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  • richardmitnick 4:01 pm on December 19, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From: “Knee meniscus fixed using revolutionary stem cell procedure” 

    Cornell Bloc

    Cornell University

    Dec. 19, 2014
    Krishna Ramanujan

    Researchers report on a revolutionary new procedure that uses 3-D printing and the body’s stem cells to regenerate knee meniscus, a tissue lining that acts as a natural cushion between the femur and tibia.

    People with damaged menisci develop arthritis and are forced to limit their activity.

    The procedure, published online Dec. 10 in the journal Science Translational Medicine, has proved successful in sheep at Cornell University six months after surgery, though the researchers will monitor the sheep for a year to ensure the animals do not develop arthritis. Sheep menisci are structurally similar to those of humans, and clinical trials in humans could begin in two to three years.

    “Most middle-aged people who end up with a degenerate meniscus have it trimmed up [surgically], but if you lose more than 20 to 30 percent, then you are very prone to arthritis,” said Lisa Fortier, professor of large animal surgery at Cornell’s College of Veterinary Medicine and a co-author of the paper; she led the meniscus surgeries on sheep. “If everybody who needed it could replace their meniscus they could slow arthritis and maintain their full function,” Fortier added.

    Lise Fortier checks the meniscus of a sheep that she operated on last summer, using a groundbreaking new procedure to regenerate knee meniscus. (Meg Goodale)

    The technique was developed by the paper’s senior author Jeremy Mao, professor of dental medicine at Columbia University Medical Center, and involves taking an MRI of the patient’s (in this case sheep’s) knee. Using a 3-D printer, Mao printed a biodegradable polyester scaffold in the exact shape of a patient’s meniscus. Through multiple lab experiments, Mao’s group discovered that two growth factors, when used in specific concentrations and at critical times, recruited the most stem cells for meniscal repair. The growth factors were then laced into the scaffold, allowing the body’s stem cells build a new meniscus four to six weeks after surgery.

    Currently, a torn meniscus requires replacement with cadaver tissue, which has a low success rate and can lead to disease and rejection, and synthetic menisci have proved ineffective and hard to fit properly in diversely built patients.

    Approximately a million people undergo meniscus surgeries each year in the United States.

    Co-authors include Scott Rodeo, orthopedic surgeon at the Hospital for Special Surgery, an affiliate of Weill Cornell Medical College; and Chang H. Lee, Chuanyong Lu and Cevat Erisken, all at Columbia University Medical Center.

    The study was funded by the National Institutes of Health, the Arthroscopy Association of North America, the American Orthopaedic Society for Sports Medicine and the Harry M. Zweig Foundation.

    See the full article here.

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    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

  • richardmitnick 3:06 pm on December 19, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From Brown: “New technique reveals immune cell motion through variety of tissues” 

    Brown University
    Brown University

    December 18, 2014
    Kevin Stacey 401-863-3766

    Neutrophils, a type of white blood cell, are the immune system’s all-terrain vehicles. The cells are recruited to fight infections or injury in any tissue or organ in the body despite differences in the cellular and biochemical composition. Researchers from Brown University’s School of Engineering and the Department of Surgery in the Warren Alpert Medical School collaborated to devise a new technique for understanding how neutrophils move in these confined spaces.

    Cell movement in 3-D tissue By placing neutrophils between two hydrogel sacks, researchers can mimic cell movement through 3-D tissue. Digital micrometers can change the characteristics — density, stiffness — of the medium through which the cells move. Frank lab/Brown University

    The technique involves two hydrogel sacks sandwiched together with a miniscule space in between. Neutrophils could be placed in that space, mimicking the confinement they experience within tissue. Time-lapse cameras measure how fast the cells move, and traction force microscopes determine the forces the cells exert on the surrounding gel.

    In a paper published in the Journal of Biological Chemistry, the researchers used the device to reveal new details about the motion of neutrophils. Bodily tissues are highly confined, densely packed, three-dimensional spaces that can vary widely in physical shape and elasticity. The researchers showed that neutrophils are sensitive to the physical aspects of their environment: They behave differently on flat surfaces than in confined three-dimensional space. Ultimately, the team hopes the system can be useful in screening drugs aimed at optimizing neutrophils to fight infection in specific tissue types.

    Traditionally, research on neutrophil motion in the lab is often done on two-dimensional, inflexible surfaces composed of plastic or glass. Those studies showed that neutrophils move using arm-like appendages called integrins. The cell extends the integrins, which grab onto to flat surfaces like tiny grappling hooks. By reeling those integrins back in, the cell is able to crawl along.

    Scientists thought that by inhibiting integrins, they could greatly reduce the cells’ ability to move through tissue. That, they thought, could be a good strategy for fighting autoimmune diseases in which neutrophils attack and damage healthy tissue.

    But in 2008, a landmark paper showed that neutrophils have a second mode of motion. The work showed that cells in which integrins had been disabled were still able to move through dense tissue.

    Christian Franck, assistant professor of engineering at Brown, and his colleagues wanted to learn more about this second mode of motion.

    “On flat 2-D surfaces there’s integrin-dependent motion, but in complicated 3-D materials there’s integrin-independent motion,” Franck said. “The question we were asking is can we find an in-vitro system that can recreate that integrin-independent motion, because you can’t get it in a regular petri dish.”

    Using their gel system and the traction force microscopes, Franck and his colleagues showed that, when confined, neutrophils exert force in several distinct spots. On the bottom of the cell, forces were generated in a way that was consistent with previous imaging of integrin engagement. But on the top of the cell, there was another source of force. The cell pushed on the upper gel surface with its nuclear lobe, the area of the cell where DNA resides.

    “It’s like a rock climber pushing against the walls of a canyon,” Franck said.

    To see if the force generated by the nuclear lobe was responsible for the cells’ ability to move without integrins, the researchers repeated the experiment with cells in which integrins were chemically inhibited. Sure enough, the cells were still able to move when confined between the gels. In fact, they were able to move faster.

    “We showed that physical confinement is the key feature to reproduce integrin-independent motion in a relatively simple setting,” Franck said. “That wasn’t possible previously on a flat surface.”

    The fact that confined cells actually move faster without their integrin suggests that even though integrins aren’t essential for the cells motion, they still play a regulatory role.

    “What we showed was that [use of integrins] is not black and white,” Franck said. “Even in this integrin-independent motion, integrins remain to regulate motion and force generation.”

    Now that they have a means of recreating how neutrophils travel through confined spaces in the lab, Franck and his team plan to do further experiments aimed at fine-tuning that motion. The system they’ve developed enables them to control the stiffness of the gel surfaces between which the cells travel, mimicking the varying stiffness of tissue in the body.

