September 17, 2007, 5:00 AM CT

Effort to 'barcode' world's species

Smithsonian scientists are among the leaders in a worldwide effort to revolutionize the way researchers identify species in the laboratory and in the field with a technique called DNA barcoding. Similar to the barcode that identifies an item at the grocery store, a DNA barcode is used to identify and distinguish biological species.

This month, researchers are gathering in Taiwan for the Second International Barcode of Life Conference (Sept. 17-21). They will discuss potential applications for using DNA barcodes, including food safety, disease prevention and better environmental monitoring. There are now more than 280,000 DNA barcode records representing about 31,000 species.

DNA barcoding is emerging as a global standard for identifying species in basic taxonomic research, biodiversity studies and in government regulation. The Smithsonians researchers are important leaders in the Barcode of Life Initiative, and the National Museum of Natural History is demonstrating the importance of museum collections, said David Schindel, executive secretary of the Consortium for the Barcode of Life, based at the Smithsonians National Museum of Natural History.

Each of the worlds estimated 1.8 million species is genetically uniqueits unique identity is carried in its DNA molecules. DNA barcoding rapidly sequences the DNA from a single, standardized gene on the DNA molecule. The technique can quickly identify species from larval forms or tissue samples that can sometimes be nearly impossible to identify through traditional methods......... Posted by: Janet      Read more         Source

September 12, 2007, 8:24 PM CT

Microinjection Of Zebrafish Embryos

Funded by an NSERC Idea to Innovations grant and an Ontario Early Researcher Award, Prof. Yu Suns group, the Advanced Micro and Nanosystems Laboratory (http://amnl.mie.utoronto.ca) at the University of Toronto (U of T) recently developed a microrobotic technology for automated microinjection of zebrafish embryos.

Based on computer vision and motion control, the automated microrobotic system is capable of immobilizing a large number of zebrafish embryos into a regular pattern within seconds and injecting 15 embryos (chorion unremoved) per minute with a success rate, survival rate, and phenotypic rate all close to 100%. The system and performance were published in the journal PLoS ONE in an article entitled, A Fully Automated Robotic System for Microinjection of Zebrafish Embryos.

Zebrafish is a model organism widely used in life sciences. High-speed injection of zebrafish embryos is important for screening genes in genetics and drug molecules in drug discovery. The automated microrobotic system proves itself as a reliable tool for determining gene functions and more generally, for facilitating large-scale molecule screening......... Posted by: Kelly      Read more         Source

September 12, 2007, 8:16 PM CT

Corals added to IUCN Red List of Threatened Species

For the first time in history, the IUCN Red List of Threatened Species includes ocean corals in its annual report of wildlife going extinct.

A comprehensive study of marine life sponsored by Conservation International (CI) and implemented jointly with the IUCN (World Conservation Union) used data from the Galapagos-based Charles Darwin Research Station and other regional institutions to conclude that three species of corals unique to the Galapagos Islands could soon disappear forever.

The 2007 IUCN Red List designates two of the corals Floreana coral (Tubastraea floreana) and Wellingtons solitary coral (Rhizopsammia wellingtoni) as Critically Endangered, while a third Polycyathus isabela is listed as Vulnerable. The Red List also includes 74 Galapagos seaweeds, or macro-algae, with 10 of them receiving the most threatened status of Critically Endangered. Previous to 2007, only one algae species had been included on the Red List.

There is a common misconception that marine species are not as vulnerable to extinction as land-based species, said Roger McManus, CIs vice president for marine programs. However, we increasingly realize that marine biodiversity is also faced with serious environmental threat, and that there is an urgent need to determine the worldwide extent of these pressures to guide marine conservation practice......... Posted by: Janet      Read more         Source

September 12, 2007, 6:50 PM CT

A small leak will sink a great ship

Flowers of higher plants are built in a similar pattern: their outermost whorl is composed of sepals, which protect the young bud, thereafter comes a whorl of often colorful petals attracting insect pollinators, followed by a whorl of stamens with pollen sacks and the innermost whorl holds carpels, which later give rise to the fruit and seeds. This basic architecture is comparable in higher plants prompting the question after common components of a genetic 'masterplan'.

