Seaglider was developed in 1997 by researchers at the School of Oceanography and Applied Physics Laboratory. In UW research the device has set records for the distance traveled and time spent alone at sea, using buoyancy to glide up and down through the ocean while using minimal power.

Kongsberg will pick up where previous licensee iRobot left off, handling orders for customers external to the UW. The Norwegian-owned company plans to hire five or six employees to build Seagliders at its Lynwood facility.  The UW Seaglider Fabrication Center, managed by Fritz Stahr, will continue to employ three full-time staff members and two students to build and service Seagliders for UW researchers, and to service units sold before there was a commercial provider for the technology.

The Boldt decision revisited
Richard R. Whitney, a UW emeritus professor of fisheries, will give a public talk about his role in the Boldt decision, a 1974 ruling that gave Washington tribes an equal share of the state’s salmon catch. The talk is at 4 p.m. Thursday, May 23, in Fishery Sciences 102, and is free and open to the public.

Richard Whitney

Whitney’s talk, “My Fisheries Management Experience with Judge George H. Boldt in his Case United States v. The State of Washington,” will provide a firsthand account of the science and politics of those years. Whitney served as technical adviser to Judge Boldt from March 1974, one month after he handed down the ruling, until 1979, when the U.S. Supreme Court reviewed and affirmed the decision.

Whitney was a UW fisheries professor from 1983 to 1993. He previously held positions at the University of Maryland, the University of California, Los Angeles, and the predecessor to the U.S. Fish and Wildlife Service. He is co-author of “Inland Fishes of Washington” and was elected in 2008 to the American Fisheries Society’s Fisheries Management Hall of Excellence.

U. of Minnesota president to speak
Eric Kaler, University of Minnesota president and former UW professor of chemical engineering, will speak on campus Tuesday, May 28, about challenges and opportunities for the nation’s top research universities.

Eric Kaler

Kaler taught at UW for seven years starting in 1982 before moving on to the University of Delaware and later to Stony Brook University in New York. He has been president at Minnesota since 2011.

He will speak to a general audience on “The Future of the American Research University” at 3 p.m. May 28 in the Lyceum of the Husky Union Building for the chemical engineering department’s first Bruce A. Finlayson Lecture. The lecture, the department’s largest event of the year, honors Finlayson, a chemical engineering professor emeritus who previously taught with Kaler. In a separate talk, Kaler will have a more technical presentation on surfactant microstructures at 10:30 a.m. May 28 in the Bill & Melinda Gates Commons (CSE 691) of the Allen Center for Computer Science & Engineering.

Both talks are free and open to the public. A reception will follow the afternoon talk at 4 p.m. in the HUB Lyceum.

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The latest version, made public April 9, was developed by a national team with input from thousands of teachers, scientists and other stakeholders, including Philip Bell, director of the University of Washington’s Institute for Science and Math Education and the College of Education, and Andrew Shouse, associate director of the institute.

Bell and Shouse are now advising schools, districts and states about how to implement the standards. They will host two public events May 22 to talk about the vision and the new standards with teachers, scientists, school administrators, parents and others interested in science education.

Bell answered questions about the new K-12 science education standards for UW Today.

Q: Why are science learning standards important?

A: Scientific literacy helps us all make better life choices and decisions. The learning standards set the baseline of what we should all know about science. We were very careful to make sure the learning goals help all youth become scientifically literate and college-ready, so they can transition more seamlessly to college and have more choices about majors they can pursue.

Q: What do the standards look like?

A: There are three dimensions that help define the performances for each standard: disciplinary practices, core ideas of science and cross-cutting concepts that apply to multiple fields of science. The standards describe ways a student integrates these dimensions, but we didn’t lay out specific ways to meet these learning goals, so there’s still a lot of work to do in developing innovative curricula and instruction.

Q: What is different about the latest standards?

