Scientists around the world may benefit from a powerful new database, available for free online, that will help them to home in on the parts of proteins most necessary for their function.  Arend Sidow, PhD, associate professor of pathology and of genetics at the Stanford University School of Medicine, recently launched the novel bioinformatics tool, which enlists evolution as the guide to determining the role different proteins play in a wide array of organisms.

ProPhylER, which Sidow has been working on since 2002, will enable a researcher studying a protein, or the gene coding for it, to more easily figure out how it works and whether something might go wrong if the gene has a mutation. “Whether you’re a cell biologist, biochemist or structural biologist, ProPhylER produces instant working hypotheses for you as to where the protein’s functional areas are,” he said. The site made its debut on Oct. 10.

Proteins—the machines of life that do everything from making your muscles move to helping you breathe and think—are long chains of small chemical units called amino acids. As soon as a protein molecule is made inside a cell from the gene encoding it, it folds up to assume the unique shape that determines its activity. To do its job, a protein needs to have specific amino acids (there are 20 to pick from) in specific places. In particular regions of the folded protein, it may be crucial that a specific amino acid sequence be there in order for the protein to function; in other regions, the swapping of one amino acid for another has little effect.

Over the course of several hundreds of millions of years myriad species have evolved, and, through eons of random mutation, so have their proteins. Yet in the face of all these changes, some things have to remain constant. “Evolution imposes stronger constraints on more-important regions of a protein molecule, from the standpoint of its biological activity, than on other, less-critical regions of that protein,” Sidow said. If a change interferes with a protein’s function, the hapless creature harboring this variant dies out; if not, the creature is fruitful and multiplies, and the variant protein persists in modern species.

It’s by no means obvious just from looking at a protein’s linear amino-acid sequence which regions are the “business districts” of the protein, and which are the sleepier bedroom communities. However, ProPhylER shows biologists which parts of a protein are key to its activity by comparing numerous versions of the same protein from different species. This is especially useful for proteins about which nothing or little is known, which is still the majority of proteins encoded in the human genome.

Human geneticists, too, will benefit from ProPhylER (a play on words derived from the bulkier term “PROtein PHYLogenetics and Evolutionary Rates”). Each of us carries tens of thousands of protein variants (due to mutations that have persisted in the human gene pool), some fraction of which affect protein function. For researchers, it is notoriously difficult to measure experimentally how much a protein’s function is impaired by a mutation. ProPhylER provides specific predictions, also based on evolutionary variation, of the impact of a mutation on the protein’s function. A mutation in an amino acid that has changed a lot in evolution is much less likely to be bad than a mutation that affects an amino acid in which evolution has not tolerated any change. “This type of analysis will be key in the interpretation of your personal genome sequence, when—not if—that becomes commonplace,” said Sidow.

After a user has searched for his or her protein of interest, the ProPhylER Web site displays data via two interfaces. The first displays all the evolutionary data graphically along the length of the protein. The second, called “Crystal Painter,” projects these degrees of evolutionary constraint onto three-dimensional structures of proteins, when those are known, by imposing a color-coded scheme on their structures. It is clear at first glance that parts of proteins obviously important to function—such as binding pockets in which the protein holds a small molecule on which it’s performing an operation—are, indeed, just the ones Sidow’s evolutionary algorithm has deemed most important.

“No other proteomics resource does this,” Sidow said.

Two studies, presented this week at the 94^th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA), concluded a novel technique can improve outcomes for patients with vertebral compression fractures (VCF) caused by malignant tumors in the spine. The American Cancer Society estimates 30 to 70 percent of more than half a million people who die annually of cancer have metastatic disease and 10 percent of the 750,000 vertebral compression fractures that occur each year are caused by metastatic spine tumors.

This new treatment uses a plasma mediated medical device, the Cavity SpineWand, developed by ArthroCare to debulk, or reduce, the lesion. Bone cement can be subsequently injected to stabilize the fracture. Stabilization of the fracture helps to ease the pain associated with VCFs. The combined therapies have been successfully used in tandem with radiation and chemotherapy.

One study, led by Mark Perman, M.D., an ArthroCare consultant, examined a synergistic approach to treating VCFs secondary to spinal metastases. The approach consisted of three treatments: removing tumor tissue to create a cavity, filling the cavity with bone cement to stabilize the vertebral body and then treating the tumor with either radiosurgery or external beam radiation to reduce the remaining tumor burden. A separate study by Bassem Georgy, M.D. found removing tumor tissue with the Cavity SpineWand increased control and predictability during cement injection.

