Archive for August, 2008

Cool Volcano Photos!

Friday, August 22nd, 2008

Next time you you worry about earth shaking events picture this:

Fish Tale Has A DNA Hook - Students Find Bad Labels

Friday, August 22nd, 2008

From the New York Times - August 22, 2008

Many New York sushi restaurants and seafood markets are playing a game of bait and switch, say two high school students turned high-tech sleuths.

In a tale of teenagers, sushi and science, Kate Stoeckle and Louisa Strauss, who graduated this year from the Trinity School in Manhattan, took on a freelance science project in which they checked 60 samples of seafood using a simplified genetic fingerprinting technique to see whether the fish New Yorkers buy is what they think they are getting.

They found that one-fourth of the fish samples with identifiable DNA were mislabeled. A piece of sushi sold as the luxury treat white tuna turned out to be Mozambique tilapia, a much cheaper fish that is often raised by farming. Roe supposedly from flying fish was actually from smelt. Seven of nine samples that were called red snapper were mislabeled, and they turned out to be anything from Atlantic cod to Acadian redfish, an endangered species.

What may be most impressive about the experiment is the ease with which the students accomplished it. Although the testing technique is at the forefront of research, the fact that anyone can take advantage of it by sending samples off to a laboratory meant the kind of investigative tools once restricted to Ph.D.’s and crime labs can move into the hands of curious diners and amateur scientists everywhere.

The project began, appropriately, over dinner about a year ago. Ms. Stoeckle’s father, Mark, is a scientist and early proponent of the use of DNA bar coding, a technique that greatly simplifies the process of identifying species. Instead of sequencing the entire genome, bar coders — who have been developing their field only since 2003 — examine a single gene. Dr. Stoeckle’s specialty is birds, and he admits that he tends to talk shop at the dinner table.

One evening at a sushi restaurant, Ms. Stoeckle recalled asking her father, “Could you bar code sushi?”

Dr. Stoeckle replied, “Yeah, I think you could — and if you did that, I think you’d be the first ones.”

Ms. Stoeckle, who is now 19, was intrigued. She enlisted Ms. Strauss, who is now 18.

Their field technique was simple, Ms. Stoeckle said. “We ate a lot of sushi.”

Or, as Dr. Stoeckle put it, “It involved shopping and eating, in which they were already fluent.”

They hit 4 restaurants and 10 grocery stores in Manhattan. Once the samples were home, whether in doggie bags or shopping bags, they cut away a small piece and preserved it in alcohol. They sent those off to the University of Guelph in Ontario, where the Barcode of Life Database project began. A graduate student there, Eugene Wong, works on the Fish Barcode of Life (dubbed, inevitably, Fish-BOL) and agreed to do the genetic analysis. He compared the teenagers’ samples with the global library of 30,562 bar codes representing nearly 5,500 fish species. (Commercial labs will also perform the analysis for a fee.)

Three hundred dollars’ worth of meals later, the young researchers had their data back from Guelph: 2 of the 4 restaurants and 6 of the 10 grocery stores had sold mislabeled fish.

Dr. Stoeckle said he was excited to see a technology used in a new way. “The smaller and cheaper you make something,” he said, “the more uses it has.” He compared bar coding to another high-tech wonder turned everyday gadget, GPS.

Eventually, he predicted, the process will become more automatic, cheaper and smaller so that a handheld device could perform a quick analysis and connect to the database remotely. What his daughter did, he said, is like dropping film off at the supermarket for developing. The next generation could be more like a digital camera that displays the results on the spot.

The results of Ms. Strauss and Ms. Stoeckle’s research are being published in Pacific Fishing magazine, a publication for commercial fishermen. The sample size is too small to serve as an indictment of all New York fishmongers and restaurateurs, but the results are unlikely to be a mere statistical fluke.

The experiment does serve as a general caveat emptor for fish lovers, particularly because the students, their parents and their academic mentor all declined to give the names of the vendors, citing fear of lawsuits. Besides, they noted, mislabeling could occur at any stage of the process.

