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Archive for December 2009

Genetics and Evolution of the Skeleton Research Initiative conference

gesriThe Genetics and Evolution of the Skeleton Research Initiative recently had its semiannual meeting in San Francisco. Organized by UCMP Faculty Curator Leslea Hlusko, the focus for this year’s meeting was Development, Diseases, and Evolution of Mineralized Tissues. Two graduate students from the Hlusko lab, Theresa Grieco and Sarah Amugongo, give us these snapshots from the conference:

Highlights from the conference, by Theresa Grieco:

The GESRI meeting draws bone biologists from all over the Bay Area — UC Berkeley, UC San Francisco, UC Davis, Stanford, and Lawrence Livermore National Lab. The speakers and attendees work in a variety of contexts, including biomed, EvoDevo, paleontology research, and veterinary/clinical research. It is great that this meeting is able to draw together a diverse group that is willing to talk across field boundaries and present their findings to the broader scientific community. We heard talks about fracture repair, bone mineralization and its changes during fossilization, osteoarthritis, tooth bioengineering, and how bones and teeth can be used to infer life history traits.

For me personally, it is a great way to meet and keep in touch with local mentors and colleagues and get fresh ideas. It’s really the best way to find out about potential resources and collaborations for research projects. It was also great to see a presentation by a biochemist or embryologist drawing questions from practicing MDs or bioengineers, and to see such different people getting excited about each other's work. One thing that I thought was interesting was that sometimes questions would be misunderstood, usually because people trained in different fields catch on to very different aspects of your research than the ones you’ve been trained to look at. Talking about these kinds of questions in a little more detail can reveal significant implications of your research in other arenas, or where the methods or data collected from another field could make your research better.

A highlight of the day was one of our plenary speakers, Dr. David Kingsley, who gave a talk about why he developed the stickleback fish as a model system for EvoDevo and a case study about pelvic reduction and hindlimb loss in these fish. Through genetic mapping, his lab identified a set of chromosome deletions in the regulatory region of a gene called Pitx1. These deletions have been selected for in many different stickleback populations around the world. These deletions only affect the molecular switch for Pitx1 expression in the hindlimb, allowing the rest of the gene’s vital functions to be preserved. He then showed us how similar phenotypes can be seen evolutionarily, with hindlimb loss and pelvic reduction in snakes, manatees, and in mice missing the Pitx1 gene. Dr. Kingsley then brought us into the clinic with case studies of club foot in humans. Wow!

A sampling of GESRI talks, by Sarah Amugongo:

Though only in its infant stages, GESRI has already become very popular among bone biologists in the Bay Area and beyond. I was astounded by the turnout, especially from the un-registered members. The range of topics covered was quite impressive: from basic bone biology, to clinical application, to evolutionary history of bone mineralization.

Here are a few of the talks that were given at the conference:

  • One talk focused on the repair of fractures. A high oxygen level was demonstrated to be very important for the healing of fractures. Interestingly, the process of fracture repair is different from the process of normal bone development in several ways. The source of bone cells is different, and the processes that regulate cell fate are different too.
  • The inverse relationship between osteoarthritis and osteoporosis was also notably interesting. With the loss of cartilage, there is an up-regulation of bone growth as demonstrated by research on osteoarthritis of the hip.
  • The growth hormones TGF-beta and IGF-1 have different signaling pathways, but both have been demonstrated to be important to the skeleton as they regulate osteoblast differentiation and proliferation. Osteoblasts are cells that are responsible for bone formation.
  • In addition to studying the extant organisms, learning that soft tissue is also preserved in the fossil record through the study of dinosaur fossils was really amazing. It made me wonder what else we’ve been missing by just focusing on bones. This might open a whole new area of research in paleo!

View the full meeting program here.

