Tuesday, October 12, 2010

'GOLD' FISH THRIVE, CANCERS DIE

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Rice University physicist Dmitri Lapotko has demonstrated that plasmonic nanobubbles, generated around gold nanoparticles with a laser pulse, can detect and destroy cancer cells in vivo by creating tiny, shiny vapor bubbles that reveal the cells and selectively explode them.

A paper in the October print edition of the journal Biomaterials details the effect of plasmonic nanobubble theranostics on zebra fish implanted with live human prostate cancer cells, demonstrating the guided ablation of cancer cells in a living organism without damaging the host.

Lapotko and his colleagues developed the concept of cell theranostics to unite three important treatment stages -- diagnosis, therapy and confirmation of the therapeutic action -- into one connected procedure. The unique tunability of plasmonic nanobubbles makes the procedure possible. Their animal model, the zebra fish, is nearly transparent, which makes it ideal for such in vivo research.

The National Institutes of Health has recognized the potential of Lapotko's inspired technique by funding further research that holds tremendous potential for the theranostics of cancer and other diseases at the cellular level. Lapotko's Plasmonic Nanobubble Lab, a joint American-Belarussian laboratory for fundamental and biomedical nanophotonics, has received a grant worth more than $1 million over the next four years to continue developing the technique.

In earlier research in Lapotko's home lab in the National Academy of Sciences of Belarus, plasmonic nanobubbles demonstrated their theranostic potential. In another study on cardiovascular applications, nanobubbles were filmed blasting their way through arterial plaque. The stronger the laser pulse, the more damaging the explosion when the bubbles burst, making the technique highly tunable. The bubbles range in size from 50 nanometers to more than 10 micrometers.

In the zebra-fish study, Lapotko and his collaborators at Rice directed antibody-tagged gold nanoparticles into the implanted cancer cells. A short laser pulse overheated the surface of the nanoparticles and evaporated a very thin volume of the surrounding medium to create small vapor bubbles that expanded and collapsed within nanoseconds; this left cells undamaged but generated a strong optical scattering signal that was bright enough to detect a single cancer cell.

A second, stronger pulse generated larger nanobubbles that exploded (or, as the researchers called it, "mechanically ablated") the target cell without damaging surrounding tissue in the zebra fish. Scattering of the laser light by the second "killer" bubble confirmed the cellular destruction.

That the process is mechanical in nature is key, Lapotko said. The nanobubbles avoid the pitfalls of chemo- or radiative therapy that can damage healthy tissue as well as tumors.

"It's not a particle that kills the cancer cell, but a transient and short event," he said. "We're converting light energy into mechanical energy."

The new grant will allow Lapotko and his collaborators to study the biological effects of plasmonic nanobubbles and then combine their functions into a single sequence that would take a mere microsecond to detect and destroy a cancer cell and confirm the results. "By tuning their size dynamically, we will tune their biological action from noninvasive sensing to localized intracellular drug delivery to selective elimination of specific cells," he said.

"Being a stealth, on-demand probe with tunable function, the plasmonic nanobubble can be applied to all areas of medicine, since the nanobubble mechanism is universal and can be employed for detecting and manipulating specific molecules, or for precise microsurgery."

Rice University

GENETIC CLUES TO EVOLUTION OF JAWS IN VERTEBRATES UNEARTHED BY CU-LED TEAM

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A half-billion years ago, vertebrates lacked the ability to chew their food. They did not have jaws. Instead, their heads consisted of a flexible, fused basket of cartilage.

An international team of researchers led by a faculty member from the University of Colorado at Boulder published evidence that three genes in jawless vertebrates might have been key to the development of jaws in higher vertebrates.

The finding is potentially significant in that it might help explain how vertebrates shifted from a life of passive "filter feeding" to one of active predation.

"Essentially what we found is that the genetic roots of the vertebrate jaw can be found in the embryos of a weird jawless fish called the sea lamprey," said Daniel Meulemans Medeiros, an assistant professor of ecology and evolutionary biology at CU-Boulder and lead author of the study.

Medeiros' team included Robert Cerny, assistant professor of zoology at Charles University in Prague; Maria Cattell, a researcher in the Medeiros lab; and Tatjana Sauka-Spengler, Marianne Bronner-Fraser and Feiqiao Yu from the California Institute of Technology. Their findings were published in the Sept. 22 edition of the Proceedings of the National Academy of Sciences.