    “If motility is specific to a neutrophil being in a specific tissue, maybe we could attenuate its response,” Franck said. “Maybe we could make it move faster in the muscle and slower everywhere else, for example.”

    This new system enables testing of drugs aimed at doing just that. Such drugs could be of great benefit to people who have disorders of the immune system.

    Franck’s co-authors on the study were Jennet Toyjanova, Estefany Flores-Cortez, and Jonathan S. Reichner. The research was supported by the National Institutes of Health (grants GM066194 and AI101469), and by a Brown University seed grant.

    See the full article here.

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    Welcome to Brown

    Rhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interiorRhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interior

    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

  • richardmitnick 10:13 am on December 19, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From ICL: “New study shows how some E. coli bacteria hijack key proteins to survive longer” 

    Imperial College London
    Imperial College London

    19 December 2014
    Laura Gallagher

    A new study shows how two strains of the intestinal bug E. coli manage to hijack host proteins used to control the body’s immune system.


    The research, carried out by scientists at Imperial College London and published in the journal Nature Communications, shows how E. coli bacteria can block key human enzymes, in a way that has not previously been shown in any other biological context.

    The enzymes, known as kinases, are molecular switches that control processes such as immune responses to infection and cancers in humans. Better understanding how the E. coli bacteria interfere with kinases will provide valuable avenues for investigating new therapies.

    There are many different strains of E. coli. While some are good bacteria, others can cause symptoms ranging from mild diarrhoea and nausea to kidney failure and death. The two strains examined in this study are E. coli O157, which causes food-borne infections, and enteropathogenic E. coli (EPEC), which is a major cause of infantile diarrhoea in low-income countries.

    At present there are no vaccines or effective drugs to combat these infections – in fact antibiotic treatment of E. coli O157 infection can cause the invading bacteria to release more toxins, making the symptoms worse. Patients are treated with fluids and nutrients to enable their immune system to fight the infection.

    One reason why these strains are so dangerous is that they inject bacterial proteins into human cells. These proteins hijack the cell’s signalling network to promote their growth and survival, for example by preventing the host from recognising them as harmful bacteria.

    The new research found that E. coli O157 and EPEC inject a protein called EspJ which inhibits the kinases from signalling.

    “The way in which the EspJ protein blocks the activity of human kinases is completely novel,” says Professor Gad Frankel, from the MRC Centre for Molecular Bacteriology and Infection. “This study will help us better understand how pathogens are able to hijack cells and how they prevent the immune system from fighting the infection.”

    The team reached their conclusions after performing biochemical, mass spectrometry and cell biology assays. This study provides valuable new avenues of investigation: further research will look at whether EspJ-like proteins in other intestinal pathogens, such as Salmonella, behave in similar ways, and also what effect EspJ proteins in E. coli O157 might have on other types of kinases.

    The research was carried out by a team of scientists at Imperial College London, working in collaboration Albert-Ludwigs-Universität Freiburg, in Germany.

    See the full article here.

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    Imperial College London is a science-based university with an international reputation for excellence in teaching and research. Consistently rated amongst the world’s best universities, Imperial is committed to developing the next generation of researchers, scientists and academics through collaboration across disciplines. Located in the heart of London, Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.

  • richardmitnick 12:56 pm on December 16, 2014 Permalink | Reply
    Tags: , Biology, , RPI   

    From RPI: “Researchers Develop ‘Radio-genetics’ – New Method Triggers Gene Expression With Radio Waves or Magnetic Field” 

    Rensselaer Polytechnic Institute

    Rensselaer Polytechnic Institute

    Rensselaer Polytechnic Institute Researchers Partner in Research Described in Nature Medicine

    December 15, 2014
    Mary L. Martialay
    Phone: (518) 276-2146
    E-mail: martim12@rpi.edu

    It’s the most basic of ways to find out what something does, whether it’s an unmarked circuit breaker or an unidentified gene — flip its switch and see what happens. New remote-control technology may offer biologists a powerful way to do this with cells and genes. A team at Rensselaer Polytechnic Institute and Rockefeller University is developing a system that would make it possible to remotely control biological targets in living animals — rapidly, without wires, implants, or drugs.

    In a technical report published today in the journal Nature Medicine, the team describes successfully using electromagnetic waves to turn on insulin production to lower blood sugar in diabetic mice. Their system couples a natural iron storage particle, ferritin, to activate an ion channel called TRPV1 such that when the metal particle is exposed to a radio wave or magnetic field, it opens the channel, leading to the activation of an insulin-producing gene. Together, the two proteins act as a nano-machine that can be used to trigger gene expression in cells.

    Researchers experimented with different configurations for their remote control system, and they found the best relies on an iron nanoparticle (blue), which is tethered by a protein (green) to an ion channel (red). Above, all three appear within cell membranes.

    “The use of a radiofrequency-driven magnetic field is a big advance in remote gene expression because it is non-invasive and easily adaptable,” said Jonathan S. Dordick, the Howard P. Isermann Professor of Chemical and Biological Engineering and vice president for research at Rensselaer Polytechnic Institute. “You don’t have to insert anything — no wires, no light systems — the genes are introduced through gene therapy. You could have a wearable device that provides a magnetic field to certain parts of the body and it might be used therapeutically for many diseases, including neurodegenerative diseases. It’s limitless at this point.”

    Dordick, Ravi Kane, the P.K. Lashmet Professor and head of Chemical and Biological Engineering, within the Rensselaer Center for Biotechnology and Interdisciplinary Studies, and doctoral student Jeremy Sauer collaborated with Rockefeller colleagues Jeffrey Friedman, Rensselaer Class of 1977, and Sarah Stanley on the project.

    Other techniques exist for remotely controlling the activity of cells or the expression of genes in living animals. But these have limitations. Systems that use light as an on/off signal require permanent implants or are only effective close to the skin, and those that rely on drugs can be slow to switch on and off.

    The new system, dubbed radiogenetics, uses a signal, in this case low-frequency radio waves or a magnetic field, to activate ferritin particles. They, in turn, prompt the opening of TRPV1, which is situated in the membrane surrounding the cell. Calcium ions then travel through the channel, switching on a synthetic piece of DNA the scientists developed to turn on the production of a downstream gene, which in this study was the insulin gene.

    In an earlier study, the researchers used only radio waves as the “on” signal, but in the current study, they also tested out a related signal – a magnetic field – that could also activate insulin production. They found it had a similar effect as the radio waves.