Fossils provide baseline for mammal diversity


Skull of a short-faced bear from northern California, an example of a species that went extinct after humans arrived in North America. Photo: Tony Barnosky

As more and more species go extinct, biologists wonder whether we are on the verge of the earth's sixth mass extinction.  A new study, by Marc Carrasco and Tony Barnosky of the UCMP and Russell Graham of Pennsylvania State University, uses the fossil record to examine mammal biodiversity in North America over the past 30 million years. Carrasco and his collaborators used data from two fossil databases, MioMap and Faunmap, to determine the baseline of mammal diversity before humans arrived in North America. Their results, published in the journal PLoS ONE, show that the arrival of humans 13 thousand years ago coincided with a 15 to 42% decline in mammal diversity. These data show that humans had a negative impact on mammals long before we factor in the effects of current industrialization and global climate change. Now that a pre-human baseline of North American mammal diversity has been established, we can compare current diversity to the continent's "normal" diversity level — an important comparison as we plan and evaluate conservation efforts in the future.

To learn more about Marc and Tony's study, read the paper on the journal PLoS ONE, the UC Berkeley News press release, and this article in the San Francisco Chronicle.

New dino described by UCMP alums

Field crew 2006

The field crew that excavated Tawa hallae in 2006: Kevin Padian, Sterling Nesbitt, Alan Turner, Nate Smith, Randy Irmis, Amy Balanoff, and Gabe Bever. Photo: Nathan Smith, Field Museum of Natural History

Last week, two University of California Museum of Paleontology alums, Sterling Nesbitt and Randall Irmis, described a new species of dinosaur in the journal Science. The new species, Tawa hallae, sheds light on early dinosaur evolution — and the importance of the UCMP's collections.

Tawa's bones were first found by hikers in Ghost Ranch, New Mexico, in 2004. Around that time, Sterling and Randy were doing fieldwork at the nearby Petrified Forest National Park in northern Arizona, excavating fossils from rock layers from the Late Triassic — the same rock formation where the new fossils were found. That fall, park paleontologist Alex Downs approached Sterling and Randy at a scientific meeting and asked them if they'd be interested in excavating and describing what appeared to be a novel species. At that time, Randy was a graduate student at Berkeley, and Sterling had finished his undergrad at Berkeley and begun graduate school at Columbia. They decided to collaborate with Alex to describe the specimens and made plans to start fieldwork during the summer of 2006.

"Three weeks before our first major expedition," says Sterling, "the provost at the American Museum of Natural History called and asked if I'd like to be accompanied by an NSF-funded IMAX movie crew."  They wanted to film the excavation of the fossils for a movie, Dinosaurs Alive!. Sterling was a little worried that the filming would interfere with his fieldwork, but he agreed. The film crew followed Sterling, Randy, and the rest of the team for a week and a half. Sterling needn't have worried about having enough time to do his research — there was plenty of down time. "IMAX film is expensive," he says, and the film crew spent a lot of time setting up each shot. During some of this down time, Sterling was excavating the area where the hikers had found the fossils. "That's when I hit the ankle bone of the articulated leg of what became the holotype."

Other early dinosaur fossils are not as complete or as well preserved as those of Tawa hallae. Sterling, Randy, and the team found two nearly complete skeletons, as well as bones from several other individuals. Some of the bones are so well preserved that you can see very fine details, like the places where the muscles once attached. The neck vertebrae and the bones of the braincase have small depressions with raised rims — suggesting that there were air sacs adjacent to these bones. The air sacs filled up the depressions. Modern birds have air sacs attached to their bones, which they use for respiration. As Sterling and Randy write in their paper (co-authored by Nate Smith, Alan Turner, Alex Downs, and Mark Norell), we can't know if Tawa's air sacs served a similar function. However, we do know that Tawa is the earliest dinosaur with a pneumatic skeleton.

Tawa is particularly important because it fills a gap between early carnivorous dinosaurs, found in South America (where dinosaurs are thought to have originated), and later carnivorous dinosaurs found throughout the world. Randy, Sterling, Nate, and Alan figured out where Tawa fit by comparing it to other specimens, many of which were in the UCMP's collection. "The UCMP collection was instrumental in helping us understand what was at Ghost Ranch," says Randy. Sterling also points out the importance of the museum's collections, both in this study and in his paleontological education. "I came to Berkeley for the paleo," he says. As an undergrad, "I was in the collections a couple times a week, learning anatomy, learning what the fossil record is really like."