“Patients with VCFs are typically in extreme pain and radiation therapy alone, which is critical to treating the cancer, may be ineffective as a palliative option,” said Dr. Perman, Chief of Radiosurgery, The CyberKnife Center at North Florida Radiology. “With this synergistic approach, my patients receive quick pain relief and mechanical stability without delaying tumor treatment, which can dramatically improve quality of life.”

The study led by Dr. Perman, “Vertebroplasty and Radiation Therapy: Synergistic Treatment of Pathologic Compression Fractures,” involved seven patients suffering from painful VCFs. After treatment, all but one patient reported significant pain relief immediately following the treatments which was sustained or reduced further during follow-up with radiation therapy. Pain levels were assessed at three different time points over the course of three months.

In the study “Percutaneous Anterior Column Stabilization in Metastatic Spine Lesions: Value of Plasma-mediated Radiofrequency Ablation and Cement Augmentation,” Dr. Georgy, interventional neuro-radiologist and Associate Professor as University of California San Diego, and a consultant to ArthroCare, reported 82.3 percent success in placing bone cement in the anterior 2/3 of the vertebral body, which is commonly believed to be a key factor in stabilizing the spine. The study included 30 patients (34 levels) with 25 (83 percent) reporting pain relief following cement augmentation.

The Cavity SpineWand is a minimally invasive device that uses a plasma based technology called Coblation to create a cavity in a malignant lesion. The Cavity SpineWand is inserted through a cannula to reach the tumor inside the vertebrae. Once inside, a low-heat, plasma cloud removes tumor tissue while minimizing damage to surrounding healthy tissue. Medical grade bone cement is subsequently injected to stabilize the fracture using the space created by the reduction of the lesion. Following vertebroplasty, patients report significant pain relief, often within 72 hours post procedure.

This minimally invasive procedure is typically performed by a specialist in consultation with a radiation oncologist. Over 200 physicians in the United States have been trained in these treatments to date.

The genome of a squirrel-sized, saucer-eyed lemur from Madagascar may help scientists understand how HIV-like viruses coevolved with primates, according to new research from the Stanford University School of Medicine. The discovery, to be published online on Dec. 1 in the Proceedings of the National Academy of Sciences, could provide insight into why non-human primates don’t get AIDS and lead to treatments for humans.

Scientists have long believed that lentiviruses—the family of viruses that includes HIV—started infecting primates within the past million years. In fact, said Rob Gifford, PhD, former postdoctoral researcher in infectious diseases and geographical medicine and lead author of the new study, lentiviruses may have been present in ancestral primates as long as 85 million years ago.

A type of retrovirus, lentiviruses replicate by inserting their RNA into a cell’s DNA. Some retroviruses have been known to infect cells that mature into sperm or eggs, incorporating viral DNA into the genome of the host. Until last year, when Gifford discovered Rabbit Endogenous Lentivirus type K among the DNA of the European rabbit, no one knew lentiviruses could be inherited in this way.

“It allows us to put a timeline on the evolution of primate lentiviruses,” said Robert Shafer, MD, associate professor (research) of infectious diseases and geographical medicine and senior author of the paper.

Gifford began computer-based screening of the DNA of 21 primates for which at least partial genome sequencing was available. He searched each species for strings of nucleotides that matched the modern lentivirus genome and found one lurking in the DNA of the tiny gray mouse lemur.

Ancestors of the modern lemur colonized Madagascar about 75 million years ago, and since then, lemurs and their lentivirus-carrying African cousins have been evolving separately. Four hundred kilometers of ocean divide the two branches, giving mainland primates limited opportunities to swap germs with lemurs. And the last of the occasional land bridges between the two disappeared beneath the sea 14 million years ago, suggesting that lentiviruses are likely at least that old, say the researchers.

High-end estimates of the age of this lentivirus, called pSIVgml, could range back 85 million years, when the primate family that includes lemurs split from the evolutionary branch that would eventually give rise to monkeys, apes and humans. “Lentiviruses could be very ancient indeed,” Gifford said.

Gifford remains cautious about overestimating the virus’s age, warning that the virus could have been spread within the last 14 million years by something that could cross the ocean, such as a bat. But Shafer says that sort of cross-species transmission is unlikely, because bats and primates are very distant relatives. The leap from primate to bat and back would be difficult for a lentivirus to make.

