolution, but nothing more than one would expect to see by "chance," citing research that shows there's nothing extraordinary about evolutionary processes on islands. He and colleagues have conducted many scientific studies comparing evolutionary patterns of island and mainland ecosystems, and the results refute the idea that islands operate under different, "magical" rules.

Man bites evolutionary dog

"My findings are a bit controversial for some evolutionary biologists," says Dr. Meiri, the author of several papers and essays on island evolution. His research is based on statistical models he developed.

"There is a tendency to think that big animals become very small on islands, and small animals become very big, due to limited resources or lack of competition. I've shown that this is just not true, at least not as a general rule. Evolution operates on islands no differently than anywhere else"......... Posted by: Janet      Read more         Source

July 9, 2010, 6:50 AM CT

Ferns and fog on the forest floor

As the mercury rises outdoors, it's a fitting time to consider the effects of summertime droughts and global warming on ecosystems. Complex interactions among temperature, water cycling, and plant communities create a tangled web of questions that need to be answered as we face a rapidly changing climate.

Drs. Emily Limm and Todd Dawson (University of California, Berkeley) recently tackled one aspect of the challenging question of how climate change can impact plant communities that obtain water from fog. Their results are reported in the recent issue of the American Journal of Botany

Fog is an important source of water to ecosystems around the world, because fog allows plants to stay hydrated even during times without rain. Fog may condense and drip to the soil, where it can be taken up by roots. Alternatively, some plants are able to absorb the water from fog through their leaves, allowing these plants to immediately benefit from the atmospheric moisture that may never reach the forest floor. The fern Polystichum munitum covers the forest floors of the redwood forests in northern California. Limm and Dawson examined variation in the ability of the leaves of P. munitum to absorb the water from fog.

The scientists observed that the quantity of water the plants absorbed varied in the different regions of the redwood forest. "Today, summertime drought conditions are greater in the southern end of the redwood forest ecosystem of Northern California, and this reduces P. munitum abundance and plant size. These smaller ferns in the south are less able to capture fog water that drips to the forest floor during the summer, and they may therefore suffer more drought stress than ferns in the northern end of the redwood forest ecosystem," Limm stated......... Posted by: Erica      Read more         Source

July 8, 2010, 6:53 AM CT

What plant genes tell us

Anyone who has seen teosinte, the wild grass from which maize (corn) evolved, might be forgiven for assuming a number of genetic changes underlie the transformation of one plant to the other.

However, a method for exploring the genetics of domestication called Quantitative Trait Locus (QTL) mapping has revealed that only modest modifications are needed to convert a wild plant to a crop plant. Some major transitions in phenotype can even be achieved by a single genetic change.

The few artificial experiments in domestication that have been conducted have also shown that it is possible to achieve domesticate-like plants in fewer than 20 generations.

None of this pleases archaeobotanists, who try to piece together the history of plant domestication from scraps of ancient plant remains.

Their data are sparse and unimpressive - a 10,000-year-old squash seed found in a cave in Oaxaca, Mexico, or four 12,000-year-old grains of rice recovered from a rock shelter in Hunan Province in China - but they have their own irrefutable reality.

"There's been an argument in the recent archeological literature that genetics gives a false picture of domestication as a rapid, geographically localized process," comments Kenneth M. Olsen, PhD, assistant professor of biology in Arts & Sciences at Washington University in St. Louis. "They argue instead that domestication likely involved much trial and error in a number of different geographic regions over a long period of time"......... Posted by: Erica      Read more         Source

July 8, 2010, 6:47 AM CT

Crop development won't satisfy future demand

Eventhough global grain production must double by 2050 to address rising population and demand, new data from the University of Illinois suggests crop yields will suffer unless new approaches to adapt crop plants to climate change are adopted. Improved agronomic traits responsible for the remarkable increases in yield accomplished during the past 50 years have reached their ceiling for some of the world's most important crops.

"Global change is happening so quickly that its impact on agriculture is taking the world by surprise," said Don Ort, U of I professor of crop sciences and USDA/ARS scientist. "Until recently, we haven't understood the urgency of addressing global change in agriculture".

The need for new technologies to conduct global change research on crops in an open-field environment is holding the commercial sector back from studying issues such as maximizing the elevated carbon dioxide advantage or studying the effects of ozone pollution on crops.