Dr. Stoeckle was willing to divulge the name of one fish market whose products were accurately labeled in the test: Leonards’ Seafood and Prime Meats on Third Avenue. John Leonard, the owner, said he was not surprised to find that his products passed the bar code test. “We go down and pick the fish out ourselves,” he said. “We know what we’re doing.” As for the technology, Mr. Leonard said, “it’s good for the public,” since “it would probably keep restaurateurs and owners of markets more on their toes.”

Ms. Stoeckle said the underlying message of the research was simple: “If you’re paying for white tuna and you’re eating tilapia, I think you’d want to know that.”

Although the students did not present the project for a grade at school, they made sure to mention it on their college applications. Both will enroll at Johns Hopkins University this fall.

Neither, however, expects to major in the sciences. “I’ve always been into art history,” Ms. Strauss said, “which is really different from this.” Ms. Stoeckle, who is the granddaughter of the entertainer and arts patron Kitty Carlisle Hart, is thinking about studying writing or psychology. But that, they said, is the point. “If we found it interesting — which we did — I think lots of people like us can do it, too,” Ms. Stoeckle said.

Peter B. Marko, a professor at Clemson University who used a more detailed genetic technique in a 2004 paper to show that red snapper was commonly mislabeled, called their project “quite remarkable,” though he added that genetic analysis had been simplified to the point that high school students could now perform the task without sending samples off.

Mr. Marko prefers to work with whole genomes — “more information is better,” he explained — which can be sequenced now with lightning speed. He plans to perform a broad genetic comparison of fishes that were separated millions of years ago by the rise of the Isthmus of Panama. “The technology is allowing us to ask questions that really would not have been possible in the past.”

The students worked under the tutelage of Jesse H. Ausubel of Rockefeller University, a champion of the DNA bar coding technique. As for Ms. Strauss and Ms. Stoeckle, Dr. Ausubel said they “have contributed to global science” by adding to the database, built on a model similar to that of Wikipedia, in which people around the world can contribute.

In a way, Dr. Ausubel said, their experiment is a return to an earlier era of scientific inquiry. “Three hundred years ago, science was less professionalized,” he said, and contributions were made by interested amateurs. “Perhaps the wheel is turning again where more people can participate


Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities

Friday, August 22nd, 2008
As Aesop said, appearances are deceiving—even in life’s tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye. The findings, reported in the August 21 online edition of the journal Nature, establish a group of organisms as a branching point of animal evolution and identify sets of genes, or a “parts list,” employed by organisms that have evolved along particular branches.
With each sequenced genome, another dataset is made available to advance the quest of evolutionary biologists seeking to reconstruct the tree of life. The analysis of the 98 million base pair genome of Trichoplax (literally “hairy-plate”) illuminates its ancestral relationship to other animals. Trichoplax is the sole member of the placozoan (”tablet,” or “flat” animal) phylum, whose relationship to other animals, such as bilaterians (humans, flies, worms, snails, et al) and cnidarians (jellyfish, sea anemones, corals, et al), and sponges is contentious.

“Our whole genome analysis supports placing the placozoans after the sponge lineage branched from other animals,” said Daniel Rokhsar, the publication’s senior author, DOE JGI’s head of Computational Genomics Program, and Professor of Genetics, Genomics and Development at the University of California, Berkeley.

“Trichoplax has had just as much time to evolve as humans, but because of its morphological simplicity, it is tempting to think of it as a surrogate for an early animal,” said Mansi Srivastava, the study’s first author, a graduate student under the direction of Rokhsar, at the Center for Integrative Genomics, U.C. Berkeley.

Earlier mitochondrial DNA studies suggested that this “mother of all metazoans,” Trichoplax, was the earliest branch, before sponges diverged, but this remains debatable—even among collaborators.

“The latest and most complex analysis again suggests that placozoans populated the oceans long before sponges evolved,” said Bernd Schierwater, director of the Institute of Animal Ecology & Cell Biology and head of the Center for Biodiversity at TiHo Hannover, Germany. Schierwater, a study co-author, joined Stephen Dellaporta and Leo Buss of Yale University in proposing the Trichoplax sequencing project in 2004 to DOE JGI’s Community Sequencing Program [].