Researchers in the group of Zsuzsanna Schwarz-Sommer investigated a mutant of snapdragon where stamens form instead of petals (Fig. 1). Interestingly, a strikingly similar mutant occurs in another plant species, in Petunia. 'We already suspected some ten years ago when we first looked at these mutants that in the two species a similar defect might disturb the genetic control resulting in the 'wrong organ at the wrong place' explains Mrs. Schwarz-Sommer. A similar example is well known in the fruit fly where a mutant carries a pair of legs at the head instead of the two antennae.

Indeed, experiments performed by the German and Dutch researchers showed that in the two plant species mutation in the same gene conferred altered identity to the floral organs. This gene turned out to code for a microRNA, a small ribonucleic acid consisting of little more than 20 nucleotides. MicroRNAs can recognize and bind to complementary sequences present in messenger RNAs (mRNA) and prevent thereby translation of the mRNA into a protein: the respective gene falls silent. By this interaction microRNAs can influence whole chains of control events......... Posted by: Erica      Read more         Source

September 12, 2007, 6:42 PM CT

One species, many genomes

To track down the variation in the genome of the different Arabidopsis strains, the scientists compared the genetic material of 19 wild strains with that of the genome of the lab strain, which was sequenced in the year 2000. Using a very elaborate procedure, they examined every one of the roughly 120 million building blocks of the genome. For their molecular sleuthing they used almost one billion specially designed DNA probes. "All together, these probes would have seven times the length of human genome," illustrates Weigel the extent of the project. The data were reviewed with several specially designed statistical methods, including a variant of machine learning.

The result of this painstaking analysis: on average, every 180th DNA building block is variable. And about four percent of the reference genome either looks very different in the wild varieties, or cannot be found at all. Almost every tenth gene was so defective that it could not fulfill its normal function anymore!

Results such as these raise fundamental questions. For one, they qualify the value of the model genomes sequenced so far. "There isn't such a thing as the genome of a species," says Weigel. He adds "The insight that the DNA sequence of a single individual is by far not sufficient to understand the genetic potential of a species also fuels current efforts in human genetics"......... Posted by: Erica      Read more         Source

September 12, 2007, 6:00 PM CT

Gray Whales Population On Decline

Gray whales in the Pacific Ocean, long thought to have fully recovered from whaling, were once three to five times as plentiful as they are now, as per a new article.

Today's population of more than 22,000 gray whales has successfully been brought back from the threat of extinction and is now the most abundant whale on the North American west coast. But the new findings from scientists at Stanford University and the University of Washington suggest that the current population is actually far below the original number--estimated by genetic methods at 96,000 animals--that once roved the Pacific Ocean.

The report also weighs in about why large numbers of gray whales have recently been discovered suffering from starvation. Previously it was assumed that the thin and starving animals are a consequence of the gray whale population exceeding its historical ecological limits. But if the Pacific normally housed 96,000 gray whales, then starving whales may be suffering reduced food supply from changing climate conditions in their Arctic feeding grounds. This possibility parallels reports last year of major climate shifts in the Arctic ecosystems in which gray whales feed. The study also suggests that lowered numbers of gray whales no longer play their normal role in ocean ecology......... Posted by: Kelly      Read more         Source

September 12, 2007, 5:57 PM CT

Color Night Vision In The Aye-Aye

A quest to gain a more complete picture of color vision evolution has led Biodesign Institute researcher Brian Verrelli to an up-close, genetic encounter with one of the world's most rare and bizarre-looking primates.

Verrelli and his ASU team have performed the first sweeping study of color vision in the aye-aye (pronounced "eye-eye"), a bushy-tailed, Madagascar native primate with a unique combination of physical features including extremely large eyes and ears, and elongated fingers for reaching hard to access insects and other foods. Verrelli, lead author George Perry, and collaborator Robert Martin's results, reported in the journal Molecular Biology and Evolution, have led to some surprising conclusions on how this nocturnal primate may have retained color vision function.

Verrelli's group focuses on color vision to better understand genetic variation between human and other primate populations and the truly big evolutionary questions as to what makes us human. "At least within humans and some other primates, we know that there are three different genes responsible for color vision," said Verrelli. The genes, called opsins, come in three forms that shape our color vision palette, one for blue, another for green, and a third for red.