Lampreys are eel-like fish with no jaws and a "very strange skeleton compared to their cousins" with jaws, Medeiros said. But "when we looked carefully at how genes are used during the development of the lamprey head, we saw that the basic plan for a jaw is there, and that only a few genes likely had to be moved around to create full-blown jaws."

Between jawless vertebrates -- called agnathans -- and vertebrates with jaws -- called gnathosomes -- only three genes of the 12 genes the team looked at appeared to be used differently, Medeiros said. This finding suggests that "creating a jaw in a jawless ancestor was a relatively simple matter of altering when and where these few genes are used."

The findings support a new scenario for jaw evolution, an area that has been an open question in vertebrate evolution. Viewing the eel-like fish, "It was hard to imagine how something like that could evolve into the strong, snapping, biting, chewing jaws of a shark, fish or mammal," Medeiros said.

(Photo: Jeff Mitton)

University of Colorado at Boulder

PENN BIOLOGISTS SAY SPECIES ACCUMULATE ON EARTH AT SLOWER RATES THAN IN THE PAST

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Computational biologists at the University of Pennsylvania say that species are still accumulating on Earth but at a slower rate than in the past.

In the study, published in the journal PLoS Biology, Penn researchers developed a novel computational approach to infer the dynamics of species diversification using the family trees of present-day species. Using nine patterns of diversification as alternative models, they examined 289 phylogenies, or evolutionary trees, representing amphibians, arthropods, birds, mammals, mollusks and flowering plants.

The study demonstrated that diversity is generally not at equilibrium. Nonetheless, speciation rates have typically decayed over time, suggesting that the diversification of species is somehow constrained, and that equilibrium may eventually be reached.

There are many competing theories for how species diversify and become extinct. Some suggest that species continually accumulate in time, always finding new ecological niches. Other theories suggest that the number of coexisting species is limited and that we will eventually have equilibrium. In other words, a species will be born only when another goes extinct.

The question that intrigued the Penn researchers was whether species diversity on Earth is in equilibrium or is still expanding. They also wondered whether the world has an invisible stop sign on species diversity that would eventually limit the diversity on the planet.

“What we see is diversification rates that are declining but not yet to zero,” said Joshua Plotkin, assistant professor in the Department of Biology in the School of Arts and Sciences at Penn. “We are not yet in equilibrium. Either there is a limit to the total species number and we haven’t reached it yet, or there is no such limit. But the rates of diversification are typically falling; when we will hit zero is not yet obvious.”

While it is clear that Earth has recently lost species due to human impact, this study dealt with much longer, geologic time scales. Understanding these long-term dynamics is central to our understanding of what controls present-day biodiversity across groups and regions.

Even though the study did not deal with the current anthropogenic loss of biodiversity, researchers were surprised at how little extinction they actually saw in the evolutionary trees of species. The fossil record shows that many species have gone extinct over geologic time. For example, the diversity of whales has decreased during the last ~12 million years. But extinction was rarely apparent in this analysis of evolutionary trees.

The study also shows how analyzing molecular phylogenies can shed light on patterns of speciation and extinction; future work may reconcile this approach with the fossil record.

“By taking advantage of existing data from the flood of genomic research, we hope to combine efforts with paleontologists gathering fossil data,” Plotkin said.

(Photo: Steve Minicola)

University of Pennsylvania

NO EVIDENCE FOR CLOVIS COMET CATASTROPHE, ARCHAEOLOGISTS SAY

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New research challenges the controversial theory that an ancient comet impact devastated the Clovis people, one of the earliest known cultures to inhabit North America.

Writing in the October issue of Current Anthropology, archaeologists Vance Holliday (University of Arizona) and David Meltzer (Southern Methodist University) argue that there is nothing in the archaeological record to suggest an abrupt collapse of Clovis populations. "Whether or not the proposed extraterrestrial impact occurred is a matter for empirical testing in the geological record," the researchers write. "Insofar as concerns the archaeological record, an extraterrestrial impact is an unnecessary solution for an archaeological problem that does not exist."

The comet theory first emerged in 2007 when a team of scientists announced evidence of a large extraterrestrial impact that occurred about 12,900 years ago. The impact was said to have caused a sudden cooling of the North American climate, killing off mammoths and other megafauna. It could also explain the apparent disappearance of the Clovis people, whose characteristic spear points vanish from the archaeological record shortly after the supposed impact.