“The outcome of the Trichoplax adhaerens genome sequencing is so exciting that we are now culturing another 13 placozoan species in order to identify the most basal placozoan lineage and genome,” said Schierwater.

“Trichoplax is an ancient lineage—a good representation of the ancestral genome that is shedding light of the kinds of genes, the structures of genes, and even how these genes were arranged on the genome in the common ancestor 600 million years ago,” said Srivastava. “It has retained a lot of primitive features relative to other living animals.”

Originally collected from the Red Sea, and cultured over the last 40 years in the laboratory, Trichoplax is a two-millimeter flat disk containing fluid sandwiched between two cell layers. It lacks organs and only has four or five cell types. Yet, despite its apparent simplicity, its genome encodes a panoply of signaling genes and transcription factors usually associated with more complex animals.

Trichoplax has no neurons, but has many genes that are associated with neural function in more complex animals. “It lacks a nervous system, but it still is able to respond to environmental stimuli. “It has genes, such as ion channels and receptors, that we associate with neuronal functions, but no neurons have ever been reported,” explained Rokhsar.

Of the 11,514 genes identified in the six chromosomes of Trichoplax, 80 percent are shared with cnidarians and bilaterians. Trichoplax also shares over 80 percent of its introns—the regions within genes that are not translated into proteins—with humans. Even the arrangement of genes is conserved between the Trichoplax and human genomes. This stands in contrast to other model systems such as fruit flies and soil nematodes that have experienced a paring down of non-coding regions and a loss of the ancestral genome organizations.

With its pancake shape, gutless feeding, and genomic primitiveness, the rich array of metabolic capabilities begs additional consideration. While it has been observed to motor around via cilia, eat by mounting its prey, and reproduce by fission (pulling itself into pieces)—it may in fact have a secret sex life.

“Some of our new placozoan species show frequent sexual reproduction while others never show any signs of sex,” said Schierwater. “The genome data allow us to search for the genes responsible for sex and life cycle complexity.”

“It’s remarkable that we have the whole genome sequence but we still know so little about this animal in the wild,” said Rokhsar. “Hopefully the genome sequence will stimulate more studies of this enigmatic creature.”

Source: DOE/Joint Genome Institute

Teacher Rocket Balloon Cars

Saturday, August 16th, 2008

I thought you’d like to hear about our successful science lesson today. We’ve been learning about Neil Armstrong and the Wright Brothers so I found an experiement called The Rocket Balloon. You are probably familiar with it. Anyway, first I demonstrated it for the class. Then I divided them into four teams of four. Each student had an assigned job and all the materials were ready on the table. I told them that part of their science grade was to see how they worked in teams because astronauts can’t argue in space about whose doing what. It was interesting to just sit back and watch them working together. After letting them do the experiment four or five times, they cleaned up and wrote about it in their journals. I’ve never seen them write so quietly and so focused before! One of the requirements was to explain what they had learned. It was a little hard for some to put it in to words but they were able to explain the activity very well. It is definitely one that I will do again next year.

Take care,

Shark-Inspired Boat Surface

Sunday, August 10th, 2008

Materials Engineers Turn to Ferocious Fish for Nonstick Ship Coating

May 1, 2005 — Researchers are using shark skin as a model for creating new coatings that prevent adhesion of algae and barnacles to boats. The new coating is modeled after sharks’ placoid scales, which have a rectangular base embedded in the skin with tiny spines or bristles that poke up from the surface that prevent things from attaching to the shark’s skin.

GAINESVILLE, Fla.–In the boating industry, a huge problem exists that can be summed up in three words — algae, barnacles and slime. Until now, the only way to prevent these organisms from growing was toxic paint. But researchers are studying a more natural approach that’s inspired by the ocean’s fiercest predator.

In movies, they’re the enemy, but in the world of science, sharks are allies.

Materials engineer Tony Brennan, of University of Florida in Gainesville, uses shark skin as a model for creating new surfaces. “The shark scales have a roughness that approximates the roughness that we had predicted would be a good roughness to stop adhesion,” he says.