However, U of I's Free Air Concentration Enrichment (FACE) research facility, SoyFACE, is allowing scientists to conduct novel studies using this technology capable of creating environments of the future in an open-field setting.

"If you want to study how global change affects crop production, you need to get out of the greenhouse," Ort said. "At SoyFACE, we can grow and study crops in an open-field environment where carbon dioxide and ozone levels can be raised to mimic future atmospheric conditions without disturbing other interactions"......... Posted by: Erica      Read more         Source

July 7, 2010, 7:06 AM CT

Deworming lambs

Deworming lambs can be minimized with rotational grazing and checking the animals' eye color, as per an Agricultural Research Service (ARS) study.

Animal scientist Joan Burke at the ARS Dale Bumpers Small Farms Research Center in Booneville, Ark., and his colleagues made this finding as part of a continuing collaboration with scientists, veterinarians, and extension agents from the Southern Consortium for Small Ruminant Parasite Control.

The consortium was formed in response to the threats posed by worms resistant to parasiticides. Unnecessary de-worming speeds development of resistant worms. Reducing the use of conventional parasiticides fits well into organic and grass-fed management systems and meets consumer preferences of minimizing chemical residues in meat.

The blood-sucking worm, Haemonchus contortus, can cause severe anemia in animals. It is called the barber pole worm for the spiraling of its white, egg-filled ovaries around blood-filled intestines. Worldwide, they cost farmers and ranchers millions of dollars in losses. Animals shed worm eggs with their manure, and the larvae that hatch can be eaten by other livestock.

Burke and his colleagues observed that gel capsules filled with copper oxide wire particles eliminated the need for conventional dewormers in all but one case. And lambs that also rotated pastures needed fewer dewormings with the copper oxide pills......... Posted by: Kelly      Read more         Source

July 7, 2010, 6:59 AM CT

Lone whales shout to overcome noise

noise increases; and just like humans, at a certain point, it appears to become too costly to continue to shout, as per marine and acoustic scientists.

"The impacts of increases in ocean noise from human activities are a concern for the conservation of marine animals like right whales," said Susan Parks, assistant professor of acoustics and research associate, Applied Research Laboratory, Penn State. "The ability to change vocalizations to compensate for environmental noise is critical for successful communication in an increasingly noisy ocean".

Right whales are large baleen whales that often approach close to shore. They may have been given the name because they were the right whales to hunt as they are rich in blubber, slow swimming and remain afloat after death. Consequently, whalers nearly hunted these whales to extinction. Currently right whales are monitored to determine the health and size of the population. The northern and southern right whales are on the endangered species list.

"Right whale upcalls are used extensively for passive acoustic monitoring in conservation efforts to protect this endangered species," said Parks.

Whales produce upcalls, sometimes called contact calls, when they are alone or in the process of joining with other whales. An upcall begins low and rises in pitch. It is the most frequent call produced by right whales......... Posted by: Kelly      Read more         Source

July 6, 2010, 7:16 AM CT

Salmon in hot water

Rearing juvenile salmon at the relatively high temperature of 16C causes skeletal deformities in the fish. Scientists writing in the open access journal BMC Physiology investigated both the magnitude and mechanisms of this effect, which occurs when salmon farmers use warmed water to increase fish growth rates.

Harald Takle worked with a team of scientists from NOFIMA (the Norwegian Institute of Food, Fisheries and Aquaculture Research), Norway, to carry out the studies. He said, "The data presented here indicate that both production of bone and cartilage were disrupted when promoting fast growth using elevated temperature. It is very likely that higher temperatures result in the increased rate of deformities observed in the 16C group".

The scientists reared 400 fish in 10C water and another 400 at 16C. The fish in the 16C water grew faster, but 28% were found to show some signs of skeletal deformity, in comparison to 8% of the fish reared in the cooler tank. Takle said, "Our results strongly indicate that temperature induced fast growth is severely affecting gene transcription in osteoblasts and chondrocyte bone cells, leading to a change in the tissue structure and composition".

In a second related study, fish with vertebral deformities were studied in detail. Takle said, "The deformity process involves molecular regulation and cellular changes similar to those found in mammalian intervertebral disc degeneration"......... Posted by: Kelly      Read more         Source