As evidence for the rapid Clovis depopulation, comet theorists point out that very few Clovis archaeological sites show evidence of human occupation after the Clovis. At the few sites that do, Clovis and post-Clovis artifacts are separated by archaeologically sterile layers of sediments, indicating a time gap between the civilizations. In fact, comet theorists argue, there seems to be a dead zone in the human archaeological record in North America beginning with the comet impact and lasting about 500 years.

But Holliday and Meltzer dispute those claims. They argue that a lack of later human occupation at Clovis sites is no reason to assume a population collapse. "Single-occupation Paleoindian sites—Clovis or post-Clovis—are the norm," Holliday said. That's because many Paleoindian sites are hunting kill sites, and it would be highly unlikely for kills to be made repeatedly in the exact same spot.

"So there is nothing surprising about a Clovis occupation with no other Paleoindian zone above it, and it is no reason to infer a disaster," Holliday said.

In addition, Holliday and Meltzer compiled radiocarbon dates of 44 archaeological sites from across the U.S. and found no evidence of a post-comet gap. "Chronological gaps appear in the sequence only if one ignores standard deviations (a statistically inappropriate procedure), and doing so creates gaps not just around [12,900 years ago] but also at many later points in time," they write.

Sterile layers separating occupation zones at some sites are easily explained by shifting settlement patterns and local geological processes, the researchers say. The separation should not be taken as evidence of an actual time gap between Clovis and post-Clovis cultures.

Holliday and Meltzer believe that the disappearance of Clovis spear points is more likely the result of a cultural choice rather than a population collapse. "There is no compelling data to indicate that North American Paleoindians had to cope with or were affected by a catastrophe, extraterrestrial or otherwise, in the terminal Pleistocene," they conclude.

(Photo: Vance Holliday)

University of Chicago

NOTRE DAME AND WYOMING SCIENTISTS GENETICALLY ENGINEER SILKWORMS TO PRODUCE ARTIFICIAL SPIDER SILK

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A research and development effort by the University of Notre Dame, the University of Wyoming, and Kraig Biocraft Laboratories, Inc. has succeeded in producing transgenic silkworms capable of spinning artificial spider silks.

"This research represents a significant breakthrough in the development of superior silk fibers for both medical and non-medical applications," said Malcolm J. Fraser Jr., a Notre Dame professor of biological sciences. "The generation of silk fibers having the properties of spider silks has been one of the important goals in materials science."

Natural spider silks have a number of unusual physical properties, including significantly higher tensile strength and elasticity than naturally spun silkworm fibers. The artificial spider silks produced in these transgenic silkworms have similar properties of strength and flexibility to native spider silk.

Silk fibers have many current and possible future biomedical applications, such as use as fine suture materials, improved wound healing bandages, or natural scaffolds for tendon and ligament repair or replacement. Spider silk-like fibers may also have applications beyond biomedical uses, such as in bulletproof vests, strong and lightweight structural fabrics, a new generation athletic clothing and improved automobile airbags.

Until this breakthrough, only very small quantities of artificial spider silk had ever been produced in laboratories, but there was no commercially viable way to produce and spin these artificial silk proteins. Kraig Biocraft believed these limitations could be overcome by using recombinant DNA to develop a bio-technological approach for the production of silk fibers with a much broader range of physical properties or with pre-determined properties, optimized for specific biomedical or other applications.

The firm entered into a research agreement with Fraser, who discovered and patented a powerful and unique genetic engineering tool called "piggyBac". PiggyBac is a piece of DNA known as a transposon that can insert itself into the genetic machinery of a cell.

"Several years ago, we discovered that the piggyBac transposon could be useful for genetic engineering of the silkworm, and the possibilities for using this commercial protein production platform began to become apparent."

Fraser, with the assistance of University of Wyoming researcher Randy Lewis, a biochemist who is one of the world's foremost authorities on spider silk, and Don Jarvis, a noted molecular geneticist who specializes in insect protein production, genetically engineered silkworms in which they incorporated specific DNAs taken from spiders. When these transgenic silkworms spin their cocoons, the silk produced is not ordinary silkworm silk, but, rather, a combination of silkworm silk and spider silk. The genetically engineered silk protein produced by the transgenic silkworms has markedly improved elasticity and strength approaching that of native spider silk.