    “The method allows one to wirelessly control the expression of genes in a living animal and could potentially be used for conditions like hemophilia to control the production of a missing protein. Two key attributes are that the system is genetically encoded and can activate cells remotely and quickly,” says Friedman, co-senior author on the project and the Marilyn M. Simpson Professor and head of the Laboratory of Molecular Genetics at Rockefeller. “We are now exploring whether the method can also be used to control neural activity as a means for noninvasively modulating the activity of neural circuits.”

    See the full article here.

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  • richardmitnick 2:20 pm on December 13, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From Wisconsin: “New theory suggests alternate path led to rise of the eukaryotic cell” 

    U Wisconsin

    University of Wisconsin

    As a fundamental unit of life, the cell is central to all of biology. Better understanding how complex cells evolved and work promises new revelations in areas as diverse as cancer research and developing new crop plants.

    But deep thinking on how the eukaryotic cell came to be is astonishingly scant. Now, however, a bold new idea of how the eukaryotic cell and, by extension, all complex life came to be is giving scientists an opportunity to re-examine some of biology’s key dogma.

    All complex life — including plants, animals and fungi — is made up of eukaryotic cells, cells with a nucleus and other complex internal machinery used to perform the functions an organism needs to stay alive and healthy. Humans, for example, are composed of 220 different kinds of eukaryotic cells — which, working in groups, control everything from thinking and locomotion to reproduction and immune defense.

    Thus, the origin of the eukaryotic cell is considered one of the most critical evolutionary events in the history of life on Earth. Had it not occurred sometime between 1.6 and 2 billion years ago, our planet would be a far different place, populated entirely by prokaryotes, single-celled organisms such as bacteria and archaea.

    Eukaryotes and some examples of their diversity

    Cell structure of a bacterium, a member of one of the two domains of prokaryotic life

    Halobacteria sp. strain NRC-1, each cell about 5 μm long

    For the most part, scientists agree that eukaryotic cells arose from a symbiotic relationship between bacteria and archaea. Archaea — which are similar to bacteria but have many molecular differences — and bacteria represent two of life’s three great domains. The third is represented by eukaryotes, organisms composed of the more complex eukaryotic cells.

    Eukaryotic cells are characterized by an elaborate inner architecture. This includes, among other things, the cell nucleus, where genetic information in the form of DNA is housed within a double membrane; mitochondria, membrane-bound organelles, which provide the chemical energy a cell needs to function; and the endomembrane system, which is responsible for ferrying proteins and lipids about the cell.

    The structure of part of a DNA double helix

    Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy

    Prevailing theory holds that eukaryotes came to be when a bacterium was swallowed by an archaeon. The engulfed bacterium, the theory holds, gave rise to mitochondria, whereas internalized pieces of the outer cell membrane of the archaeon formed the cell’s other internal compartments, including the nucleus and endomembrane system.

    “The current theory is widely accepted, but I would not say it is ‘established’ since nobody seems to have seriously considered alternative explanations,” explains David Baum, a University of Wisconsin-Madison professor of botany and evolutionary biologist who, with his cousin, University College London cell biologist Buzz Baum, has formulated a new theory for how eukaryotic cells evolved. Known as the “inside-out” theory of eukaryotic cell evolution, the alternative view of how complex life came to be was published recently (Oct. 28, 2014) in the open access journal BMC Biology.


    The inside-out theory proposed by the Baums suggests that eukaryotes evolved gradually as cell protrusions, called blebs, reached out to trap free-living mitochondria-like bacteria. Drawing energy from the trapped bacteria and using bacterial lipids — insoluble organic fatty acids — as building material, the blebs grew larger, eventually engulfing the bacteria and creating the membrane structures that form the cell’s internal compartment boundaries.

    “The idea is tremendously simple,” says David Baum, who first began thinking about an alternate theory to explain the rise of the eukaryotic cell as an Oxford University undergraduate 30 years ago. “It is a radical rethinking, taking what we thought we knew (about the cell) and turning it inside-out.”

    From time to time, David Baum dusted off his rudimentary idea and shared it with others, including the late Lynn Margulis, the American scientist who developed the theory of the origin of eukaryotic organelles. Over the past year, Buzz and David Baum refined and detailed their idea, which, like any good theory, makes predictions that are testable.

    “First, the inside-out idea immediately suggested a steady stepwise path of evolution that required few cellular or molecular innovations. This is just what is required of an evolutionary model,” argues Buzz Baum, an expert on cell shape and structure. “Second, the model suggested a new way of looking at modern cells.”

    “The current theory is widely accepted, but I would not say it is ‘established’ since nobody seems to have seriously considered alternative explanations.”

    David Baum

    Modern eukaryotic cells, says Buzz Baum, can be interrogated in the context of the new theory to answer many of their unexplained features, including why nuclear events appear to be inherited from archaea while other features seem to be derived from the bacteria.

    “It is refreshing to see people thinking about the cell holistically and based on how cells and organisms evolved,” says Ahna Skop, a UW-Madison professor of genetics and an expert on cell division. The idea is “logical and well thought out. I’ve already sent the paper to every cell biologist I know. It simply makes sense to be thinking about the cell and its contents in the context of where they may have come from.”

    The way cells work when they divide, she notes, requires the interplay of molecules that have evolved over many millions of years to cut cells in two in the process of cell division. The same molecular functions, she argues, could be repurposed in a way that conforms to the theory advanced by the Baums. “Why spend the energy to remake something that was made thousands of years ago to pinch in a cell? The functions of these proteins just evolve and change as the organism’s structure and function change.”

    Knowing more about how the eukaryotic cell came to be promises to aid biologists studying the fundamental properties of the cell, which, in turn, could one day fuel a better understanding of things like cancer, diabetes and other cell-based diseases; aging; and the development of valuable new traits for important crop plants.

    One catch for fleshing out the evolutionary history of the eukaryotic cell, however, is that unlike many other areas of biology, the fossil record is of little help. “When it comes to individual cells, the fossil record is rarely very helpful,” explains David Baum. “It is even hard to tell a eukaryotic cell from a prokaryotic cell. I did look for evidence of microfossils with protrusions, but, not surprisingly, there were no good candidates.”

    A potentially more fruitful avenue to explore, he suggests, would be to look for intermediate forms of cells with some, but not all, of the features of a full-blown eukaryote. “The implication is that intermediates that did exist went extinct, most likely because of competition with fully-developed eukaryotes.”

    However, with a more granular understanding of how complex cells evolved, it may be possible to identify living intermediates, says David Baum: “I do hold out hope that once we figure out how the eukaryotic tree is rooted, we might find a few eukaryotes that have intermediate traits.”