Brennan designed the surfaces to prevent algae and barnacles from growing on boats. He says, “We started making surfaces that are mimicking the shark’s skin.”

A computer program helped researchers create the pattern and structure…

“Whatever we can draw, we can make into a surface,” says UF graduate student, Jim Schumacher.

And just like shark skin, spores can’t fit in the ridges and don’t want to balance on top of the surface Brennan and his team designed in the lab. “That’s a tremendous benefit to energy consumption, dollars and maintenance,” Brennan says.

Getting rid of those barnacles and other organisms would mean less cleaning and not having to drag around the extra weight would lower fuel costs.

“If it’s effective, it would tremendously affect the industry,” Emerson says.

When the surface hits the market in the next year, it could impact private boaters and Navy vessels, too. Researchers are also studying the shark-coated surface for medical applications.

Exploring Energy Conservation Through Shark Research

Sunday, August 10th, 2008

Web address:

Dr. Amy Lang and a graduate student work in UA’s water tunnel lab researching skin friction over solid surfaces. (Credit: University of Alabama Photography)ScienceDaily (Dec. 1, 2007) — The stars of the “Jaws” films–sharks–have recently become the subject of a University of Alabama engineering research project. Conducted by Dr. Amy Lang, assistant professor of aerospace engineering and mechanics, the project explores energy conservation and boundary layer control in regard to a shark’s surface.

The project findings will allow researchers to explore natural solutions for the reduction of skin friction over solid surfaces, which could result in new innovations and applications concerning energy conservation. This research will not only provide a greater understanding of the evolutionary development of sharks, but it will also investigate methods of flow control and drag reduction that can be easily applied to mobile vehicles.

Research has shown the issue of reducing drag over solid surfaces can save thousands of dollars. For example, it is estimated that even a 1 percent reduction in drag can save an airline company up to $200,000 and at least 25,000 gallons of fuel per year per aircraft. The resulting reduction in emissions into the air is equally impressive.

Funded through a National Science Foundation Small Grant, the project is investigating the boundary layer flow over a surface that mimics the skin of a fast-swimming shark. The boundary layer is the area closest to the surface where viscous conditions cause drag–in this instance a shark’s skin.

Lang hopes to explain why fast sharks that swim upwards of 60 mph have smaller denticles, or scales, than slower shark species. Evidence suggests that sharks with smaller denticles have the ability to stick out their scales when they swim, allowing them to swim faster and creating a unique surface pattern on the skin that results in various mechanisms of boundary layer control.

“We hope to explain how a shark’s skin controls the boundary layer to decrease drag and swim faster,” said Lang. “If we can successfully show there is a significant effect, future applications to reduce drag of aircraft and underwater vehicles could be possible.”

Lang’s research is being conducted using a water tunnel facility in Hardaway Hall. The water tunnel lab can increase the shark skin geometry by 100 times with a corresponding decrease in flow over the model. This makes the flow over the skin observable, and it allows for the visualization and measurement of flow using modern experimental techniques.

In addition to the National Science Foundation Small Grant, Lang recently received a Lindbergh Grant for this research project. Lindbergh Grants are made in amounts up to $10,580, a symbolic amount representing the cost of building Charles Lindbergh’s plane, the Spirit of St. Louis.
University of Alabama (2007, December 1). Exploring Energy Conservation Through Shark Research. ScienceDaily. Retrieved August 10, 2008, from­ /releases/2007/11/071130155548.htm

Herpes Research Uncovers Possible Clue To Alzheimer’s Disease

Sunday, August 10th, 2008

ScienceDaily (Nov. 7, 2003) — Providence, R.I. — Researchers at Brown University and the Marine Biological Laboratory at Woods Hole, Mass., have found a physical connection between the herpes simplex virus and amyloid precursor protein, a protein that breaks down to form a major component of the amyloid plaques that are consistently present in the brains of persons with Alzheimer’s disease.

Amyloid precursor protein – or APP – breaks down to form beta-amyloid. There is strong evidence, according to the researchers, that beta-amyloid is the underlying cause of Alzheimer’s.