"We've also made strides in improving the process of genetic engineering of these animals so that the development of additional transgenics is facilitated," Fraser said. "This will allow us to more rapidly assess the effectiveness of our gene manipulations in continued development of specialized silk fibers."

Since silkworms are already a commercially viable silk production platform, these genetically engineered silkworms effectively solve the problem of large scale production of engineered protein fibers in an economically practical way.

"Using this entirely unique approach, we have confirmed that transgenic silkworms can be a potentially viable commercial platform for production of genetically engineered silk proteins having customizable properties of strength and elasticity," Fraser said. "We may even be able to genetically engineer fibers that exceed the remarkable properties of native spider silk."

(Photo: UND)

University of Notre Dame

RESEARCHERS FIND FIRST GENETIC EVIDENCE FOR LOSS OF TEETH IN THE COMMON ANCESTOR OF BALEEN WHALES

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In contrast to a toothed whale, which retains teeth that aid in capturing prey, a living baleen whale (e.g., blue whale, fin whale, humpback, bowhead) has lost its teeth and must sift zooplankton and small fish from ocean waters with baleen or whalebone, a sieve-like structure in the upper jaw that filters food from large mouthfuls of seawater.

Based on previous anatomical and fossil data studies, scientists have widely believed that both the origin of baleen and the loss of teeth occurred in the common ancestor of baleen whales about 25 million years ago. Genetic evidence for these, however, was lacking.

Now biologists at the University of California, Riverside provide the first genetic evidence for the loss of mineralized teeth in the common ancestor of baleen whales. This genomic record, they argue, is fully compatible with the available fossil record showing that the origin of baleen and the loss of teeth both occurred in the common ancestor of modern baleen whales.

"We show that the genetic toolkit for enamel production was inactivated in the common ancestor of baleen whales," said Mark Springer, a professor of biology, who led the research. "The loss of teeth in baleen whales marks an important transition in the evolutionary history of mammals, with the origin of baleen laying the foundation for the evolution of the largest animals on Earth."

Previous studies have shown that the dental genes enamelin, ameloblastin, and amelogenin are riddled with mutations that disable normal formation of enamel, but these debilitating genetic lesions postdate the loss of teeth documented by early baleen whale fossils in the rock record.

Springer's team focused on the evolution of the enamelysin gene, which is critical for enamel production in cetaceans and other mammals. Cetacea includes toothed whales (e.g., sperm whales, porpoises, dolphins) and baleen whales.

They found that the enamelysin gene was inactivated in the common ancestor of living baleen whales by the insertion of a "transposable genetic element" – a mobile piece of DNA.

"Our results demonstrate that a transposable genetic element was inserted into the protein-coding region of the enamelysin gene in the common ancestor of baleen whales," Springer said. "The insertion of this transposable element disrupted the genetic blueprint that provides instructions for making the enamelysin protein. This means we now have two different records, the fossil record and the genomic record, that provide congruent support for the loss of mineralized teeth in the common ancestor of baleen whales."

The study, which appeared online last week (Sept. 22) in the Proceedings of the Royal Society B: Biological Sciences, included eight baleen whale species and representatives of all major living lineages of Cetacea. The researchers examined protein-coding regions of the enamelysin gene for molecular cavities that are shared by all baleen whales.

Next, the researchers plan to piece together the complete evolutionary history of a variety of different tooth genes in baleen whales to provide an integrated record of the macroevolutionary transition from ancestral baleen whales that captured individual prey items with their teeth to present-day behemoths that entrap entire schools of minute prey with their toothless jaws.

(Photo: John Gatesy and Carl Buell)

University of California

SCIENTISTS RECREATE EXTREME CONDITIONS DEEP IN EARTH’S INTERIOR

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Scientists have wondered for some time why certain seismic waves travel more quickly through the core-mantle boundary, a thin layer of the Earth’s interior that lies between about 1675 and 1800 miles below the surface. Now a new study by Yale University and the University of California, Berkeley sheds light on the mystery by showing how this region behaves under the extreme conditions found so deep in the Earth. The findings, which appear in the Sept. 24 issue of the journal Science, have important implications for understanding how the Earth’s internal heating and cooling processes work.