    “This is a whole new take (on the eukaryotic cell), which I find fascinating,” notes UW-Madison biochemistry Professor Judith Kimble. “I have no idea if it is right or wrong, but they’ve done a good job of pulling in detail and providing testable hypotheses. That, in itself, is incredibly useful.”

    See the full article here.

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    In achievement and prestige, the University of Wisconsin–Madison has long been recognized as one of America’s great universities. A public, land-grant institution, UW–Madison offers a complete spectrum of liberal arts studies, professional programs and student activities. Spanning 936 acres along the southern shore of Lake Mendota, the campus is located in the city of Madison.

  • richardmitnick 9:44 am on December 12, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From NYT: “An Evolutionary Battle Against Bacteria” 

    New York Times

    The New York Times

    DEC. 11, 2014
    Carl Zimmer

    Every disease has a history. Some of that history is written in books, and some is written in our DNA.

    The earliest records of meningitis — an infection of the membranes that line the brain — reach back to 1685. The British physician Thomas Willis described fevered patients, some of whom suffered from “continual raving” and others who suffered from “horrible stiff extensions in the whole body.”

    But meningitis was a threat long before Willis put quill to paper. In a new study, published Thursday in the journal Science, two University of Utah scientists have uncovered a 40-million-year struggle between our ancestors and the bacteria that cause meningitis: As our ancestors evolved new defenses, our enemies evolve counter-defenses. By understanding the history of this struggle, we may be able to fight meningitis more effectively in the future.

    A number of species of bacteria can cause meningitis, but two — Haemophilus influenzae and Neisseria meningitidis — are the top threats. Like all bacteria, these pathogens need iron to grow. But we don’t make it easy for them to find iron inside our bodies.

    Haemophilus influenzae

    Neisseria meningitidis

    To move iron atoms from one cell to another, we seal them inside a kind of molecular lockbox, called transferrin. A cell can load two iron atoms into a single transferrin molecule and deliver it to another cell, which draws the transferrin inside and then opens it.


    Transferrin lets us starve bacteria by making free iron atoms scarce. Simply withholding it from the bacteria “becomes an immune strategy,” said Nels C. Elde, an evolutionary geneticist and an author of the new study.

    A few years ago, Dr. Elde became puzzled by transferrin. Studies by other scientists suggested that it had experienced strong natural selection, changing its molecular structure over generations. But transferrin still does the same job it has been doing for hundreds of millions of years. It ferries iron atoms inside mammals, reptiles, amphibians and even fish.

    To understand what has driven transferrin’s evolution, Dr. Elde teamed with Matthew F. Barber, a postdoctoral researcher in his lab. They carried out an unprecedented study on the evolution of the gene that encodes transferrin, comparing our own version to those in 20 species of apes and monkeys.

    The two scientists confirmed that over the past 40 million years, our transferrin protein had undergone drastic changes. Transferrin is made up of two lobes, each of which grabs an iron atom. By far the most changes had occurred in only one of the lobes. The other one barely evolved.

    This finding gave Dr. Elde a clue as to what was driving the evolution of transferrin: meningitis-causing bacteria.

    Neisseria and Haemophilus can both steal iron from transferrin. They do so with a protein, TbpA, that pries open one of transferrin’s two lobes, exposing the iron atom inside. The lobe under attack is the one that has been evolving swiftly; the unmolested lobe has barely changed.


    As the two Utah scientists were studying these evolutionary changes, researchers at the National Institutes of Health published the molecular details of how TbpA grabs transferrin. When Dr. Barber and Dr. Elde compared their results with the molecular structure, they were shocked. Almost every point at which transferrin made contact with TbpA has evolved, while little has changed beyond them.

    “That was the moment it all snapped together,” said Dr. Elde.

    Dr. Barber and Dr. Elde were able to reconstruct the history of transferrin. Each time its shape changed, it became harder for the bacteria to grab it and steal its iron.

    The scientists wondered if the bacteria had evolved in response to these changes. To find out, they got strains of Haemophilus influenzae and Neisseria meningitis from patients. They looked at the bacteria’s TbpA genes to see where they had evolved new structures.

    It turns out they changed where they made contact with transferrin. “It’s basically a mirror image,” said Dr. Elde.

    He and Dr. Barber argue that our ancestors and meningitis-causing bacteria have been locked in an arms race for 40 million years. Each time we make it harder for the bacteria to steal our iron, the bacteria change their structure to get a better grip on our transferrin.

    The race isn’t over. A new variant of transferrin has evolved in humans, and it is found in 6 to 25 percent of people, depending on their ethnic group. The Utah scientists found that Haemophilus influenzae bacteria can’t steal iron from the new variant. “It’s basically invisible,” Dr. Elde said.

    Harmit S. Malik, an evolutionary geneticist at the Fred Hutchinson Cancer Research Center who was not involved in the research, said that until he saw it, he doubted there were enough clues left in living primates to reconstruct the evolutionary arms race.

    But Dr. Barber and Dr. Elde proved him wrong. “It’s an extremely crisp result,” Dr. Malik said, adding, “Frankly, I didn’t think this could be done.”

    Despite all the defenses our ancestors evolved against these bacteria, they still pose a major threat to humanity. Haemophilus influenzae alone has been estimated to kill 371,000 people a year. Some researchers have investigated treating such infections by giving patients extra transferrin to starve bacteria.

    Dr. Malik suggested that this treatment would be even more effective if scientists used the evolutionary history of transferrin as a guide for designing transferrin that the bacteria can’t attack.

    “I suspect it could be a very, very important therapeutic,” he said. If he is right, our monkeylike ancestors could have a hand in saving the lives of our descendants.

    See the full article here.

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  • richardmitnick 8:48 pm on December 11, 2014 Permalink | Reply
    Tags: , Biology, Mitochondria,   

    From Wisconsin: “New studies power legacy of UW-Madison mitochondrial research “ 

    U Wisconsin

    University of Wisconsin

    Dec. 11, 2014
    Kelly April Tyrrell

    It was the yellow color of the solution, pulled from cauliflower, that set Frederick Crane’s hallmark achievement into its final motion.

    Crane was a researcher under David E. Green in the early days of the University of Wisconsin-Madison Enzyme Institute, in a lab group on a mission to determine, bit by bit, how mitochondria — the power plants of cells — generate the energy required to sustain life.