A: There are several major changes from the last incarnation of documents that have laid out standards for science education in the mid-1990s:

1. More emphasis on specific disciplinary practices used by scientists and engineers, such as developing and using a model, writing an argument from evidence, engaging in computational thinking and developing causal explanations about the natural world. The eight practices for science and engineering help focus what has previously been described as “inquiry” or “hands-on” instruction.
2. Greater focus on engineering and design. This is particularly important now that there’s an increased emphasis on science, technology, mathematics and engineering and thinking about how to integrate those subjects to solve complex problems. And a greater emphasis on engineering in K-12 is especially important because of the technology industries in the state of Washington and the lack of qualified people for jobs in those fields.
3. More challenging goals for preschoolers and kindergarten students. Research studies show that our youngest learners are capable of thinking that’s more complex than we previously believed, so the new standards have more ambitious learning goals for this age group.

Q: Won’t this just be more work for teachers?

A: I have known many elementary school teachers who feel like they haven’t had as much opportunity to teach science over the last decade because of the increased attention being given to reading, writing and mathematics. The new science standards have greater overlap with the existing standards for mathematics and English language arts so that teachers can teach science in ways that accomplish multiple goals. We hope this will make the lives of classroom teachers more manageable while allowing all students to meaningfully learn about science.

Q: Why should people who don’t want a science career have to meet these standards?

A: The science standards help people develop core knowledge and ways of thinking that can be used in a broad variety of everyday situations and other careers, including the ability to skeptically critique information, build an argument based on evidence and design a solution to fit an everyday need.

Q: How are the standards put into action?

A: Each state will decide whether they’ll try to adopt them and on what timeline. Washington state is working toward adoption, and my sense is there’s a lot of excitement around embracing these standards. The state’s Office of Superintendent of Public Instruction is coordinating the process of figuring out what the new science standards would mean for the state.

Q: Why are you excited about the new science learning goals?

A: It’s an exciting time for helping the public think more deeply about how science and technology relate to their lives and how they can leverage it for their own interests, such as solving problems their communities may be facing. This compels us in a lot of the work that we do.

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For more information, contact Bell at 206-221-3642 or pbell@uw.edu or Shouse at 206-897-1461 or awshouse@uw.edu.

Jeffrey Richey / UW

The team used rented boats to collect samples in the mouth of the world’s largest river.

Until recently people believed much of the rain forest’s carbon floated down the Amazon River and ended up deep in the ocean. University of Washington research showed a decade ago that rivers exhale huge amounts of carbon dioxide – though left open the question of how that was possible, since bark and stems were thought to be too tough for river bacteria to digest.

A study published this week in Nature Geoscience resolves the conundrum, proving that woody plant matter is almost completely digested by bacteria living in the Amazon River, and that this tough stuff plays a major part in fueling the river’s breath.

The finding has implications for global carbon models, and for the ecology of the Amazon and the world’s other rivers.

“People thought this was one of the components that just got dumped into the ocean,” said first author Nick Ward, a UW doctoral student in oceanography. “We’ve found that terrestrial carbon is respired and basically turned into carbon dioxide as it travels down the river.”

Tough lignin, which helps form the main part of woody tissue, is the second most common component of terrestrial plants. Scientists believed that much of it got buried on the seafloor to stay there for centuries or millennia. The new paper shows river bacteria break it down within two weeks, and that just 5 percent of the Amazon rainforest’s carbon ever reaches the ocean.

“Rivers were once thought of as passive pipes,” said co-author Jeffrey Richey, a UW professor of oceanography. “This shows they’re more like metabolic hotspots.”

Jeffrey Richey / UW

Nick Ward collects samples of Amazon River water.

When previous research showed how much carbon dioxide was outgassing from rivers, scientists knew it didn’t add up. They speculated there might be some unknown, short-lived carbon source that freshwater bacteria could turn into carbon dioxide.

“The fact that lignin is proving to be this metabolically active is a big surprise,” Richey said. “It’s a mechanism for the rivers’ role in the global carbon cycle – it’s the food for the river breath.”

The Amazon alone discharges about one-fifth of the world’s freshwater and plays a large role in global processes, but it also serves as a test bed for natural river ecosystems.

