Virtual reality helps Marine fight PTSD

“It was killing me,” Joshua Musser told CNN about the effects of post-traumatic stress disorder (PTSD). Musser, a Marine Corps veteran who fought in the battle of Fallujah in Iraq, realized that he needed help. He turned to Emory clinical psychologist Maryrose Gerardi, who uses virtual reality to treat PTSD.

The treatment required Musser to relive the sights and sounds of war through computer simulation, as Gerardi talked him through the experience.

“They put you back in Iraq where you kind of have one foot here and one foot there,” Musser told CNN. “The only thing outside of Iraq that you hear is her voice. I would shake really bad and I would sweat, but she would be in my ear and pull me back.”

“People often try not to think about what happened to them, and what we’ve found is that’s the worst thing that you can do when you experience a trauma,” Girardi said. “If you don’t process it and deal with it, that’s what can eventually cause PTSD and a chronic problem.”

'Galaxy' makes genomics more user-friendly

iStockphoto/AlanPhilips

Kevin Davies writes in Bio-IT World about an open-source platform for computational analysis:

Enter the term “galaxy” in a Web search engine, Penn State’s Anton Nekrutenko muses, and the top hits are likely to be an astrophysical entity or “a very bad soccer team.” But making fast strides up the web charts is the Galaxy open-source tool, which is coming into its own as more and more researchers seek ways to easily handle and manipulate next-gen sequencing (NGS) and other large datasets.

“Galaxy allows you to do analyses you cannot do anywhere else, without the need to install or download anything,” says Nekrutenko. “We can make genomics better, easier and more efficient. You can analyze multiple sequence alignments, compare genomic annotations, profile metagenomic samples and much, much more.” Galaxy was originally developed by Nekrutenko, who is based in the Center for Comparative Genomics and Bioinformatics at Penn State, and his former Penn State colleague James Taylor, who is now an assistant professor in biology and math and computer science at Emory University. Both are quick to cite the many contributions to Galaxy’s evolution from the genomics community.

Taylor was finishing his Ph.D. when the pair started to develop Galaxy, and they have devoted much of their time to that effort ever since. Nekrutenko is the more biologically inclined of the pair. “I can script a bit,” he says, “but Galaxy could only be developed with proper software engineering practices, which was only possible after James got involved.”

Galaxy is primarily a platform for making computational tools accessible. Nekrutenko and Taylor observed “a huge disconnect” between computer science development tools and algorithms on the one hand, and the researchers wanting to use them on the other. Galaxy is designed to fill that gap. …

Most of the Galaxy tools are in the genomics and gene evolution space, but researchers are also adapting the platform to proteomics and other areas. “When this started, NGS didn’t exist,” says Nekrutenko. “Initially, we were addressing problems with whole genome sequence, comparative genomics, etc. In reality, very few people can use this information. We’re still the only resource to meaningfully manipulate genome alignments on a large scale.”

The basic model is a Web-based platform. “We believe that’s really important for collaboration and communication,” says Taylor. “Having no barrier to using Galaxy other than a Web browser is very important.”

Read the whole article at Bio-ITWorld.com.

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Jewish law in the era of bio-engineering

iStockphoto.com/DanBrandenburg

Mary Loftus writes in the Huffington Post:

Cats with bits of luminescent jellyfish DNA. Sheep-goat hybrids, "geep," with furry legs and floppy ears. Human stem cells inserted into the brains of newborn mice. Embryonic screening that allows parents to choose to implant an embryo without the breast cancer gene. Human-human chimeras that allow gay couples to have children that belong, biologically, to both of them.

To paraphrase Dickens, these are not things that will happen in time, these are things that are happening.

Speaking from a Jewish law perspective about the ethics of reproductive technologies, Rabbi Michael Broyde, a law professor at Emory University and a member of the Beth Din of America, the largest Jewish law court in the country, is just getting warmed up in his delivery of the Decalogue Lecture for Emory's Center for the Study of Law and Religion Sept. 13.

He's enjoying the reaction this bioethically edgy information, complete with slides of an adorable glowing kitten and a geep, is getting from his audience.

Broyde has covered artificial insemination: "No adultery is associated with AI. The dominant Jewish law view doesn't look at misplaced paternity, absent sexual conduct, as a moral or religious wrong... It's even discussed in the Talmud."