    An assortment of biochemical approaches, both modern and classic, is pictured with a 3-D model of the COQ9 protein structure used by UW-Madison researchers. The university’s mitochondrial research dates back nearly 60 years. Photo: Matthew Stefely/Pagliarini Lab

    Mitochondrion ultrastructure. A mitochondrion has a double membrane; the inner one contains its chemiosmotic apparatus and has deep grooves which increase its surface area. While commonly depicted as an “orange sausage with a blob inside of it” (like it is here), mitochondria can take many shapes[17] and their intermembrane space is quite thin.

    In the early 1950s, the lab was looking for the missing piece that connected each of the individual parts of the mitochondrial energy machine — the electron transport chain — like the gears needed to operate an engine.

    What Crane found, a compound called coenzyme Q, was to become a major part of the legacy of mitochondrial research at UW-Madison, but it was no accident. It was “the result of a long train of investigation into a mechanism of, and compounds involved in, biological energy conversion,” Crane wrote in a 2007 review article of his discovery.

    coenzyme Q

    Photo: Dave Pagliarini

    Almost six decades later, that “long train” has grown even longer. Dave Pagliarini, a UW-Madison assistant professor of biochemistry, has established a new laboratory studying these dynamic organelles, the mitochondria. He recently published two studies shedding more light on coenzyme Q and how it’s made, one in the Proceedings of the National Academy of Science (PNAS) in October and another today in Molecular Cell.

    “Mitochondria are tiny structures in nearly all of our cells that are essential for producing our cellular energy and that house a wide array of metabolic processes,” Pagliarini says. “When mitochondria don’t work properly, many different human diseases can arise.”

    These include cerebellar ataxia, certain kidney diseases and severe childhood-onset multisystemic disease. Coenzyme Q deficiency is a hallmark of these diseases, but scientists aren’t sure why.

    “Nearly 60 years later, there is still much we don’t know about how mitochondria make coenzyme Q and that has complicated our ability to target this pathway therapeutically,” Pagliarini says.

    The new studies, he says, are about two proteins known to be important in the coenzyme Q production pathway. Mutations in them lead to human disease. But before now, no one knew a thing about their biochemical functions.

    One of these proteins is COQ9, and graduate student Danielle Lohman, co-lead author of the PNAS study, explains it’s somehow involved in making coenzyme Q in mitochondria. The other lead author is Farhad Forouhar at Columbia University.

    The study team — which includes researchers from UW-Madison and other universities in the U.S. and Spain — found COQ9 is essential for coenzyme Q production in mice. To study what it looks like, they created crystals of COQ9 in the lab and found it binds fatty substances like those Crane first observed in his studies, like coenzyme Q.

    With these mitochondrial proteins and many others, much is still unknown. They represent an untapped resource, Pagliarini says, but the mining for answers is happening right here, where coenzyme Q was first found.

    In his day, while others were looking for proteins to be the missing part of the mitochondrial energy chain, Crane was looking for fatty, vitamin-like compounds. His hunch turned out to be correct.

    Today, Pagliarini and Lohman have a hunch, too, that COQ9 may be grabbing hold of an immature form of coenzyme Q and helping it develop. The prevailing notion in the mitochondrial field is that coenzyme Q is made through the actions of a collaborative complex of proteins, of which CoQ9 may be a part.

    Only time and future study will tell, but lending credence to the idea is the research team’s additional finding that COQ9 cooperates with another protein called COQ7.

    “We went from not knowing why this protein would be needed to make coenzyme Q, to having a model for what it might be doing,” Lohman says.

    Two other graduate students in Pagliarini’s lab, Jonathan Stefely and Andrew Reidenbach, worked together to lead the Molecular Cell study of a human mitochondrial protein also involved in building coenzyme Q, called ADCK3.

    “Like COQ9, there are patients with mutations in ADCK3 who have really bad cerebellar ataxia, described in the medical literature not too long ago,” says Stefely.

    Also like COQ9, ADCK3’s biochemical function was previously unknown. The research team — from UW-Madison, the University of Georgia and the University of San Diego — similarly created a crystal of the protein and determined the protein family it’s related to: the kinase superfamily. Craig Bingman, a research scientist at UW-Madison, performed the challenging crystal work.

    While solving the crystal structure revealed the protein’s genealogy, the findings also provided the researchers with information that could have implications for cancer and other cellular processes that may rely on the actions of this protein and its close relatives. It provides a platform for further discovery.

    “It has some very specific and unique features that separate it from the rest of this kinase superfamily,” says Reidenbach.

    “We were also able to show the first enzymatic activity for ADCK3, which was a major milestone in this field,” Stefely adds.

    For Pagliarini and his students — the future of UW-Madison mitochondrial research — the old, yet still-wide-open field of study offers plenty of opportunity for curiosity, and promise.

    With these mitochondrial proteins and many others, much is still unknown. They represent an untapped resource, Pagliarini says, but the mining for answers is happening right here, where coenzyme Q was first found.

    In his lab, Pagliarini is on a quest to describe the hundreds of mitochondrial proteins with functions yet unknown. With colleagues, he has amassed a collection of them in an inventory they’ve called the MitoCarta.

    “I stumbled into mitochondrial biology early in my graduate career and spent my postdoctoral years systematically identifying new mitochondrial proteins” says Pagliarini. “Now, I am very interested in annotating the functions of these ‘orphan’ proteins.”

    It’s this same natural curiosity that fueled Crane and eventually led to his discovery of coenzyme Q. As part of Green’s group, he was also systematically separating the parts of the mitochondrial energy machinery, asking questions along the way.

    He was using beef hearts — which he got from the Oscar Mayer plant in Madison — to isolate mitochondria, and they came out in a brown solution. But Crane was originally trained as a plant physiologist and in his spare time, he started isolating mitochondria from cauliflower, too. They came out in a yellow solution, which told him to keep looking for fatty, vitamin-A-like molecules, leading him ultimately to coenzyme Q.

    The give-away color was simply masked by the brown-colored elements of the beef.

    For Pagliarini and his students — the future of UW-Madison mitochondrial research — the old, yet still-wide-open field of study offers plenty of opportunity for curiosity, and promise.

    “It gives you a sense of wonder; for me, like all scientists, I just want to know how things work,” says Lohman. “This seemed like fruit ripe for the picking.”

    See the full article here.

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  • richardmitnick 7:45 pm on December 11, 2014 Permalink | Reply
    Tags: , Biology, ,   

    From Scientific American via Cornell University: “Are Algae Blooms Linked to Lou Gehrig’s Disease?” 

    Scientific American

    Scientific American

    Cornell Bloc

    December 11, 2014
    Lindsey Konkel and Environmental Health News

    Medical researchers are now uncovering clues that appear to link some cases of ALS to people’s proximity to lakes and coastal waters.

