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Archive - 2014

January 25th

Large-Scale Analysis of Over 20 Tumor Types Increases Catalog of Cancer Genes by 25 Percent

A landmark study across many cancer types reveals that the universe of cancer mutations is much larger than previously thought. By analyzing the genomes of thousands of patients' tumors, a Broad Institute-led research team has discovered many new cancer genes — expanding the list of known genes tied to these cancers by 25 percent. Moreover, the study shows that many key cancer genes still remain to be discovered. The team's work, which lays a critical foundation for future cancer drug development, also shows that creating a comprehensive catalog of cancer genes for scores of cancer types is feasible with as few as 100,000 patient samples. "For the first time, we know what it will take to draw the complete genomic picture of human cancer," said Broad Institute founding director Dr. Eric Lander, a senior co-author of the paper. "That's tremendously exciting, because the knowledge of genes and their pathways will highlight new, potential drug targets and help lead the way to effective combination therapy." Over the past 30 years, scientists had found evidence for about 135 genes that play causal roles in one or more of the 21 tumor types analyzed in the study. The new report not only confirms these genes, but, in one fell swoop, increases the catalog of cancer genes by one-quarter. It uncovers 33 genes with biological roles in cell death, cell growth, genome stability, immune evasion, as well as other processes. The researchers' results appear in print in the January 23, 2014 issue of Nature. "One of the fundamental questions we need to ask ourselves is: Do we have a complete picture yet? Looking at cancer genomes tells us that the answer is no: there are more cancer genes out there to be discovered," said the paper's first author Dr. Mike Lawrence, a computational biologist at the Broad.

January 23rd

Fruit Flies Can Detect Cancer Cells and Differentiate Subgroups via Olfactory Sense; Related Fluorescent System May Provide Early Cancer Screening Tool

A research unit in an international cooperation project led by the University of Konstanz (Germany)-based neurobiologist and zoologist Professor Dr. Giovanni Galizia, has been the first to demonstrate that fruit flies are able to distinguish cancer cells from healthy cells via their olfactory sense. In an article, published on January 6, 2014 in an open-access article in the international scientific journal "Scientific Reports" by the Nature Publishing Group, researchers of the University of Konstanz and the University La Sapienza in Rome, Italy, describe how characteristic patterns in the olfactory receptors of transgenic Drosophilae can be recorded when activated by scent. Not only could a clear distinction be made between healthy cells and cancer cells; moreover, groupings could be identified among the different cancer cells. "What really is new and spectacular about this result is the combination of objective, specific, and quantifiable laboratory results and the extremely high sensitivity of a living being that cannot be matched by electronic noses or gas chromatography," explains Dr. Galizia. Natural olfactory systems are better suited to detecting the very small differences in scent between healthy cells and cancer cells. This fact has already been shown in experiments with dogs; however, these results are not objectifiable and are thus not applicable for a systematic medical diagnosis. The researchers from Konstanz and Rome used the fact that single odorant molecules dock to the receptor neurons of the flies' antenna and thus activate the neurons. In an imaging technique developed by the researchers, the different odorant molecules of the respective scent samples create different patterns of activated neurons, which fluoresce under the microscope when active, thanks to a genetic modification.

January 23rd

Genome of 11,000-Year-Old Transmissible Dog Cancer Reveals Its Secrets

A cancer normally lives and dies with a person, however this is not the case with a particular sexually transmitted cancer in dogs. In a study published in the January 24, 2014 issue of Science, a team of researchers led by Professor Sir Mike Stratton (image), Director of the Sanger Institute, has described the genome and evolution of this cancer that has continued living within the dog population for the past 11,000 years. A commentary on these results, written by canine genetics experts Dr. Heidi Parker and Dr. Elaine Ostrander, is also published in the same issue of Science. Scientists have sequenced the genome of the world’s oldest continuously surviving cancer, a transmissible genital cancer that affects dogs. This cancer, which causes grotesque genital tumors in dogs around the world, first arose in a single dog that lived about 11,000 years ago. The cancer survived after the death of this dog by the transfer of its cancer cells to other dogs during mating. The genome of this 11,000-year-old cancer carries about two million mutations – many more mutations than are found in most human cancers, the majority of which have between 1,000 and 5,000 mutations. The team used one type of mutation, known to accumulate steadily over time as a “molecular clock,” to estimate that the cancer first arose 11,000 years ago. “The genome of this remarkable long-lived cancer has demonstrated that, given the right conditions, cancers can continue to survive for more than 10,000 years despite the accumulation of millions of mutations,” says Dr. Elizabeth Murchison, first author of the Science article from the Wellcome Trust Sanger Institute and the University of Cambridge.

