“Fossil evidence of early reptiles' last meal - Nature.com” plus 4 more

Fossil evidence of early reptiles' last meal - Nature.com
While Darwin observed evolution, synthetic biologists are learning to ... - Minnpost.com
Harpursville senior wins award from Keuka - Press & Sun-Bulletin
Yakima: New medical school receives federal grant - Tacoma News Tribune
Direct Oncology Foundation Seeks $100,000 to Sequence Genome of Cancer ... - PR.com

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Fossil evidence of early reptiles' last meal - Nature.com

Posted: 23 Dec 2009 08:35 AM PST

In the caves of a hilly Oklahoma ghost town, researchers have found what may be the first evidence of preserved insect remains in the mouths of fossilized vertebrates. The find is compelling evidence that early reptiles, the equivalent of modern-day lizards, fed on insects.

Sean Modesto, a biologist at Cape Breton University in Nova Scotia, Canada, and his colleagues found pieces of arthropod skeleton on the teeth inside two 280-million-year-old skulls of a species of reptile they have yet to fully describe. They report the discovery in the journal Biology Letters¹.

One skull contained a cuticle with five segments that seemed to be part of an antenna, and the other had a long cuticle fragment that was narrow at one end and broader at the tip. This could have been part of a rear appendage.

"It is extremely uncommon to find the remains of organisms in the mouths of fossilized predators," says Matthew Vickaryous, who studies the anatomy of fossil vertebrates at the University of Guelph in Ontario, Canada. "To the best of my knowledge, this is a one of a kind find."

Lucky find

Modesto and his collaborators made this discovery entirely by chance. "You don't expect to see the last meal lodged in the teeth of fossils," Modesto says. "The modern equivalent is finding a popcorn kernel shell in the tooth of an ancient Mayan."

The two skulls come from an enigmatic group called parareptiles, which first appeared nearly 300 million years ago and for the most part became extinct by the end of the Permian period, with just a few species lingering into the age of dinosaurs.

"To have pieces of both vertebrate and invertebrate preserved at the same time is very unusual," Vickaryous says. Vertebrate palaeontologists may overlook small pieces of invertebrate remains when excavating spectacular vertebrate fossils. Beyond the initial detection, preserving the remains requires careful recovery and preparation, he adds.

In younger specimens, researchers have found mollusc shell fragments in the gut of a fossil sea turtle², preserved fish remains in a bird's stomach³, lizard and mammal skeletons in fossil dinosaur stomachs⁴ and dinosaur remains in a fossil mammal's stomach⁵. In fossil reptiles from the Permian, scientists have found plant material in the gut⁶ and reptile bones in the mouth⁷.

But little other evidence is available for the dietary habits of the vertebrates that lived during the Permian, says Conrad Labandeira, palaeoecologist at the National Museum of Natural History in Washington DC. "This paper may be more important in the long run than the original description of the fossil bones."

Insectivorous evidence

Roy Beckemeyer, palaeoentomologist at the University of Kansas Natural History Museum in Lawrence, has studied Permian insect fossils in Oklahoma. He evaluated photographs of the finds and verified that the fragments were from an arthropod. "We know of roughly 200 species of insects in this area during that time," Beckemeyer says. "There's a very good chance that these reptiles were insectivorous."

Scientists had long suspected that early reptiles were insectivorous because of the shape of their teeth, which are sharp and curve inward, making them ideal for piercing insect skeletons and holding struggling prey in place. But that evidence is indirect because it relies on comparisons between extinct and living animals.

"It's pretty much smoking-gun type of evidence when you actually have the organism in the part of the anatomy responsible for feeding," Labandeira says. "It's very compelling evidence that closes the case."

References
1. Modesto, S. P. , Scott, D. M. & Reisz, R. R. Biol. Lett. 5, 838-840 (2009).
2. Kear, B. P. Biol. Lett. 2, 113-115 (2006).
3. Mayr, G. J. Ornithol. 145, 281-286 (2004).
4. Currie, P. J. & Chen, P.-J. Can. J. Earth Sci. 38, 1705-1727 (2001).
5. Hu, Y. , Meng, J. , Wang, Y. & Li, C. Nature 433, 149-152 (2005).
6. Karlsruhe, W. M. & Sues, H.-D. Paläontol. Zeitschr. 67, 169-176 (1993).
7. Eaton, T. H. Jr American Museum Novitates No. 2169 (1964).

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While Darwin observed evolution, synthetic biologists are learning to ... - Minnpost.com

Posted: 23 Dec 2009 06:27 AM PST

"We put new genes in there that encode the enzyme machinery," Schmidt-Dannert said. "We either recombine them from different organisms, and put them together and test them. Or, maybe we even modify the genes so we get better function."

That's the simple description. The actual process takes many rounds of modeling and testing.

"You have to first engineer all of these systems and test drive them," she said.

But the pace is picking up. Automated DNA sequencing, ever more sophisticated computer power and the ability to mass produce DNA molecules are propelling biology much the way digital technology raced ahead during the 20th century.