    For 28 years, Bill Gilmore lived in a New Hampshire beach town, where he surfed and kayaked. “I’ve been in water my whole life,” he said. “Before the ocean, it was lakes. I’ve been a water rat since I was four.”

    Now Gilmore can no longer swim, fish or surf, let alone button a shirt or lift a fork to his mouth. Earlier this year, he was diagnosed with Amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease.

    In New England, medical researchers are now uncovering clues that appear to link some cases of the lethal neurological disease to people’s proximity to lakes and coastal waters.

    About five years ago, doctors at a New Hampshire hospital noticed a pattern in their ALS patients—many of them, like Gilmore, lived near water. Since then, researchers at Dartmouth-Hitchcock Medical Center have identified several ALS hot spots in lake and coastal communities in New England, and they suspect that toxic blooms of blue-green algae—which are becoming more common worldwide—may play a role.

    Now scientists are investigating whether breathing a neurotoxin produced by the algae may raise the risk of the disease. They have a long way to go, however: While the toxin does seem to kill nerve cells, no research, even in animals, has confirmed the link to ALS.

    No known cause

    As with all ALS patients, no one knows what caused Bill Gilmore’s disease. He was a big, strong guy—a carpenter by profession. One morning in 2011, his arms felt weak. “I couldn’t pick up my tools. I thought I had injured myself,” said Gilmore, 59, who lived half his life in Hampton and now lives in Rochester, N.H.

    Three years and many doctors’ appointments later, Gilmore received the news in June that the progressive weakening in his limbs was caused by ALS.

    Neither Hampton nor Rochester is considered a hot spot for ALS. Gilmore is one of roughly 5,600 people in the United States diagnosed each year with the disease. The average patient lives two to five years from the time of diagnosis.

    There is no cure, and for the majority of patients, no known cause. For 90 to 95 percent of people with ALS, there’s no known genetic mutation. Researchers assume that some unknown interaction between genes and the environment is responsible.

    In recent years, some of this research has focused on blue-green algae, also known as cyanobacteria.


    “There’s a growing awareness of the importance of gene/environment interactions with neurodegenerative diseases. There is more interest in examining environmental exposures, including exposures to cyanobacteria, as possible risk factors for sporadic ALS,” said Paul Alan Cox, director of the nonprofit Institute of Ethnomedicine in Wyoming, which focuses on treatments for ALS and other neurodegenerative diseases.

    Cyanobacteria—some of the oldest organisms on the planet—can occur wherever there is moisture. Blooms are fed largely by nutrients in agricultural and urban runoff.

    Some cyanobacteria produce toxic compounds that can sicken people. In August, hundreds of thousands of people in Toledo, Ohio, were left without tap water for days when toxins from an algal bloom in Lake Erie were found in the water supply.

    While the cyanobacteria toxin that prompted the Toledo water crisis can cause diarrhea, intestinal pain and liver problems, other toxins produced by the blue-green algae can harm the nervous systems of humans and wildlife.

    Scientists have long suspected that a cyanobacteria toxin could play a role in some forms of ALS. After World War II, U.S. military doctors in Guam found that many indigenous Chamorro suffered from a rapidly progressing neurological disease with symptoms similar to both ALS and dementia. Years later, scientists found the neurotoxin BMAA in the brains of Chamorro people who died from the disease. Cyanobacteria that grow on the roots and seeds of cycad trees produce the toxin.

    Cox, a researcher in Guam in the 1990s, hypothesized that BMAA worked its way up the food chain from the cycad seeds to bats to the Chamorro who hunted them. But Cox and his colleagues also found BMAA in the brains of Canadian Alzheimer’s patients who had never dined on Guam’s fruit bats. In patients who had died from other causes, they found no traces of it. The source of the BMAA in the Canadians remains unknown.

    Some researchers have suggested that fish and shellfish from waters contaminated with cyanobacteria blooms may be one way that people ingest BMAA. In southern France, researchers suspect ALS cases may be linked to consumption of mussels and oysters. Lobsters, collected off the Florida coast near blooms, also have been found with high levels of BMAA.

    Scientists around the world are investigating how the neurotoxin gets into the body and whether it contributes to disease.

    “We don’t really know what exposure routes are most important,” Cox said.

    New England’s ALS hot spots

    In New Hampshire, Dartmouth neurologist Elijah Stommel noticed that several ALS patients came from the small town of Enfield in the central part of the state. When he mapped their addresses, he saw that nine of them lived near Lake Mascoma.

    Around the lake, the incidence of sporadic ALS—cases for which genetics are not a likely cause—is approximately 10 to 25 times the expected rate for a town of that size.

    “We had no idea why there appeared to be a cluster around the lake,” Stommel said.

    Based on the link between ALS and the neurotoxin in other parts of the world, Stommel and his colleagues hypothesize that the lake’s cyanobacteria blooms could be a factor.

    Across northern New England, the researchers have continued to identify ALS hot spots—a large one in Vermont near Lake Champlain and a smattering of smaller ones among coastal communities in New Hampshire and Maine.

    Earlier this year, the researchers reported that poorer lake water quality increased the odds of living in a hot spot. Most strikingly, they discovered that living within 18 miles of a lake with high levels of dissolved nitrogen—a pollutant from fertilizer and sewage that feeds algae and cyanobacteria blooms—raised the odds of belonging to an ALS hot spot by 167 percent.

    The findings, they wrote, “support the hypothesis that sporadic ALS can be triggered by environmental lake quality and lake conditions that promote harmful algal blooms and increases in cyanobacteria.”

    How people in New England communities could be ingesting the neurotoxin remains largely a mystery. While fish in the lakes do contain it, not everyone in the Dartmouth studies eats fish.

    “We’ve sent questionnaires to patients and there’s really no common thread in terms of diet or activities,” Stommel said. “The one common thing that everybody does is breathe.”

    In other words, it’s possible that a boat, jet ski or even the wind could stir up tiny particles of cyanobacteria in the air, where people then breathe it in.

    Testing the air for a neurotoxin

    Last August, at Lake Attitash, Jim Haney, a University of New Hampshire biologist, waded knee-deep into swirling green water. Cyanobacteria were blooming at the small lake in the northeastern corner of Massachusetts. Haney had rigged up three vacuum-like devices with pipes, plastic funnels and paper to suck up and filter air near the lake’s surface.

    He took the filter papers back to his laboratory and measured the cyanobacteria cells, BMAA and other toxins stuck to them.

    “We want to know what level lake residents may be exposed to through airborne particles,” said Haney, who is sampling the air at Massachusetts and New Hampshire lakes in collaboration with the Dartmouth team.