January 22nd

Beautiful Life Science Fashion Now Available through Link on BioQuick

BioQuick News has added an exciting new advertiser we would like you to know about. It is “A Slice of Life Scarves” (http://www.asliceoflifescarves.com/), which produces highly artistic fashion products such as scarves and ties that feature images of biological structures observed with light and electron microscopy by their creator, Eve Reaven, Ph.D. Images include such structures as mitochondria, Golgi bodies, the endoplasmic reticulum, hormone secretory granules, actin filaments, and centrioles, all rendered in beautiful artistic patterns by Dr. Reaven. Dr. Reaven earned her Ph.D. in anatomy at the University of Chicago, working in a lab that had one of the first electron microscopes in the United States. Her work over the last several decades has helped elucidate the scavenger receptor pathway responsible for the bulk uptake and utilization of lipoprotein cholesterol by cells. Until her retirement, Dr. Reaven was a career research scientist at the Veteran’s Administration Hospital in Palo Alto, California, and for many years had been a senior research associate in the department of medicine at Stanford University. You can find an ad for “A Slice of Life Scarves” in BioQuick’s right-hand column and if you click on the ad, you will be taken to Dr. Reaven’s site, where you can view her beautiful collection of life science fashion items that are for sale. Once you see these beautiful products we believe you will become a life-time fan of Dr. Reaven’s fabulous work. We also hope that you will be convinced to purchase some of her uniquely magnificent creations. [A Slice of Life Scarves web site]

Some Salamanders Have Unique Torso-Based Jumping Ability, Possible Clue to Engineering Advances

A small, secretive creature with unlikely qualifications for defying gravity may hold the answer to an entirely new way of getting off the ground. Salamanders—or at least several species of the Plethodontidae family—can jump, and humans would like to know a lot more about it. “This particular jump is unique in the world,” said graduate researcher Anthony Hessel, as quoted in a January 21, 2014 press release from Northern Arizona University (NAU). “That’s why I think a lot of people are finding this very interesting.” The NAU student calls the move a “hip-twist jump” that powers a “flat catapult,” describing the biomechanics in language the public can access. But the work has caught the attention of a highly technical crowd. Hessel, who studies muscle physiology and biomechanics, recalled the moment he fully grasped the reach of his findings. An email from a premier journal reached him over the holiday break with the subject line “Science is interested in your work.” The contact arose from his presentation at the Society for Integrative and Comparative Biology symposium. There will likely be more who are interested. “It’s a new way to get vertical lift for animals,” Hessel said. “Something that is flat on the ground, that is not pushing directly down on the ground, can still get up in the air. I’d say that hundreds of engineers will now toy with the idea and figure out what cool things can be built from it.” Hessel used high-speed film, a home-built cantilever beam apparatus, some well-established engineering equations, and biomechanical analysis to produce the details of how a slippery little amphibian with short legs can propel itself six to 10 times its body length into the air. The key is that the salamander’s legs don’t provide the push that most creatures would require.

De Novo Schizophrenia Mutations Cluster in Specific Sets of Proteins in Key Brain Pathways

Genetic mutations in people with schizophrenia cluster in specific proteins offering a new window into the disorder, according to a team of scientists from major institutions around the world. In the largest genetic study of its kind, published online on January 22, 2014 in Nature, an international team led by scientists from Cardiff University examined the occurrence of new “de novo” genetic mutations in people with schizophrenia. Their study was entitled, “De Novo Mutations in Schizophrenia Implicate Synaptic Pathways:” lead author: Dr. Menachem Fromer—see link below). Working alongside teams from leading research institutions including the Icahn School of Medicine at Mount Sinai, New York, the Broad Institute of the Massachusetts Institute of Technology (MIT), and Harvard and Cambridge Universities, the scientists examined DNA blood samples from 623 schiophrenia sufferers and their parents. The study showed that de novo mutations, which are found in affected individuals, but not their parents, play a role in triggering the disorder but more importantly that they preferentially disrupt specific sets of proteins which have related functions in the brain. These pathways are involved in modulating the strength of connections between nerve cells and play important roles in brain development, learning, memory, and cognition. “We already had evidence from previous work in Cardiff supporting the importance of these pathways but the new findings, together with those from a related study published on the same day in Nature (“A Polygenic Burden of Rare Disruptive Mutations in Schizophrenia;” lead author: Dr.

January 21st

Pathogenic RNA Plant Virus Jumps to Honeybees

A viral pathogen that typically infects plants has been found in honeybees and could help explain their decline. Researchers working in the United States and Beijing, China reported their findings on January 21, 2014 in mBio, the online open-access journal of the American Society for Microbiology. The routine screening of bees for frequent and rare viruses "resulted in the serendipitous detection of Tobacco Ringspot Virus (image), or TRSV, and prompted an investigation into whether this plant-infecting virus could also cause systemic infection in the bees," says Dr. Yan Ping Chen from the U.S. Department of Agriculture's Agricultural Research Service (ARS) laboratory in Beltsville, Maryland, an author on the study. "The results of our study provide the first evidence that honeybees exposed to virus-contaminated pollen can also be infected and that the infection becomes widespread in their bodies," says lead author Dr. Ji Lian Li, from the Chinese Academy of Agricultural Science in Beijing. "We already know that honeybees, Apis melllifera, can transmit TRSV when they move from flower to flower, likely spreading the virus from one plant to another," Dr. Chen adds. Notably, about 5% of known plant viruses are pollen-transmitted and thus potential sources of host-jumping viruses. RNA viruses tend to be particularly dangerous because they lack the 3'-5' proofreading function which edits out errors in replicated genomes. As a result, viruses such as TRSV generate a flood of variant copies with differing infective properties. One consequence of such high replication rates are populations of RNA viruses thought to exist as "quasispecies," clouds of genetically related variants that appear to work together to determine the pathology of their hosts.