And cloning: "When people think of cloning, they think of Star Wars, or The Boys from Brazil. They are opposed to cloning because they think it will allow creation of armies or will be used in some way that's dehumanizing. But cloning could be a form of assisted reproduction for profoundly infertile people."

Broyde moves on to reproductive xenotransplants -- the placing of a fertilized embryo of one species into the uterus of another species.

"Like human-animal chimeras, when cells of a human are mixed with cells of another mammal, basic ideas of human identity come into play," Broyde says.

"Of course, one definition of humanity is, that which comes from a human mother is human," he adds. "Yet, if you put a human fetus in a gorilla and it gives birth to a human being who, six years later, is playing chess or reading or engaging in other human activity, there's no doubt at all that Jewish thought would label that a human being even if the mother is not."

Broyde says these frightful, fascinating visions are no reason to halt the advance of assisted reproduction, no matter how rapidly the biotech may be slip-sliding into areas that make us uncomfortable.

Read the whole article in the Huff Post.

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Mary Anning and the art of fossil hunting

Robey Tapp loves history and science and has served as a docent at Emory’s Carlos Museum for the past six years. She is also an independent artist who works in fiber. When she was invited to create a piece for the Fernbank Museum’s special Darwin exhibit, opening on Saturday, Sept. 24, Tapp started reading up on the England of Darwin’s time. That’s how she stumbled across Mary Anning.

Anning was a contemporary of Darwin’s, a self-taught paleontologist, who made key findings that supported Darwin’s theory of evolution. She grew up poor on the southern England coast and did not receive full scientific credit for her work during her lifetime, due to her gender and working-class status.

A painting of Mary Anning, left, hangs in the Natural History Museum of London.

“Every day she walked along the water in Lyme Regis where she lived,” Tapp says. “She saw things in the rocks and she dug them out.”

In 1811, when Anning was just 12 years old, she and her brother Joseph discovered the fossil of an entirely new animal, later named Ichthyosaurus. Throughout her life, Anning continued to make discoveries, working tirelessly along the rugged coastline.

“What inspires me about her is that she believed in herself and her findings despite the fact that it went against the religion of the time,” Tapp says. “She was really upsetting the apple cart. And she didn’t stop because she was a woman, and people told her that women couldn’t be scientists.”

Anning died poor but “her work lives on,” Tapp says. In 2010 the Royal Society included Anning in a list of the 10 British women who have most influenced the history of science.

Tapp’s fiber art inspired by Anning is part of the “Selections” show at Fernbank. Local artists, including scientists from Emory’s department of environmental studies, have created pieces influenced by evolution. The art will remain on display during the museum’s special exhibit commemorating the life and mind of Darwin, which continues through January 1.

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In the Congo, a secret world of bonobos

Anthropologist Amy Cobden's fieldwork is challenging stereotypical ideas about chimpanzees, left, and bonobos, right. Photos copyrighted by Frans de Waal.

Journalist Kate Roach writes in New Scientist about the research of an Emory graduate student of anthropology:

A dark, chiseled face looks at us from way up in the branches of a vast rainforest tree. Deep-set, inky eyes peer suspiciously through the foliage, throwing an occasional glance towards movement in a tree beyond. This is Ruby, a mature female bonobo. She lingers, almost as if to separate us from the rest of her party, who are moving on in search of more fruit. Then she leaps away.

Such encounters are typical of the pleasure and frustration of studying bonobos in their natural habitat. Found only in the heart of the Democratic Republic of the Congo, these were the last great apes to be discovered and are the least studied. Their range, beneath a huge arc made by the Congo river, is fragmented across a region of lowland rainforest that approximates 350,000 square kilometres, about the size of Germany. It is a hauntingly beautiful landscape, encompassing both swamp and dry forest, all of it inaccessible, with travel mostly restricted to following forest trails by foot or trail bike, or navigating the rivers in unsteady flat-bottomed pirogues.

But physical remoteness is not the only reason why bonobos are so elusive. A succession of wars in the Democratic Republic of the Congo between 1996 and 2003 has severely disrupted research. In 1998, scientists were forced to leave the area where I am staying with primatologist Amy Cobden from Emory University in Atlanta. … Cobden knows it will be many months, possibly years, before the apes once again become sufficiently used to humans to behave naturally. With so much still to learn about these animals, she is hopeful that her patience will be rewarded.

Click here to read the whole article. You will have to log in to access it, but it’s free to do so.

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