Geologists believe that most of the Earth’s mantle—an almost 1800-mile-thick layer between the crust and the core that makes up more than three quarters of the planet’s volume—is mostly made up of a mineral called magnesium silicate perovskite MgSiO3, or “perovskite” for short. Below this, the 125-mile-thick core-mantle boundary is composed in large part of a high-pressure phase of perovskite known as post-perovskite.

Because post-perovskite is created only under the extremely high temperatures and pressures that exist so deep in the Earth’s interior, it is not found on the planet’s surface. As a result, understanding the physics of this unique substance, and therefore the physics of the core-mantle boundary, has proven difficult.

Now a team led by Yale researcher Lowell Miyagi has managed to heat and compress post-perovskite to the conditions found at the core-mantle boundary, where temperatures soar to nearly 6000 degrees Fahrenheit and pressures are more than one million times the ambient pressure at the surface of the Earth.

Once Miyagi had formed the post-perovskite and squeezed it to these extreme pressures using a vise-like device that crushes substances between the tips of two diamonds, he discovered that the mineral behaved in a surprising way. “The preferred orientation of the post-perovskite’s crystal structure was very counterintuitive,” he said. “Post-perovskite has a layered crystal structure, but instead of deforming along the layers when compressed, like almost every other layered structure does, it deforms on a plane cutting across the layers.” Knowing more about the structure of the material that makes up much of the core-mantle boundary will help scientists understand how seismic waves travel through this region of the Earth’s interior.

Based on their experimental results, the team found that their model for mantle mixing correlates well with seismic observations. “The findings could explain why seismic waves tend to travel faster in certain directions near the core-mantle boundary,” said Kanani Lee, assistant professor of geology and geophysics at Yale and one of the study’s co-authors. “The alignment of post-perovskite’s crystal structure likely determines in which direction seismic waves travel fastest in that region. Understanding this structure gives us much more insight into the extreme physics taking place 1800 miles below the surface.”

It will also provide clues as to how Earth’s internal convection works there. After descending from the ocean floor, cool tectonic plates pass through the mantle and approach the dense, liquid-iron outer core, where they heat up and begin moving upward again in a repeated cycle of mantle mixing.

“Understanding how post-perovskite behaves is a good start to understanding what’s happening near the mantle’s lower reaches,” Miyagi said. “We can now begin to interpret flow patterns in this deep layer in the Earth.”

(Photo: Lowell Miyagi/Yale University)

Yale University

OCEAN VIRUSES: HIDDEN MOVERS AND SHAKERS OF THE EARTH SYSTEM

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All but overlooked until the past decade, marine viruses far outnumber any other biological entity on the planet. Scientists are only beginning to discover the invisible particles that are the cogs of Earth's system, changing dynamics in food webs, fisheries, even climate.

In his lab in the University of Arizona's Life Sciences South Building, Matthew Sullivan opens the door of an incubator cabinet. Rows of glass flasks crowd the shelves. Their bottoms are covered with liquids shimmering in various hues of green; each bears a label for identification. Sullivan takes out one of the flasks and sets it onto a lab bench.

"The green color comes from microscopically small algae," he says. "We use them to culture the viruses. These microbes serve as their hosts in the wild."

Sullivan's lab just received a $1.6 million research grant from the Gordon and Betty Moore Foundation to "develop and apply novel virus ecology approaches that enable deeper investigations of the structure and activities of natural marine virus communities and the linkages between viruses and their microbial hosts."

In other words, how viruses run the planet by manipulating their microbial hosts.

"Marine viruses are integral cogs of the Earth system," Sullivan says. "The food webs on Earth are fueled by microbes, and microbes in the ocean provide a big chunk of that."

On average, a drop of seawater contains about 10 million viruses, or 10 times as many microbes. These viruses are not the kind that spread around and cause the flu. Instead they infect microbes in the ocean, altering the way they impact ecosystems.

Most biologists do not consider viruses living organisms because they don't feed, grow, have a metabolism and can't reproduce on their own. Instead, they infect host cells, inject their own genetic material and hijack the cell's molecular machinery to make more viruses. In many cases, the viral reproduction cycle kills the host cell, which bursts and releases an army of new virus particles into the environment, ready to infect other cells.