Gifford’s find suggests lentiviruses could be discovered in other places they’ve never been seen, like Asian and New World monkeys. “As far as we’re aware, nobody’s really looked that hard,” said Gifford. He is one of few researchers using genome databases to search for retroviruses.

Finding widespread lentivirus-primate interaction might open doors for HIV/AIDS research. Primates infected with the simian version of HIV are protected from developing AIDS by several genes which code for proteins in the immune system that slow or block retroviral reproduction. Previous research suggests these genes evolved in response to millions of years of retrovirus infection.

Until now, scientists thought lentiviruses were too young to have participated in this evolutionary back-and-forth. But if Gifford and his colleagues find more evidence that lentiviruses and primates have been in each other’s genetic business for many millions of years, they could turn that assumption on its head. In the process, they might lead the way to a deeper understanding of the evolution of ancient innate immune defenses against retroviruses, which could have implications for HIV treatments or vaccines.

The research “raises a bunch of interesting questions about how mammals have dealt with these types of viruses over a minimum of 14 million years, what kind of defenses they have developed, and why some mammal species have lost these type of viruses,” said Beatrice Hahn, PhD, a professor in the department of medicine at the University of Alabama at Birmingham who studies human retroviruses. She hopes to see more research into the presence of lentiviruses in mammal genomes. “This is molecular archaeology,” she said. “There may be a lot of gold in these sequences that hasn’t been mined yet.”

Dr. Leonel Fernandez Liriano, Professor of Medicine at Pontifical Catholic University School of Medicine (PCUSM), announced nine month follow up results for the first patient treated with engineered stem cells in a clinical study of primary pulmonary hypertension. The stem cells are extracted from patients’ own blood and trained to become new blood vessels.

Zannos Grekos, M.D., Assistant Clinical Professor of Cardiology at Nova Southeastern University and head of the international team that developed the stem cell treatment protocol, says, “It goes against traditional theory that we should try to fix the existing pulmonary vasculature, but we are generating new blood vessels with impressive results.” According to Grekos, the clinical study is a collaborative effort amongst physicians at Regenocyte Therapeutic, a Florida-based stem cell clinic; researchers from TheraVitae, a biotechnology company in Tel Aviv, Israel; and physicians from Regenocyte’s Dominican Republic division. The patient’s base line and follow up testing is being conducted in part by Mayo Clinic, Jacksonville, Florida.

Patient Karl Wagner, age 46 of Macon, Georgia, underwent the Adult Stem Cell therapy in February 2008. Wagner says since being diagnosed with pulmonary hypertension, he was on a rapid decline. “I was being managed by medication, but still had violent chest pains, heart palpitations, extreme fatigue, and severe shortness of breath…I could barely do anything with my daughters and was on oxygen almost all the time. Doctors at Mayo Clinic gave me a three year prognosis.”

Dr. Héctor José Rosario, Professor of Cardiology at PCUSM and Director of Cardiovascular Therapy for Regenocyte’s Dominican division, says Wagner’s reduction in pulmonary artery mean pressure from 41mmHg (severe pulmonary hypertension) to 24 mmHg (normal) is extremely encouraging, and to date, the other patients in the study are following the same pattern.

“This is the first time medical science has successfully reversed the disease process in pulmonary hypertension, a previously untreatable condition with a very grim prognosis,” Rosario states.

“Using advanced engineered stem cell technology and innovative delivery methods,” Grekos explains, “we’ve been able to harness the regenerative power of stem cells and literally replace the damaged blood vessels in the lungs of the pulmonary hypertension patients.”

Wagner’s saturations are now consistently high, and he no longer needs to be supplemented with oxygen or considered for a lung transplant. “I feel great,” he says, “and have a normal life again. I take my girls to school every morning and work all day…my quality of life is ten-fold what it used to be. I also am off almost all of my medications and the doctors at Mayo Clinic have given me a new prognosis.”

Athina Kyritsis, M.D. and chair of Regenocyte’s Scientific Advisory Board, says the work announced today is based upon several years of Regenocyte’s clinical experience in the treatment of cardiac and vascular disease using Autologous Adult Stem Cell therapy. “In treating diseases like Cardiomyopathy and Peripheral Vascular Disease, we’ve had consistent success in generating viable heart tissue and growing new vessels; with the increased circulation, healing of wounds, and improvement in ejection fractions, it seemed a natural progression to approach pulmonary hypertension in the same manner. I believe we have only begun to discover what Adult Stem Cells can accomplish in altering the course of diseases now thought to be untreatable.”