February 4, 2009, 11:03 PM CT

Did Early Whales Gave Birth on Land?

Two newly described fossil whales--a pregnant female and a male of the same species--reveal how primitive whales gave birth and provide new insights into how whales made the transition from land to sea.

The 47.5 million-year-old fossils, discovered in Pakistan in 2000 and 2004, are described in a paper published Feb. 4, 2009, in the online journal PLoS.

"This stunning discovery reinforces the belief that modern cetaceans originated from terrestrial ancestors," said H. Richard Lane, program director in the National Science Foundation (NSF)'s Division of Earth Sciences, which funded the research.

Paleontologist Philip Gingerich of the University of Michigan, who led the team that made the discoveries, was at first perplexed by adult female and fetal bones found together.

"When we first saw the small teeth, we thought we were dealing with a small adult whale, but then we continued to expose the specimen and found ribs that seemed too large to go with those teeth," Gingerich said. "By the end of the day, we realized we had found a female whale with a fetus".

It is the first discovery of a fetal skeleton of an extinct whale in the group known as Archaeoceti, and the find represents a new species dubbed Maiacetus inuus. (Maiacetus means "mother whale," and Inuus was a Roman fertility god.)......... Posted by: Kelly      Read more         Source

February 4, 2009, 10:55 PM CT

Largest Prehistoric Fossil Snake

Researchers have recovered fossils from a 60-million-year-old South American snake whose length and weight might make today's anacondas seem like garter snakes.

Named Titanoboa cerrejonensis by its discoverers, the size of the snake's vertebrae suggest it weighed 1,140 kilograms (2,500 pounds) and measured 13 meters (42.7 feet) nose to tail tip.

A paper describing the find appears in this week's issue of the journal Nature.

"At its greatest width, the snake would have come up to about your hips," said geologist David Polly of Indiana University, who identified the position of the fossil vertebrae, which made an estimate possible. "The size is pretty amazing. We went a step further and asked, how warm would the Earth have to be to support a body of this size?".

Smithsonian Tropical Research Institute geologist Carlos Jaramillo and University of Florida vertebrate paleontologist Jonathan Bloch discovered the fossils in the Cerrejon Coal Mine in northern Colombia, and investigated what the snake's environment might have been like.

Paleontologist Jason Head of the University of Toronto, the Nature paper's main author, made an estimate of Earth's temperature 58 to 60 million years ago in an area encompassed by modern-day Colombia......... Posted by: Kelly      Read more         Source

February 4, 2009, 6:22 AM CT

Methyl bromide for North Carolina tomato production

Methyl bromide (MeBr) is a highly effective broad-spectrum fumigant used extensively in U.S. agriculture to control a wide variety of pests. Under the Montreal protocol of 1991, however, MeBr was defined as one of the chemicals that contributed to the depletion of the stratospheric ozone layer, resulting in an incremental reduction in the amount of MeBr produced and imported in the U.S. In January 2005, a total phase out of MeBr (except for emergency and critical-use exceptions) was imposed.

The U.S. Department of Agriculture has indicated that the phaseout of MeBr as a preplant soil fumigant may have substantial impact on the production levels of a number of agricultural crops. No known single alternative fumigant, chemical, or other technology exists that can readily substitute for MeBr in efficacy, cost, ease of use, availability, worker safety, and environmental safety.

Fresh-market tomatoes were planted on 124,400 acres in the United States in 2007, with a gross production value of almost $1300 million. Southeastern states, including Georgia, North Carolina, South Carolina, Tennessee, and Virginia, accounted for about 17% of the total tomato production in the U.S. Tomatoes accounted for 25% of the use of MeBr in the U.S., making tomato growers one of the main groups impacted by the MeBr regulations......... Posted by: Erica      Read more         Source

February 4, 2009, 6:20 AM CT

Does hotter mean healthier?

Phytophthora blight, caused by Phytophthora capsici, is a major plant disease that affects a number of crop species worldwide, including chile peppers in New Mexico. Farmers' observations suggested that Phytophthora capsici caused less damage in pepper crops of the hot pepper varieties than low-heat pepper varieties.

A study reported in the October 2008 issue of HortScience by the research team of Mohammed B. Tahboub (postdoctoral researcher), Soumaila Sanogo (plant pathologist and team leader), Paul W. Bosland (chile pepper breeder), and Leigh Murray (statistician) set out to determine whether or not the severity of Phytophthora blight would be greater in low-heat than in hot chile peppers.

The most effective means for controlling Phytophthora blight are chile pepper cultivars that are genetically resistant to the disease. Some resistant lines have been identified, but currently there are no cultivars that are resistant to the blight in all environments.