"What makes that very interesting is that the green and red are found on the X chromosome [sex chromosome], and it is the manipulation of those two genes alone which is correlation to color blindness for eight to ten percent of the male population," explains Verrelli. In a 2004 study in the American Journal of Human Genetics by Verrelli and collaborator Sarah Tishkoff of the University of Maryland, they suggested that natural genetic selection has provided women with a frequent ability to better discriminate between colors than men......... Posted by: Kelly      Read more         Source

September 12, 2007, 5:51 PM CT

Tasmanian Tiger No Match For Dingo

The wily dingo out-competed the much larger marsupial thylacine by being better built anatomically to resist the "mechanical stresses" linked to killing large prey, say Australian scientists.

Despite being armed with a more powerful and efficient bite and having larger energy needs than the dingo, the thylacine was restricted to eating relatively small prey while the dingo's stronger head and neck anatomy allowed it to subdue large prey as well.

Earlier studies had given ambiguous results regarding the size of prey favoured by the thylacine, and had suggested that changes in mainland Aboriginal culture may have driven its extinction 3,000 years ago in mainland Australia.

This new conclusion, published recently in Proceedings B of the Royal Society, is based on sophisticated computer simulations revealing bite forces and stress patterns applying to dingo and thylacine skull specimens.

A team led by UNSW palaeontologist Stephen Wroe, along with Karen Moreno (UNSW) and University of Newcastle colleagues, Colin McHenry and Philip Clausen, conducted the research.

The simulations illustrate mechanical stresses and strains applying to the skull, jaw, teeth and cranial muscles of both animals across a range of biting, tearing and shaking motions that simulate the impact of controlling and killing a struggling prey......... Posted by: Kelly      Read more         Source

September 11, 2007, 11:48 PM CT

Biological invasions can begin with just 1 insect

A new study by York University biologists Amro Zayed and Laurence Packer has shown that a lone insect can initiate a biological invasion.

Zayed, a recent graduate of Packers lab, examined patterns of genetic diversity in both native European and invasive North American populations of a solitary bee. He concluded that the invasion was most likely founded by one mated female. The study was published recently in the open access journal PLoS ONE.

This is a shocking result, particularly since bees suffer from huge genetic problems in small populations, says Zayed, now a postdoctoral fellow in the Department of Entomology at the University of Illinois.

Were now seeing that the introduction of even one single insect can cause a potentially costly invasion, so we have to be extremely vigilant with reducing the number of animals that are unintentionally transported around the globe, he says.

The study contradicts a popular theory of invasive biology: the more individuals introduced to an area, the higher the success of the invasion. This concept is usually referred to as the propagule pressure hypothesis.

Zayed adds that numbers are not the only factor controlling the success of invasions. Chance and the specific characteristics of invasive species and their introduced habitats can be more important, he says......... Posted by: Kelly      Read more         Source

September 11, 2007, 11:46 PM CT

Scientists fear rare dolphin driven to extinction

An international research team, including biologists from NOAA Fisheries Service, has reported in an online scientific journal that it had failed to find a single Yangtze River dolphin, or baiji, during a six-week survey in China. The researchers fear the marine mammal is now extinct due to fishing and commercial development, which would make it the first cetacean to vanish as result of human activity.

The research paper, published last month in the online journal Biology Letters, reports that an intensive acoustical and visual survey of the main Yangtze River where the baiji live failed to find what was already considered to be one of the worlds most endangered species.

The last time these animals were surveyed was in the 1990s when only 13 were found, said Barbara Taylor, a marine biologist at NOAAs Southwest Fisheries Science Center in La Jolla, Calif., and one of the scientists on the scientific team that was working with local researchers at the invitation of the Chinese government. This time, we detected no baiji, either visually or acoustically. This would be the first human-caused extinction of a dolphin or whale and it is especially sad for the last member of a family of a species that is over 20 million years old.

The baiji is one of only a few dolphin species that is known to have adapted from the ocean to a freshwater environment. The likely cause of the baijis decline is from the use of fishing nets with hooks that snag and drown the dolphins as bycatch. Other causes may include habitat degradation......... Posted by: Kelly      Read more         Source