    Stommel said,“it’s very compelling to look at the filter paper and see it just coated with cyanobacteria.”

    At this point, Haney and graduate students are trying to understand under what conditions the toxins might be coming out of the lake and whether the airborne particles are an important route of exposure.

    Preliminary findings suggest that BMAA and other cyanobacteria cells are being aerolized. “There is potentially a large quantity of cyanobacteria that could be inhaled,” Haney said. He noted, however, that the measurements were taken about eight inches above the water’s surface, making it likely that concentrations would be much lower farther away.

    While the toxins are likely to be most abundant in the air around lakes, they exist all over the planet, even in deserts.

    In 2009, BMAA was even detected in the sands of Qatar. Crusts containing cyanobacteria may lie dormant in the soil for most of the year, but get kicked up during spring rainstorms. Cox and colleagues hypothesized that breathing in toxins from dust might be a trigger for a doubling of ALS incidence in military personnel after Operation Desert Storm.

    Near Haney’s workstation at Lake Attitash, a child splashed in the shallow water off a dock. Haney scooped up a cupful of water. He peered at the tiny green particles in the cup that reflect the sunlight, making the mixture resemble a murky pea soup.

    “We’ve developed this view of nature as idyllic, which is wonderful, but not everything in nature is benign,” he said. “Rattlesnakes are natural and you wouldn’t get too close to one of those.”

    “Proximity does not equal causality”

    The hypothesis that exposure to BMAA may trigger the disease in some people remains controversial.

    Researchers have evidence that people living close to lakes with blooms may be at increased risk for ALS. They’ve even found BMAA in the diseased brain tissue of people who have died of neurodegenerative diseases. Nevertheless, “proximity does not equal causality,” said Deborah Mash, a neuroscientist at the University of Miami in Florida.

    The big, unanswered question is whether the toxin can actually cause the disease. So far, there’s little evidence to show how it could induce the type of brain changes seen in people with ALS.

    Tests of human cells have found that BMAA kills the motor neurons—nerve cells that control muscles—implicated in ALS. Primates fed high levels of BMAA in the 1980s showed signs of neurological and muscular weakness. But the toxin did not kill their motor neurons.

    “What is lacking at this point is a clear animal model that demonstrates that BMAA exposure results in ALS-like neuropathy,” Cox said.

    So what is a possible mechanism for how the toxin may lead to the disease? The body may mistake BMAA for the amino acid L-serine, a naturally occurring component of proteins. When the toxin is mistakenly inserted into proteins, they become “misfolded,” meaning they no longer function properly and can damage cells.

    Cox and colleagues soon will test two drugs in FDA-approved clinical trials. They’re about to enter second-phase testing with L-serine. The idea, explained Sandra Banack, a researcher at the Institute for Ethnomedicine, is that large doses of L-serine may be able to “outcompete” low levels of BMAA in the body, preventing it from becoming incorporated into proteins.

    For ALS patients like Gilmore, the research can’t come soon enough. “If they can figure out a cause, then hopefully they can find a cure,” Gilmore said.

    [We need to remember that cyanobacteria are responsible for the first free oxygen in our atmosphere, without which we would not exist. This, from a 2009 Scientific American article:

    It’s hard to keep oxygen molecules around, despite the fact that it’s the third-most abundant element in the universe, forged in the superhot, superdense core of stars. That’s because oxygen wants to react; it can form compounds with nearly every other element on the periodic table. So how did Earth end up with an atmosphere made up of roughly 21 percent of the stuff?

    The answer is tiny organisms known as cyanobacteria, or blue-green algae. These microbes conduct photosynthesis: using sunshine, water and carbon dioxide to produce carbohydrates and, yes, oxygen. In fact, all the plants on Earth incorporate symbiotic cyanobacteria (known as chloroplasts) to do their photosynthesis for them down to this day.]

    See the full article here.

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  • richardmitnick 5:55 pm on December 10, 2014 Permalink | Reply
    Tags: , Biology, , ,   

    From isgtw: “Supercomputer compares modern and ancient DNA” 

    international science grid this week

    December 10, 2014
    Jorge Salazar, Texas Advanced Computing Center

    What if you researched your family’s genealogy, and a mysterious stranger turned out to be an ancestor? A team of scientists who peered back into Europe’s murky prehistoric past thousands of years ago had the same surprise. With sophisticated genetic tools, supercomputing simulations and modeling, they traced the origins of modern Europeans to three distinct populations.The international research team’s results are published in the journal Nature.

    The Stuttgart skull, from a 7,000-year-old skeleton found in Germany among artifacts from the first widespread farming culture of central Europe. Right: Blue eyes and dark skin – how the European hunter-gatherer appeared 7,000 years ago. Artist depiction based on La Braña 1, whose remains were recovered at La Braña-Arintero site in León, Spain. Images courtesy Consejo Superior de Investigaciones Cientificas.

    “Europeans seem to be a mixture of three different ancestral populations,” says study co-author Joshua Schraiber, a National Science Foundation postdoctoral fellow at the University of Washington, in Seattle, US. Schraiber says the results surprised him because the prevailing view among scientists held that only two distinct groups mixed between 7,000 and 8,000 years ago in Europe, as humans first started to adopt agriculture.

    Scientists have only a handful of ancient remains well preserved enough for genome sequencing. An 8,000-year-old skull discovered in Loschbour, Luxembourg provided DNA evidence for the study. The remains were found at the caves of Loschbour, La Braña, Stuttgart, a ritual site at Motala, and at Mal’ta.

    The third mystery group that emerged from the data is ancient northern Eurasians. “People from the Siberia area is how I conceptualize it,” says Schraiber. “We don’t know too much anthropologically about who these people are. But the genetic evidence is relatively strong because we do have ancient DNA from an individual that’s very closely related to that population, too.”

    The individual is a three-year-old boy whose remains were found near Lake Baikal in Siberia at the Mal’ta site. Scientists determined his arm bone to be 24,000 years old. They then sequence his genome, making it the second oldest modern human sequenced. Interestingly enough, in late 2013 scientists used the Mal’ta genome to find that about one-third of Native American ancestry originated through gene flow from these ancient North Eurasians.

    The researchers took the genomes from these ancient humans and compared them to those from 2,345 modern-day Europeans. “I used the POPRES data set, which had been used before to ask similar questions just looking at modern Europeans,” Schraiber says. “Then I used software called Beagle, which was written by Brian Browning and Sharon Browning at the University of Washington, which computationally detects these regions of identity by descent.”

    The National Science Foundation’s XSEDE (Extreme Science and Engineering Discovery Environment) and Stampede supercomputer at the Texas Advanced Computing Center provided computational resources used in the study. The research was funded in part by the National Cancer Institute of the National Institutes of Health.