Arctic Warmth Unprecedented in 44,000 Years, Reveal Samples of Ancient Moss

When the temperature rises on Baffin Island, in the Canadian high Arctic, ancient Polytrichum mosses (image), trapped beneath the ice for thousands of years, are exposed. Using radiocarbon dating, new research in the November 16, 2013 issue of Geophysical Research Letters has calculated the age of relic moss samples that have been exposed by modern Arctic warming. Because the moss samples would have been destroyed by erosion had they been previously exposed, the authors suggest that the temperatures in the Arctic now must be warmer than during any sustained period since the mosses were originally buried. The authors collected 365 samples of recently exposed biological material from 110 different locations, cutting a 1,000-kilometers-long transect across Baffin Island, with samples representing a range of altitudes. From their samples, the authors obtained 145 viable measurements through radiocarbon dating. They found that most of their samples date from the past 5,000 years, when a period of strong cooling overtook the Arctic. However, the authors also found even older samples that were buried from 24,000 to 44,000 years ago. The records suggest that, in general, the eastern Canadian Arctic is warmer now than in any century in the past 5,000 years, and in some places, modern temperatures are unprecedented in at least the past 44,000 years. The observations, the authors suggest, show that modern Arctic warming far exceeds the bounds of historical natural variability. “The great time these plants have been entombed in ice, and their current exposure, is the first direct evidence that present summer warmth in the Eastern Canadian Arctic now exceeds the peak warmth there in the Early Holocene era,” said Dr. Gifford Miller, from the University of Colorado.

Anti-Swine Flu Vaccination Linked to Increased Risk of Narcolepsy in Children and Adolescents

Pandemrix is an influenza vaccination, created in 2009 to combat H1N1 virus (image), known as Swine Flu. Now, according to a January 21, 2014 press release from the Journal of Internal Medicine, a team of Swedish clinicians testing the vaccine for links to immune-related or neurological diseases has linked Pandemrix to an increased risk of narcolepsy in young adults. Using a population-based prospective cohort study, the team analyzed data from regional vaccination registries and national health registries, covering seven healthcare regions and 61% of the Swedish population. While the team did not identify any link to a large number of immune-related or neurological diseases, they did confirm an increased risk in diagnosis of narcolepsy in individuals younger than 20 years of age, and observed a trend towards an increased risk amongst young adults between 21 and 30. “The follow-up of Pandemrix vaccinations in a large registry based study in Sweden confirms an increased risk of narcolepsy in children and adolescents, while also providing reassuring results for a large number of other neurological and immune related diseases,” said Dr. I. Persson from the Karolinska Institutet, Stockholm. [Press release]

Zone in with Zon—Will Wooly Mammoths and Passenger Pigeons Return?

Dr. Gerald Zon’s latest blog post, dated January 20, 2014, and published by TriLink BioTechnologies of San Diego, focuses on the issue of “De-Extinction: Hope or Hype?” In this thought-provoking post, Dr. Zon asks if the wooly mammoth can be revived and if the passenger pigeon might be returned to flight. He then suggests that “facilitated adaptation” might be a more realistic approach. Initially, Dr. Zon describes a CBS News interview with Dr. Hendrik Poinar on the possibility of reestablishing wooly mammoths. Dr. Poinar specializes in the novel techniques to extract and analyze “molecular information (DNA and/or protein sequences)” from ancient samples and has already sequenced the mitochondrial genome of the long-extinct wooly mammoth. Dr. Poinar believes that it might indeed be possible to bring these extinct creatures back to life in 30 to 50 years time. When asked to describe how this would be done, he said, “First thing you have to do is to get the entire blueprint. We have mapped the genome of the woolly mammoth. We’re almost completely done with that as well as a couple other extinct animals. We can look at the discrete differences between a mammoth and an Asian elephant. We would take an Asian elephant chromosome and modify it with mammoth information. Technology at Harvard can actually do that. Take the modified chromosomes and put them into an Asian elephant egg. Inseminate that egg and put that into an Asian elephant and take it to term. It could be as soon as 20 years.” Dr. Zon next described the work of a determined young ecologist with no graduate degree, Ben Novak, who has devoted all his recent efforts to resurrecting the exinct passenger pigeon. This was once the United States’ most numerous bird at approximately 5 billion strong, according to Audubon, but died out completely by 1914.