Chile pepper fruit become infected during prolonged periods of heavy rain and high humidity in flooded and poorly drained fields. Previous to this study, there had been no systematic assessment of the relationship of chile pepper heat level to chile pepper response to Phytophthora capsici If such a connection could be found, information might have been revealed that would assist breeding programs intended for developing disease-resistant cultivars of pepper......... Posted by: Erica      Read more         Source

February 2, 2009, 6:29 AM CT

Preparing for climate change

The global climate is changing, and this change is already impacting food supply and security. People living in regions already affected by aridity need plants that can thrive / grow under dry conditions.

One example is sorghum: Also known as milo, durra, or broomcorn, sorghum is a grass species that can grow up to five meters in height and is extremely resistant to aridity and hot conditions. The grass, which originates from Africa, can thrive under conditions and locations where other cereal plants cannot survive due to lack of water. In arid-warm and moderate regions of the Americas, Asia and Europe it is mainly utilized for food and fodder and is also gaining in significance as a basis for bio-fuel. The plant also provides fibers as well as combustible material for heating and cooking.

As part of an international consortium of scientists, scientists at Helmholtz Zentrum München are analyzing the genes of sorghum, the first plant of African origin whose genome has been sequenced.

Dr. Klaus Mayer of the Institute of Bioinformatics and Systems Biology of the Helmholtz Zentrum München described the scientists' research goal: "We want to elucidate the functional and structural genomics of sorghum." He went on to explain: "That is the prerequisite for making this important grain even more productive through targeted breeding strategies. As German Research Center for Environmental Health, sustaining the food supply is one of our most important research topics. That is why we are trying to learn something about the molecular basis of the plant's pronounced drought tolerance in order to apply this knowledge to other crop plants in our latitude zone as well. "The first results of the study have been reported in the current issue of Nature......... Posted by: Erica      Read more         Source

February 2, 2009, 6:13 AM CT

New class of genes found in mammals

A research team at the Broad Institute of Harvard and MIT and Beth Israel Deaconess Medical Center has uncovered a vast new class of previously unrecognized mammalian genes that do not encode proteins, but instead function as long RNA molecules. Their findings, presented in the February 1st advance online issue of the journal Nature, demonstrate that this novel class of "large intervening non-coding RNAs" or "lincRNAs" plays critical roles in both health and disease, including cancer, immune signaling and stem cell biology.

"We've known that the human genome still has a number of tricks up its sleeve," said Eric Lander, founding director of the Broad Institute and co-senior author of the Nature paper. "But, it is astounding to realize that there is a huge class of RNA-based genes that we have almost entirely missed until now".

Standard "textbook" genes encode RNAs that are translated into proteins, and mammalian genomes harbor about 20,000 such protein-coding genes. Some genes, however, encode functional RNAs that are never translated into proteins. These include a handful of classical examples known for decades and some recently discovered classes of tiny RNAs, such as microRNAs.

By contrast, the newly discovered lincRNAs are thousands of bases long. Because only about ten examples of functional lincRNAs were known previously, they seemed more like genomic oddities than critical components. The new Nature study shows that there are actually thousands of such genes and that they have been conserved across mammalian evolution......... Posted by: Kelly      Read more         Source

January 30, 2009, 6:22 AM CT

Surprising lion stronghold in central Africa

Times are tough for wildlife living at the frontier between Uganda and the Democratic Republic of the Congo. Armies are reportedly encamped in a national park and wildlife preserve on the Congolese side, while displaced herders and their cattle have settled in an adjoining Ugandan park.

And yet, the profusion of prey in the region could potentially support more than 900 individuals of the emblematic African lion, as per new research but only if immediate conservation steps are taken.

"Those two protected areas that straddle the frontier could be the stronghold for lions in central Africa the largest population," says University of Wisconsin-Madison environmental studies professor Adrian Treves, the study's main author. "Therefore, (the population) is critically important, because the lion is now considered threatened throughout Africa".

He and fellow scientists from the Wildlife Conservation Society and the Panthera Foundation report their findings in the recent issue of the journal Oryx, which published online today (Jan. 29).

While the conflict raging in D.R. Congo makes conservation efforts in that country's Parque National Virungas (PNVi) nearly impossible right now, says Treves, action can be taken in Uganda's Queen Elizabeth National Park (QENP). In an attempt to protect their livestock, cattlemen there have reportedly poisoned and shot predators in large numbers, stirring fears that the king of beasts appears to be driven to extinction in Uganda......... Posted by: Kelly      Read more         Source

January 29, 2009, 6:16 AM CT

Genetic blueprint of key biofuels crop

Researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and several partner institutions have published the sequence and analysis of the complete genome of sorghum, a major food and fodder plant with high potential as a bioenergy crop. The genome data will aid researchers in optimizing sorghum and other crops not only for food and fodder use, but also for biofuels production. The comparative analysis of the sorghum genome appears in the January 29 edition of the journal Nature

Prized for its drought resistance and high productivity, sorghum is currently the second most prevalent biofuels crop in the United States, behind corn. Grain sorghum produces the same amount of ethanol per bushel as corn while utilizing one-third less water. As the technology for producing "cellulosic" (whole plant fiber-based) biofuels matures, sorghum's rapid growth--rising from eight to 15 feet tall in one season--is likely to make it desirable as a cellulosic biofuels "feedstock."