While the scientists caution that no conclusions about Alzheimer’s can be drawn from their findings, Dr. Elaine Bearer, senior research scientist and associate professor in Brown’s Department of Pathology and Laboratory Medicine, believes the work does in fact link the common herpes virus of cold sores with the neurodegenerative disorder. Bearer isalso a summer investigator at the Marine Biological Laboratory at Woods Hole, Mass.

Past studies have implicated the herpes virus in the onset of Alzheimer’s disease, but agreement within the scientific community on the value of that research is far from universal. Bearer expects that the discovery of a physical interaction between APP and the herpes virus will trigger further investigations into the role the virus may play in the disease, and even into possible uses of the virus in therapy.

The scientists stress that none of what they found should cause alarm among those who have at one time had a cold sore. According to Bearer, nearly 85 percent of us harbor the herpes simplex virus and most of us never develop Alzheimer’s.

The researchers discovered the interaction between the herpes simplex virus (HSV) and APP while conducting experiments in the giant axon of squid at the Marine Biological Laboratory. Prasanna Satpute-Krishnan and Joseph A. DeGiorgis, both doctoral candidates in Brown’s graduate program at the time of the research, were seeking to learn how viruses are carried around the body – within cells and from one cell to another. Specifically, they were examining how the herpes simplex virus travels back to the lip area to form a recurring blister after remaining latent for some time in the trigeminal ganglion, a collection of nerve cells next to the brain.

What they found was that the herpes virus was interacting with APP, a putative motor receptor that recruits a microtubular motor, kinesin, for transport through neurons. This was the first time scientists had observed any physical interaction between the herpes virus and APP.

Without the APP, the virus moves backward up an axon (a long extension of a neuron) from the area of the lip towards the trigeminal ganglion. But the Brown researchers discovered that once it interacts with the APP, the virus travels in the opposite direction – what scientists describe as anterograde transport – back down to the lip. The researchers also found that once coupled with the APP, the virus moves remarkably fast.

“It’s as if the virus hijacks a car – which in this case would be the kinesin – and the APP is the driver,” explains Bearer. “The virus takes the APP where it wants to be, not where the APP wants to be.”

The build-up of beta-amyloid (formed in the breakdown of APP) is found consistently in the brains of Alzheimer’s patients, and many scientists are now convinced it is involved in the disease, according to Satpute-Krishnan. Questions persist, however, as to what that involvement is, and why, when APP is found in all of us, it causes problems only in a few.

Perhaps, Bearer speculates, when the APP is co-opted by the herpes virus, the APP breaks down at a location where it would not normally appear – and at a very different rate. “When APP piles up around neurons, the neurons die,” she explains. “But we don’t yet know if this is a secondary or a primary cause of Alzheimer’s.”

“At this point, of course, we don’t yet know whether herpes plays a causal role in Alzheimer’s disease,” DeGiorgis notes. “But our research does provide some interesting new insight into both diseases.”

A paper outlining the findings of the Brown/MBL researchers – titled “Fast Anterograde Transport of Herpes Simplex Virus: Role of Amyloid Precursor Protein” – will appear in the December issue of Aging Cell, published by Blackwell Publishing in England and at the publisher’s “OnlineEarly” site [].

Satpute-Krishnan, the first author of the paper, is a graduate student in Brown’s Molecular Biology, Cell Biology and Biochemistry Graduate Program. Bearer, who holds both an M.D. and a Ph.D., is an experimental pathologist. DeGiorgis, who earned his Ph.D. in Bearer’s lab last year, is now with the National Institutes of Health.

Experiments in this study were conducted in the giant axon of squid, a model widely used in research because with a diameter of nearly a millimeter it is 1,000 times thicker than a human axon. Researchers are able to inject substances into the giant axon and then observe the behavior of those substances through high-powered microscopes.

“It is pretty extraordinary that breakthroughs in Alzheimer’s disease and in the pathogenesis of herpes virus should be made using the squid of the North Atlantic sea,” notes Bearer.