"This project really had its genesis when we were all graduate students," says Randy. "This study speaks to what a fantastic program we have at Berkeley, that we can have such fantastic research coming out of a graduate student-led project."

Randy is now an Assistant Professor at the University of Utah, and Sterling is a post-doc at the University of Texas Austin. Both intend to continue working at Ghost Ranch — "I plan to go back for many years to come," says Randy. "It's an amazing site." And, they plan to continue working in the UCMP collections – they'll be back in January. Check the UCMP blog for an update!

Sterling and Randy are currently collaborating with UCMP graduate student Sarah Werning, Kevin Padian, Nate Smith, and Alan Turner, to examine the growth and bone histology of early dinosaurs (including Tawa) and their relatives from Ghost Ranch. Stay tuned for an upcoming blog about dinosaur bone histology in the New Year.

Sterling and Randy's work was funded by a National Geographic grant to UCMP Faculty Curator Kevin Padian and by grants from Integrative Biology, UCMP’s Welles Fund, and the UCMP Graduate Student Research Award. Learn how you can support graduate student research at the UCMP.

There has been some great news coverage about Tawa hallae. To learn more, check the National Science Foundation's Special Report: Tawa hallae – it includes an audio slide show, a press conference, and lots of photos. There is an interview with Sterling in this Science magazine podcast, and an interview with Randy in this blog from the Utah Museum of Natural History. Also check out this article from the San Francisco Chronicle.

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Ardi is Breakthrough of the Year

Credit: Jay Matternes © 2005

Credit: Jay Matternes © 2005

Ardipithecus ramidus has been named Science magazine's Breakthrough of the Year. At 4.4 million years old, Ardi is the oldest hominid skeleton. This fall, a series of 11 papers about Ardi and her paleoenvironment were published in Science. UCMP Faculty Curator and Human Evolution Research Center (HERC) director Tim White was one of the lead scientists on the project, which involved an international team of researchers, including UCMP Faculty Curator Leslea Hlusko. To learn more about Ardi, Breakthrough of the Year, read this article in today's issue of Science, watch this video, also on Science's website, and read this article on BBC news. For more links and more info on the discovery of Ardi, visit the UCMP's previous blog post.

Judy Scotchmoor named AAAS Fellow

Judy ScotchmoorCongratulations Judy Scotchmoor, UCMP Assistant Director for Education and Public Programs! Judy was named an American Association for the Advancement of Science (AAAS) Fellow. Judy receives this prestigious award "for leadership in defending teaching of evolution and quality science education through nationally recognized websites on these issues and through leadership of Coalition on the Public Understanding of Science."

The websites, for which Judy is project coordinator, include The Paleontology Portal, Understanding Evolution, and Understanding Science.  She is also a founder of the Coalition on the Public Understanding of Science (COPUS), a grassroots network of science organizations.

Upon learning of her award, Judy exclaimed "This was a huge and wonderful surprise — a real 'Oh WOW!' kind of moment!"

Judy will receive her award in February 2010 at the AAAS Annual Meeting, in San Diego.

Evo in the news: Fighting the evolution of malaria in Cambodia


Mosquitos like this one spread the malaria pathogen. Photo: CDC.

Evolution doesn't just happen in a textbook — evolution is happening right now, and one example is the pathogen that causes malaria. Malaria kills nearly one million people each year. The disease can be treated, but new drug-resistant strains of the pathogen, Plasmodium falciparum, have recently been discovered in western Cambodia. These strains are resistant to artemisinin, the most effective anti-malarial drug available. Learn more about the evolution of drug resistant malaria pathogens, and how combination drug therapies help prevent the evolution of drug resistance, in the latest Evo in the News story, Fighting the evolution of malaria in Cambodia. This story is on UCMP’s Understanding Evolution website and is released in conjunction with the Year of Science. This month's theme is science and health.