"This is an important step on the road to the development of cost-effective biofuels made from nonfood plant fiber," said Anna C. Palmisano, DOE Associate Director of Science for Biological and Environmental Research. "Sorghum is an excellent candidate for biofuels production, with its ability to withstand drought and prosper on more marginal land. The fully sequenced genome will be an indispensable tool for scientists seeking to develop plant variants that maximize these benefits."........ Posted by: Erica      Read more         Source

Thu, 29 Jan 2009 06:18:02 GMT

Fluorescent timers

While we’re waiting for the most exciting future biophysics tool to get built, there are all kinds of practical improvements to current-generation microscopy that would still be exciting and useful. We’ve talked a lot about increasing the spatial resolution of optical microscopy, but it would also be useful to have tools for temporal measurements of dynamics in a living cell. Many cellular processes occur on temporal scales of many hours, and being able to track such processes with current-generation optical microscopes would still give exciting information about intracellular trafficking and dynamics. To do this, a tagging system that would give temporal information as well as spatial information is necessary.

A paper in the February issue of Nature Chemical Biology discusses just such a technique. Subach et al’s Monomeric fluorescent timers that change color from blue to red report on cellular trafficking introduces a new fluorescent timer system based on directed evolution of mCherry, a protein that fluoresces in the red. By carrying out mutagenesis on selected amino acids that interact with the chromophore of the GFP-like protein, it was possible to generate variants of the protein that had differing maturation rates for the chromophore (leading to different fluorescence intensities over time), as well as a temporal shift in the fluorescence spectrum from blue to red. Different mutants resulted in fast-, medium-, and slow-fluorescent timer molecules where the maturation rate of the fluorescence change varied as their namesake.

An example of the maturation of the slow-FT reporter fused to a protein in mammalian cells is shown in the figure below. This shows the ratio of blue to red fluorescence as a function of time in vivo, where even in the complex environment of the cell, the temporal properties of the fluorescent timers remain intact.

This system of fluorescent reporters was then used to study the dynamics of lysosome-associated membrane protein 2A, a protein that must reach lysosomes either via the Golgi complex directly, or via endocytosis from the plasma membrane. The medium-FT molecules had an ideal timescale to study the LAMP-2A intracellular dynamics, and the figure below shows the result of expressing a LAMP-2A-medium-FT fusion protein in mammalian cells.

Careful analysis of the localization and colours of fluorescence made it possible to conclude that a primarily indirect pathway for LAMP-2A trafficking is taken, based on the blue-to-red ratios both near the plasma membranes and in the Golgi. While the details of this specific experiment are complex, the above figure shows that this is a very powerful new technique to study both localization and temporal dynamics in vivo, and a range of fluorescent timer mutants with fast to slow dynamics should give the ability to study a wide range of intracellular processes. Indeed, the authors point out a number of interesting things to study in their conclusion:

FT proteins will also allow for identification of recycling events among compartments, temporal tracking of molecules before and after a particular cellular event (without the need for additional labeling or artificial photoswitching) and timing of particular intracellular post-translational modifications traceable by fluorescent procedures such as ubiquitination and farnesylation. The optical microscope has a lot of science left to do. Posted by: PhilipJ      Read more     Source

January 28, 2009, 6:26 AM CT

Biofeedback from the Zoo

Almost three percent of all Americans suffer from Obsessive-Compulsive Disorder (OCD). But when do you cross the line between a neurotic compulsion to check your email every five minutes and mental illness?

As per new Tel Aviv University research, the best way to understand and effectively treat OCD is to look at ourselves as though we're animals in a zoo. "We've developed a program that allows us to videotape people that suffer from overt compulsions and compare their behavior to classic displays of neurotic or healthy behavior from the animal kingdom, observed in the wild or in captivity," says Prof. David Eilam from the Department of Zoology at Tel Aviv University.

Studying bears, gazelles, and rats, among other animals, the Tel Aviv University researchers have developed a model to identify and understand abnormal behavior. The model is, in effect, a reference database that gives mental health practitioners a way to classify different behaviors when they observe a patient at the clinic or on video.

A Descriptive Tool Becomes a Treatment Tool.

Watching animals in the wild, and then in captivity at Tel Aviv University's Research Zoo, Prof. Eilam noticed that a uniform repetition of motor patterns occurs in wild animals in captivity. He then understood that the rituals performed by animals in captivity could give clues about OCD and unnecessary actions, such as excessive hand washing, performed by humans. "In the wild, animals perform automated routines, not rituals," says Prof. Eilam. "But in captivity, the animals' attention focus is on perseverating rituals, with an explicit emphasis on performance ? just like they had OCD"......... Posted by: Kelly      Read more         Source