"This is, of course, a gigantic leap forward, and it's getting faster and faster," she said.

"Certain things I simply don't do"
Schmidt-Dannert has patented some of her creations — for bacterial production of food supplements, for example — and licensed them to companies.

But she turned down a request from the Office of Naval Research to design a bacterial pathway for making explosive compounds.

"We can do this, but the question is, 'Should we?' " she said. "It's everybody's responsibility to think about that question: 'Do you really want to do everything that you could do?' There are certain things I simply don't do."

In November, Schmidt-Dannert joined other synthetic biologists at a symposium organized by the National Academies to discuss the ethics of their work, among other topics. Related podcasts are here.

The Hastings Center, a nonpartisan research group devoted to bioethics and the public interest, is one of many other organizations grappling with the ethics.

"This rapidly advancing technology raises ethical questions about benefits and harms that have not been thoroughly addressed," said the Hastings Center's overview.

"Some of these are concrete physical worries, akin to the safety and security concerns first identified with the invention of recombinant DNA technology," Hastings researchers said. "Other concerns tap into ... our inner instincts about what is natural, and what is our relationship to the natural world, as well as scientific freedom, justice and access to the benefits of technology, and intellectual property rights."

A critical set of questions confronts the prospects for creating whole synthetic organisms — not just hijacking the scaffolding of an E. coli molecule, but building free-standing organisms that never have existed before.

J. Craig Venter, who plowed new ground in the sequencing of the human genome a few years ago, now leads research that has produced an entire genome from scratch, using nothing but chemicals in a laboratory. The scientific press dubbed the creation "Synthia." Now Venter's team is taking the crucial next step, working to transplant synthetic genomes into independent cells where they could function as new species.

An affront to God?
"This feat will surely be achieved in the next few years," the journal Nature editorialized.

"Many a technology has at some time or another been deemed an affront to God, but perhaps none invites the accusation as directly as synthetic biology," Nature's editors wrote. "The idea that such creation is a momentous step has deep roots running from the medieval homunculus portrayed by Paracelsus and the golem of Jewish legend to the modern faustian myth of Frankenstein."

If anything, though, modern-day biologists are forcing us to reconsider the profound question of what constitutes life. Nature's editors suggested that is not a question to be answered by scientists alone: "It would be a service to more than synthetic biology if we might now be permitted to dismiss the idea that life is a precise scientific concept."

Life is not Synthia — not a solitary genome or even one complex collection of cells. It is a rich array of colonies and ecosystems.

And, after all, the synthetic biologists are not creating whole new parts for life. They are using nature's pre-existing parts to spell out new forms: DNA's natural alphabet of A, C, T and G.

Even that bold step does not explain how life began in the first place. Darwin didn't do that either. The landmark theory he published 150 years ago explained in profound fashion the origin of the species — not the origin of life.

When it comes right down to basics, "we don't know how to define life very well," said U of M professor Mark Borrello, a science historian.

"It's a very complicated idea," he said. "And similar to Darwin in some ways, we still don't know what the pre-biotic soup looked like. ... This is something that Aristotle grappled with, something that theologians grapple with and something that scientists grapple with."

Many scientists thought they were close, including James Watson and Francis Crick who changed biology forever in 1953 with a discovery they made in a laboratory at the same university where Darwin worked, Cambridge University in England.

"They figure out the structure of DNA, and they go wheeling into the Eagle Pub in Cambridge saying, 'We found the secret of life!' " Borrello said.

Not quite.

"Most people would say, 'No, not really ... you have a big pile of DNA on your table. If you were to dump it into the garbage I don't think anyone would say you've thrown life into the garbage. You've thrown a molecule in the garbage."

Full grandeur of life
In the same vein, a lineup of synthetic genes is not the same thing as life itself in all of its grandeur and complexity.

Still, it is not surprising that synthetic biology spurs intense opposition on religious grounds. Schmidt-Dannert said she has received angry hand-written letters objecting to her work.

More surprising is that theologians representing many religions are prepared to take this development in stride.

"We still don't have a decent scientific theory of where life came from although they are getting closer," said Alan Padgett, who teaches systematic theology at Luther Seminary in St. Paul.

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Harpursville senior wins award from Keuka - Press & Sun-Bulletin

Posted: 23 Dec 2009 07:45 AM PST

Harpursville High School senior Desiree Ford received Keuka College's Experiential Learner of the Month Award for December.

Ford will receive a partial academic fellowship to Keuka and qualify for the Experiential Learner of the Year Award, which carries a full academic scholarship to the college. She was nominated by guidance counselor Cynthia Sodeur, who praised Ford for leading an initiative to make Harpursville a drug-free school.

"Last year we had a drug problem on our high school campus," Sodeur said. "Desiree participated in the superintendent's focus group and subsequently stood up in front of the student body and challenged them to take a stand with her to clean up the school."

Ford is a member of the student council, marching band, biology club, yearbook committee and cheerleading. She also does volunteer work at the fire department, Red Cross and library.