In 2008, Sullivan, an assistant professor with joint appointments in the UA's departments of ecology and evolutionary biology and molecular and cell biology, started the Tucson Marine Phage Lab to study how marine viruses interact with microbes that in turn are drivers of the most fundamental global processes.

"Viruses are only as interesting as their microbial hosts," Sullivan says. "And those are pretty important: they drive the global biogeochemical cycles of carbon, nitrogen, sulfur and oxygen; elements that are crucial for running all kinds of energy conversions on the planet."

"We're learning that enormous numbers of marine viruses are right at the heart of all this," he adds. "They act as a driving evolutionary force of these microbial processes: They kill their host cells, move genes to new hosts, modulate host metabolisms during infection and may even serve as food for their hosts."

"Given the abundance and important roles of viruses in global processes, we ask what kinds of viruses are out there and what they are doing, how they impact the microbes and how they interact with the environment. From our preliminary data we can already say we couldn't have dreamed of all the different interactions, all those biological processes in the oceans that viruses are involved in."

Up to 50 percent of the world's population of marine microbes are turned over each day, killed by viruses, scientists estimate.

"By killing such vast numbers of microbes, the viruses in the wild are probably keeping a lot of energy and carbon from getting into higher levels in the food webs," Sullivan says.

"One can think of carbon as a sort of currency for energy in the Earth system, and 50 percent of that comes from the ocean," Sullivan says. "Only a little over 10 years ago, we thought that number was much lower."

Our planet and all living beings could not survive without the work of vast numbers of invisible organisms inhabiting the ocean waters and the sea floor. Single-celled algae and bacteria known as phytoplankton use energy from sunlight to extract carbon dioxide from the water (and ultimately from the atmosphere) and convert it into organic matter that forms the basis of the food chain. This process is called photosynthesis.

In most textbooks, the food chain starts with the microscopically small algae and cyanobacteria that make nutrients from carbon dioxide and sunlight. Now it turns out there is a whole layer that lies beneath: viruses.

"There are about 10 viruses for every microbe pretty much anywhere you look," Sullivan says. "At this point, we can culture only about 1 percent of microbes in the lab, which means there are 99 percent we really don't know much about. That is where our new methods fit in – finding ways to chase down the other 99 percent."

The greatest challenge to studying viruses is their tiny size. A single-celled alga, undetectable with the naked eye, can accommodate up to several hundreds of virus particles. Researchers must therefore come up with ways to collect viruses from samples and concentrate them and separate them according to their different types.

"Our research is currently in the discovery phase," Sullivan says. "Developing new methods of collecting and identifying viruses makes up a huge part of our work."

With existing methods, scientists were able to extract only a quarter of all the viruses floating in a sample of seawater. Working in the UA's Biosphere 2 Ocean, Sullivan's co-workers recently discovered that by simply adding iron chloride to the water sample, they could trap 95 percent of the viruses in their collecting containers.

Most of the oxygen we breathe is released into Earth's atmosphere by two species of microbes: the cyanobacteria Prochlorococcus and Synechococcus. They are the most abundant photosynthetic cells on the planet and the Sullivan lab is especially interested in studying them and the viruses that infect them.

In previous studies, Sullivan discovered something unexpected: The viruses infecting those microbes have genes necessary to build an important part of the photosynthetic machinery used by the microbes to make oxygen.

But why would a virus, a lifeless particle with no metabolism of its own that depends on living microbes to replicate, carry genes it can't use?

"When the virus infects the cell, it shuts down the hosts' ability to do anything," Sullivan explains. "It basically takes over the biochemical machinery and forces the host into making more viruses. It leaves intact only what the cell needs to stay alive and make copies of the virus genome."

To survive, the host depends on its photosynthetic machinery. During photosynthesis, one of the core proteins of this apparatus is subject to such high wear and tear that it needs to be replaced about every 30 minutes.

"The virus has the blueprint for that protein because it will need to replace it once it has taken control of the cell," Sullivan says. "So we discover that viruses directly impact the photosynthetic capacity of their hosts, in addition to killing them and changing their ecology and their evolutionary trajectory."

"Arguably, that is only the tip of the iceberg. That just happens to be the one ocean virus system that has been looked at in any detail."

