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Archive - Jun 12, 2013

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Microbes Found Alive 500 Feet Beneath Sea Floor

Microbes are living more than 500 feet beneath the seafloor in 5-million-year-old sediment, according to new findings by researchers at the University of Delaware (UD) and Woods Hole Oceanographic Institution (WHOI). Genetic material in mud from the bottom of the ocean — called the deep biosphere —revealed an ecosystem of active bacteria, fungi, and other microscopic organisms at depths deeper than a skyscraper is high. The findings were published online in Nature on June 12, 2013. “This type of examination shows active cells,” said co-author Dr. Jennifer F. Biddle, assistant professor of marine biosciences in UD’s College of Earth, Ocean, and Environment. “We knew that all of these cells were buried, but we didn’t know if they were doing anything.” In fact, the microbes are reproducing, digesting food, and even moving around despite the extreme conditions found there: little to no oxygen, heavy pressure, and minimal nutrient sources. The organisms could shed light on how carbon and other elements circulate in the environment, the scientists reported. The researchers analyzed messenger RNA (mRNA) in sediment from different depths collected off the coast of Peru in 2002 during Leg 201 of the Ocean Drilling Program. This first glimpse into the workings of the heretofore hidden ecosystem was made possible by the first successful extraction of total mRNA, or the “metatranscriptome,” from the deep biosphere. mRNA is highly sought-after by microbial ecologists because its presence indicates that the cells that made it are alive and because it carries the instructions for the proteins the cells are making. But because the metabolic rates in the deep biosphere are very low and mRNA is present in small amounts, extracting enough of it to analyze from deep sediments had been thought by many scientists to be impossible.

Solution-Based Circuit Chip Permits Rapid and Multiplexed Pathogen Identification

Life-threatening bacterial infections cause tens of thousands of deaths every year in North America. Increasingly, many infections are resistant to first-line antibiotics. Unfortunately, current methods of culturing bacteria in the lab can take days to report the specific source of the infection, and even longer to pinpoint the right antibiotic that will clear the infection. There remains an urgent, unmet need for technologies that can allow bacterial infections to be rapidly and specifically diagnosed. Researchers from the University of Toronto have created an electronic chip that operates with record-breaking speed and can analyze samples for panels of infectious bacteria. The new technology can report the identity of the pathogen in a matter of minutes, and looks for many different bacteria and drug resistance markers in parallel, allowing rapid and specific identification of infectious agents. The advance was reported online on June 12, 2013 in Nature Communications. "Overuse of antibiotics is driving the continued emergence of drug-resistant bacteria," said Dr. Shana Kelley (Pharmacy and Biochemistry), a senior author of the study. "A chief reason for use of ineffective or inappropriate antibiotics is the lack of a technology that rapidly offers physicians detailed information about the specific cause of the infection." The researchers developed an integrated circuit that could detect bacteria at concentrations found in patients presenting with a urinary tract infection. "The chip reported accurately on the type of bacteria in a sample, along with whether the pathogen possessed drug resistance," explained Chemistry Ph.D. student Brian Lam, the first author of the study. One key to the advance was the design of an integrated circuit that could accommodate a panel of many biomarkers.

Harbor Porpoises Can Thank Arch Enemy for Their Success

The harbor porpoise (Phocoena phocoena) is a whale species that is doing quite well in coastal and busy waters. They are found in large numbers throughout the Northern Hemisphere from Mauritania to Alaska, and now researchers from the University of Southern Denmark explain why these small-toothed whales are doing so well: The harbor porpoises can thank their worst enemy, the killer whale, for their success. Coastal areas are more challenging and potentially dangerous for a small whale. There is a risk of beaching and being caught in a fisherman's net, but there are also benefits. Fish are plentiful and easier to find in coastal waters than in the open sea. Therefore, coastal waters are attractive for porpoises, and they are extremely skilled at navigating, locating prey and avoiding hazards near the coast. Like other toothed whales porpoises use echolocation for orientation and to detect prey. They emit a constant stream of sonar clicks, which, when these hit a rock, a fish, or a ship nearby an echo is sent back to the porpoise. From the echo, the porpoise can distinguish the location of the object and often also can identify the object. Porpoises can locate even small fish and small objects such as net floats and fine fishing nets. This ability sets them apart from many other toothed whales, which do not have such sophisticated echolocation abilities. The secret of this ability is that the porpoise uses very short clicks and these are higher in frequency than those of many other toothed whales, explains Dr. Lee Miller from the Institute of Biology, University of Southern Denmark (SDU). Porpoise clicks last just a hundred-millionth of a second, and are about 130 kHz. For comparison, a human can hear up to 20 kHz and a dog up to about 60 kHz. Dr. Miller and his colleague Dr.