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Yakima: New medical school receives federal grant - Tacoma News Tribune

Posted: 23 Dec 2009 06:12 AM PST

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The Pacific Northwest University of Health Sciences has received a $400,000 federal grant to help expand programs at the new medical school.

The school announced Tuesday it had received the money with help from U.S. Rep. Doc Hastings for the 2010 academic year.

Acting school president Dr. Lloyd Butler says the funding will help the school move forward with program expansion and is an "extraordinary financial boost" to the private funds already raised.

The school's College of Allied Health Sciences opened this year after it conducted a feasibility study of greatest need for services in its five state region Washington, Oregon, Alaska, Idaho and Montana. The College operates in conjunction with Central Washington University. Students are working on a master of science in biology.

The university's College of Osteopathic Medicine has two classes of 75 students training to become physicians.

The Associated Press

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Direct Oncology Foundation Seeks $100,000 to Sequence Genome of Cancer ... - PR.com

Posted: 23 Dec 2009 05:51 AM PST

Riverside, CA, December 23, 2009 --(PR.com)-- In an effort to accelerate the development of a cancer treatment based on innate cancer immunity, the Direct Oncology (DO) Foundation is launching an appeal to raise $100,000 to sequence cancer resistant mice at Wake Forest University. The project is being coordinated by Livly, a Silicon Valley based non-profit corporation dedicated to the development of sustainable cures for the major diseases plaguing humankind.

A colony of cancer resistant mice has been bred by scientists at Wake Forest University's Comprehensive Cancer Center since 2003, led by the Pathology Department's Zheng Cui and Mark Willingham. The immune systems of the mice successfully fight off different types of advanced cancer. Immune cells from these Spontaneous Regression / Complete Resistance (SR/CR) mice can be used to protect other mice from advanced cancer. Evidence suggests that there is a single place in the SR/CR mouse's genome that confers the remarkable cancer resistance. Ironically, the gene for the cancer resistance has proven inaccessible to standard mouse genetic methods, and its identity and sequence have remained elusive. The progress of clinical efforts was hampered by lack of knowledge of the genetics underlying the cancer resistance.

Whole genome sequencing is a brute force method to identify any genetic differences between SR/CR and normal mice. In recent years, the price of whole genome sequences has plummeted from billions of dollars to only $60,000 per genome. This is still a large amount of money for the six to ten mice that will likely need to be sequenced. Genome sequencing costs, however, are slated to continue their parabolic descent, and a new tier of 3rd generation sequencing companies is expected to have methods available by Spring 2009 to sequence the necessary amount of mice for $100,000. The sequencing results will be published so that multiple research teams can contribute to the effort to find the genomic basis to cancer resistance in the mice.

Dr. Zheng Cui commented: "Past research has shown that whole genome sequencing will be necessary to determine the basis of the SR/CR mouse's remarkable cancer resistance. I am excited by the possibilities opened up by cheap genome sequencing. We will take advantage of this opportunity as early as we can."

About SR/CR mice

While conducting a series of experiments with mouse sarcoma 180 (S180) cells, which form highly aggressive cancers in all normal mice at Wake Forest University's Comprehensive Cancer Center, lead scientist Dr. Zheng Cui and his colleagues happened upon a single mouse that surprised them with its ability to resist several forms of cancer, despite repeated injections of the sarcoma cells. Breeding the mouse produced offspring that also exhibited cancer resistance, suggesting a likely genetic link. Further experiments showed that in it was a massive infiltration of white blood cells that destroyed cancer cells in these mice without damaging normal, healthy cells. Based on these results, Drs. Cui and Willingham and their colleagues suggest that a previously unknown immune response may be responsible for spontaneous regression. More recent studies demonstrated the ability to cure cancer in normal mice by transferring purified immune cells from the cancer-resistant mice. These newer studies show that specific types of innate immune cells, such as macrophages, can migrate to the site of cancer in normal mice and selectively kill all of the cancer cells without harming normal cells. Such studies suggest that this type of mechanism might one day be able to help design a new strategy for cancer therapy.

About Direct Oncology Foundation

Direct Oncology (DO) Foundation was founded in 2009 to raise funding for research and development of human therapies based on Dr. Zheng Cui's remarkable cancer resistant SR/CR mice. The charity funds research into analysis of the genomics of Dr. Cui's mice, as well as into the research into cancer therapies that use the immune system to attack cancer. 100% of funds raised are redirected into research.

About Livly

Livly is a non-profit corporation based in Mountain View, California, dedicated to accelerating the development of cures for the major diseases plaguing humankind. To this end Livly pursues two programs: First, Livly's in-house research program studies new ways of stimulating the immune system to attack cancer. Second, through its "BioCurious" (Curious about Biology?) incubator program, Livly makes its research equipment available at low cost for "biohackers," hobbyists, and entrepreneurs participating in the burgeoning DIY (do-it-yourself), "garage" biology movement, enabling them to work on pet projects and test their own favorite ideas for curing major diseases.

Contact:

Damian Crowe damianjcrowe@gmail.com
John Schloendorn PhD john@livly.org

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Biology

Wednesday, December 23, 2009