Marine viruses add a whole new dimension to evolution: It is easy to imagine how a virus takes over genetic material from a host that turns out to be advantageous and transfers it to another microbe during another cycle of infection and virus replication.
"It seems like a good way to speed up molecular evolution," Sullivan says. "The host species could even be using these viruses to jump ahead, to try out new ways to evolve more quickly."

Sullivan's group expects its discovery-based research to generate knowledge directly applicable to better understand and predict marine ecosystems and fisheries. The scientists focus on viruses from environments on which a lot of information is available.
For example, his team sampled viruses from a so-called oxygen minimum zone in the subarctic Pacific, where vast swaths of ocean contain little or no oxygen at depths from about 500 meters down to 2,000 meters.

"This zone has huge implications for fisheries," Sullivan says, "so scientists have studied it for the past 50 years to find out how the ocean is breathing. We are interested in the interaction between viruses and microbes in that area, but in the context of the physics and chemistry of that important pacific subarctic environment."

Interestingly, one group of marine microbes, named Marine Group A, which is found all over the globe but in extremely low numbers, appears to flourish in the oxygen-depleted waters of oxygen minimum zone where it is found in considerable numbers.

"We don't know anything about them," Sullivan says. "We know it occurs from its genetic ‘footprint' but we can't culture it, so we have no idea what it's doing."

"Oxygen minimum zones in the open ocean are areas where microbes are producing greenhouse gases such as methane and nitrous oxides. The zones can be a bad thing when they expand, so we need to understand why they form and how they influence the marine food webs. So we're interested in the Marine Group A microbes, because they're so abundant in these regions and may produce some of these important green house gases."

"Other scientists are developing computer models of microbial communities to better understand their role at the base of the food chain," he adds. "Our experiments can provide the data that is needed to set realistic parameters for these simulations."

"All this is very exploratory," he says. "We can do this kind of science because of the UA's outstanding capabilities for high-throughput genomics, proteomics and bioinformatics. If you want to study complex biological interactions on the level of ecosystems, you need that kind of infrastructure. It allows you to open new windows into biology."

(Photo: U. Arizona)

University of Arizona

MILKY WAY SIDELINED IN GALACTIC TUG OF WAR

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The Magellanic Stream is an arc of hydrogen gas spanning more than 100 degrees of the sky as it trails behind the Milky Way's neighbor galaxies, the Large and Small Magellanic Clouds. Our home galaxy, the Milky Way, has long been thought to be the dominant gravitational force in forming the Stream by pulling gas from the Clouds. A new computer simulation by Gurtina Besla (Harvard-Smithsonian Center for Astrophysics) and her colleagues now shows, however, that the Magellanic Stream resulted from a past close encounter between these dwarf galaxies rather than effects of the Milky Way.

"The traditional models required the Magellanic Clouds to complete an orbit about the Milky Way in less than 2 billion years in order for the Stream to form," says Besla. Other work by Besla and her colleagues, and measurements from the Hubble Space Telescope by colleague Nitya Kallivaylil, rule out such an orbit, however, suggesting the Magellanic Clouds are new arrivals and not long-time satellites of the Milky Way.

This creates a problem: How can the Stream have formed without a complete orbit about the Milky Way?

To address this, Besla and her team set up a simulation assuming the Clouds were a stable binary system on their first passage about the Milky Way in order to show how the Stream could form without relying on a close encounter with the Milky Way.

The team postulated that the Magellanic Stream and Bridge are similar to bridge and tail structures seen in other interacting galaxies and, importantly, formed before the Clouds were captured by the Milky Way.

"While the Clouds didn't actually collide," says Besla, "they came close enough that the Large Cloud pulled large amounts of hydrogen gas away from the Small Cloud. This tidal interaction gave rise to the Bridge we see between the Clouds, as well as the Stream."

"We believe our model illustrates that dwarf-dwarf galaxy tidal interactions are a powerful mechanism to change the shape of dwarf galaxies without the need for repeated interactions with a massive host galaxy like the Milky Way."

While the Milky Way may not have drawn the Stream material out of the Clouds, the Milky Way's gravity now shapes the orbit of the Clouds and thereby controls the appearance of the tail.

"We can tell this from the line-of-sight velocities and spatial location of the tail observed in the Stream today," says team member Lars Hernquist of the Center.

(Photo: Plot by G. Besla, Milky Way background image by Axel Mellinger)

Harvard-Smithsonian Center for Astrophysics

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