    See the full article here.

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    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, iSGTW is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

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  • richardmitnick 2:47 pm on December 10, 2014 Permalink | Reply
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    From astrobio.net: “Warmer Pacific Ocean could release millions of tons of seafloor methane” 

    U Washington

    University of Washington

    December 9, 2014
    Hannah Hickey

    Off the West Coast of the United States, methane gas is trapped in frozen layers below the seafloor. New research from the University of Washington shows that water at intermediate depths is warming enough to cause these carbon deposits to melt, releasing methane into the sediments and surrounding water.

    Researchers found that water off the coast of Washington is gradually warming at a depth of 500 meters, about a third of a mile down. That is the same depth where methane transforms from a solid to a gas. The research suggests that ocean warming could be triggering the release of a powerful greenhouse gas.

    Sonar image of bubbles rising from the seafloor off the Washington coast. The base of the column is 1/3 of a mile (515 meters) deep and the top of the plume is at 1/10 of a mile (180 meters) deep.Brendan Philip / UW

    “We calculate that methane equivalent in volume to the Deepwater Horizon oil spill is released every year off the Washington coast,” said Evan Solomon, a UW assistant professor of oceanography. He is co-author of a paper to appear in Geophysical Research Letters.

    While scientists believe that global warming will release methane from gas hydrates worldwide, most of the current focus has been on deposits in the Arctic. This paper estimates that from 1970 to 2013, some 4 million metric tons of methane has been released from hydrate decomposition off Washington. That’s an amount each year equal to the methane from natural gas released in the 2010 Deepwater Horizon blowout off the coast of Louisiana, and 500 times the rate at which methane is naturally released from the seafloor.

    Dissociation of Cascadia margin gas hydrates in response to contemporary ocean warming
    Geophysical Research Letters | Dec. 5, 2014

    “Methane hydrates are a very large and fragile reservoir of carbon that can be released if temperatures change,” Solomon said. “I was skeptical at first, but when we looked at the amounts, it’s significant.”

    Methane is the main component of natural gas. At cold temperatures and high ocean pressure, it combines with water into a crystal called methane hydrate. The Pacific Northwest has unusually large deposits of methane hydrates because of its biologically productive waters and strong geologic activity. But coastlines around the world hold deposits that could be similarly vulnerable to warming.

    “This is one of the first studies to look at the lower-latitude margin,” Solomon said. “We’re showing that intermediate-depth warming could be enhancing methane release.”
    map of Washington coast

    The yellow dots show all the ocean temperature measurements off the Washington coast from 1970 to 2013. The green triangles are places where scientists and fishermen have seen columns of bubbles. The stars are where the UW researchers took more measurements to check whether the plumes are due to warming water.Una Miller / UW

    Una Miller, a UW oceanography undergraduate, first collected thousands of historic temperature measurements in a region off the Washington coast as part of a separate research project in the lab of co-author Paul Johnson, a UW professor of oceanography. The data revealed the unexpected sub-surface ocean warming signal.

    “Even though the data was raw and pretty messy, we could see a trend,” Miller said. “It just popped out.”

    The four decades of data show deeper water has, perhaps surprisingly, been warming the most due to climate change.

    “A lot of the earlier studies focused on the surface because most of the data is there,” said co-author Susan Hautala, a UW associate professor of oceanography. “This depth turns out to be a sweet spot for detecting this trend.” The reason, she added, is that it lies below water nearer the surface that is influenced by long-term atmospheric cycles.

    The warming water probably comes from the Sea of Okhotsk, between Russia and Japan, where surface water becomes very dense and then spreads east across the Pacific. The Sea of Okhotsk is known to have warmed over the past 50 years, and other studies have shown that the water takes a decade or two to cross the Pacific and reach the Washington coast.

    Map of the Sea of Okhotsk

    “We began the collaboration when we realized this is also the most sensitive depth for methane hydrate deposits,” Hautala said. She believes the same ocean currents could be warming intermediate-depth waters from Northern California to Alaska, where frozen methane deposits are also known to exist.

    The yellow dots show all the ocean temperature measurements off the Washington coast from 1970 to 2013. The green triangles are places where scientists and fishermen have seen columns of bubbles. The stars are where the UW researchers took more measurements to check whether the plumes are due to warming water.Una Miller / UW

    Researchers used a coring machine to gather samples of sediment off Washington’s coast to see if observations match their calculations for warming-induced methane release. The photo was taken in October aboard the UW’s Thomas G. Thompson research vessel.Robert Cannata / UW

    Warming water causes the frozen edge of methane hydrate to move into deeper water. On land, as the air temperature warms on a frozen hillside, the snowline moves uphill. In a warming ocean, the boundary between frozen and gaseous methane would move deeper and farther offshore. Calculations in the paper show that since 1970 the Washington boundary has moved about 1 kilometer – a little more than a half-mile – farther offshore. By 2100, the boundary for solid methane would move another 1 to 3 kilometers out to sea.

    Estimates for the future amount of gas released from hydrate dissociation this century are as high as 0.4 million metric tons per year off the Washington coast, or about quadruple the amount of methane from the Deepwater Horizon blowout each year.

    Still unknown is where any released methane gas would end up. It could be consumed by bacteria in the seafloor sediment or in the water, where it could cause seawater in that area to become more acidic and oxygen-deprived. Some methane might also rise to the surface, where it would release into the atmosphere as a greenhouse gas, compounding the effects of climate change.
    researchers on ship

    Evan Solomon (right) and Marta Torres (left, OSU) aboard the UW’s Thomas G. Thompson research vessel in October, with fluid samples from the seafloor that will help answer whether the columns of methane bubbles are due to ocean warming.Robert Cannata / UW

    Researchers now hope to verify the calculations with new measurements. For the past few years, curious fishermen have sent UW oceanographers sonar images showing mysterious columns of bubbles. Solomon and Johnson just returned from a cruise to check out some of those sites at depths where Solomon believes they could be caused by warming water.

    “Those images the fishermen sent were 100 percent accurate,” Johnson said. “Without them we would have been shooting in the dark.”

    Johnson and Solomon are analyzing data from that cruise to pinpoint what’s triggering this seepage, and the fate of any released methane. The recent sightings of methane bubbles rising to the sea surface, the authors note, suggests that at least some of the seafloor gas may reach the surface and vent to the atmosphere.

    The research was funded by the National Science Foundation and the U.S. Department of Energy. The other co-author is Robert Harris at Oregon State University.

    See the full article here.

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