Last summer Brown University and the Marine Biological Laboratory formalized their alliance for teaching and research. The affiliation between the two institutions established the Brown-MBL Graduate Program in Biological and Environmental Sciences. In addition, it will promote faculty exchanges and research collaborations, such as the one conducted by Satpute-Krishnan, DeGiorgis and Bearer.

### The affiliation between MBL and Brown takes advantage of the geographic proximity of the two institutions, uniting their faculty expertise in biology and medicine, particularly for molecular biology, genomics, ecosystems studies, environmental science, global infectious diseases, neuroscience and public health. Student recruitment for the Brown-MBL Graduate Program got under way this fall, with the first students expected to begin their studies next year.

MBL is an internationally known, independent, nonprofit institution dedicated to improving the human condition through creative research and education in the biological, biomedical and environmental sciences. Founded in 1888, the MBL is the oldest private marine laboratory in the Western Hemisphere.

Adapted from materials provided by Brown University.
Brown University (2003, November 7). Herpes Research Uncovers Possible Clue To Alzheimer’s Disease. ScienceDaily. Retrieved August 10, 2008, from­ /releases/2003/11/031107055048.htm

World’s Smallest Snake Discovered

Sunday, August 3rd, 2008
World’s smallest snake discovered

By Jennifer Carpenter
Science reporter, BBC News

The world’s smallest snake, averaging just 10cm (4 inches) and as thin as a spaghetti noodle, has been discovered on the Caribbean island of Barbados.

The snake, found beneath a rock in a tiny fragment of threatened forest, is thought to be at the very limit of how small a snake can evolve to be.

Females produce only a single, massive egg - and the young hatch at half of their adult body weight.

This new discovery is described in the journal of Zootaxa.

The snake - named Leptotyphlops carlae - is the smallest of the 3,100 known snake species and was uncovered by Dr Blair Hedges, a biologist from Penn State University, US.

“I was thrilled when I turned over that rock and found it,” Dr Hedges told BBC News.

“After finding the first one, we turned hundreds of other stones to find another one.”

In total, Dr Hedges and his herpetologist wife found only two females.

Defining species

Dr Hedges thinks that the snake eats termites and is endemic to this one Caribbean island. He said that, in fact, three very old specimens of this species were already in collections - one in London’s Natural History Museum and two in a museum in Martinique.

However, these specimens had been misidentified.

Dr Hedges explained the difficulty in defining a new species when the organism is so small.

“Differences in small animals are much more subtle and so are frequently over-looked,” he said.

Modern genetic fingerprinting is often the only way to tell species apart.

“The great thing is that DNA is as different between two small snakes as it is between two large snakes, allowing us to see the differences that we can’t see by eye,” explained Dr Hedges.

Researchers believe that the snake - a type of thread snake - is so rare that it has survived un-noticed until now.

But with 95% of the island of Barbados now treeless, and the few fragments of forest seriously threatened, this new species of snake might become extinct only months after it was discovered.

Smallest of the small

In contrast to other species of snake - some of which can lay up to 100 eggs in a single clutch - the world’s smallest snake only produces a single egg.

“This is unusual for snakes but seems to be a feature of small animals,” Dr Hedges told BBC News.

By having a single egg at a time, the snake’s young are one-half the length of the adult. That would be like humans giving birth to a 60-pound (27kg) baby

Dr Hedges added that the snake’s size might limit the size of its clutch.

“If a tiny snake were to have more than one offspring, each egg would have to share the same space occupied by the one egg and so the two hatchlings would be half the normal size.”

The hatchlings might then be too small to find anything small enough to eat.

This has led the researchers to believe that the Barbadian snake is as small as a snake can evolve to be.


The smallest animals have young that are proportionately enormous relative to the size of the adults producing the offspring   As in the case of Leptotyphlops carlae , the hatchlings of the smallest snakes are one-half the length of an adult  The hatchlings of the biggest snakes on the other hand are only one-tenth the length of the adult producing the offspring  Tiny snakes produce only one massive egg - relative to the size of the mother. This is evolution at work, says Dr Hedges  The pressure of natural selection means the size of hatchlings cannot be smaller than a critical limit if they are to survive.