Richey and his collaborators have studied the Amazon River for more than three decades. Earlier research took place more than 500 miles upstream. This time the U.S. and Brazilian team sought to understand the connection between the river and ocean, which meant working at the mouth of the world’s largest river – a treacherous study site.

NASA

The mouth of the Amazon River has three main channels, with an island the size of Switzerland in the middle.

“There’s a reason that no one’s really studied in this area,” Ward said. “Pulling it off has been quite a challenge. It’s a humongous, sloppy piece of water.”

The team used flat-bottomed boats to traverse the three river mouths, each so wide that you cannot see land, in water so rich with sediment that it looks like chocolate milk. Tides raise the ocean by 30 feet, reversing the flow of freshwater at the river mouth, and winds blow at up to 35 mph.

Under these conditions, Ward collected river water samples in all four seasons. He compared the original samples with ones left to sit for up to a week at river temperatures. Back at the UW, he used newly developed techniques to scan the samples for some 100 compounds, covering 95 percent of all plant-based lignin. Previous techniques could identify only 1 percent of the plant-based carbon in the water.

Based on the results, the authors estimate that about 40 percent of the Amazon’s lignin breaks down in soils, 55 percent breaks down in the river system, and 5 percent reaches the ocean, where it may break down or sink to the ocean floor.

“People had just assumed, ‘Well, it’s not energetically feasible for an organism to break lignin apart, so why would they?’” Ward said. “We’re thinking that as rain falls over the land it’s taking with it these lignin compounds, but it’s also taking with it the bacterial community that’s really good at eating the lignin.”

The research was supported by the Gordon and Betty Moore Foundation, the National Science Foundation and the Research Council for the State of São Paulo. Co-authors are Richard Keil at the UW; Patricia Medeiros and Patricia Yager at the University of Georgia; Daimio Brito and Alan Cunha at the Federal University of Amap in Brazil; Thorsten Dittmar at Carl von Ossietzky University in Germany; and Alex Krusche at University of São Paulo in Brazil.

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For more information, contact Ward at nickward@uw.edu or 858-531-1558 and Richey at jrichey@uw.edu or 206-368-1906.

CIA World Factbook

The Antarctic Peninsula (in box) extends northward from the main part of the continent toward South America.

But new University of Washington research shows that the Southern Hemisphere’s fall months – March, April and May – are the only time when there has been extensive warming over the entire peninsula, and that is largely governed by atmospheric circulation patterns originating in the tropics.

The autumn warming also brings a notable reduction in sea ice cover in the Bellingshausen Sea off the peninsula’s west coast, and more open water leads to warmer temperatures on nearby land in winter and spring (June through November), said Qinghua Ding, a UW research associate in Earth and space sciences. In fact, the most significant warming on the west side of the peninsula in recent decades has occurred during the winter.

“Local northerly wind pushes warmer air from midlatitudes of the Southern Ocean to the peninsula, and the northern wind favors warming of the land and sea ice reduction,” said Ding.

He is the lead author of a paper explaining the findings, published online this month in the Journal of Climate. Eric Steig, a UW professor of Earth and space sciences, is co-author. The work was funded by the National Science Foundation.

The scientists analyzed temperature data gathered from 1979 through 2009 at eight stations on the Antarctic Peninsula. The stations were selected because each has reliable monthly data for at least 95 percent of the study period. They also used two different sets of data, one from Europe and the other from NASA, that combine surface observations, satellite temperature data and modeling.

Hannes Grobe/Alfred Wegener Institute for Polar and Marine Research

A German research vessel, Polarstern, is shown off the Rothera station on the west coast of the Antarctic Peninsula. Rothera is one of eight stations that provided temperature data for this research.

The researchers concluded that the nonsummer Antarctic Peninsula warming is being driven by large-scale atmospheric circulation originating in the equatorial Pacific Ocean. There, the warm sea surface generates an atmospheric phenomenon called a Rossby wave train, which reaches the Antarctic Peninsula and alters the local circulation to warm the region.

The sea-surface temperature trend in the tropical Pacific is related to natural phenomena such as the El Niño Southern Oscillation (El Niño and La Niña) and cycles that occur on longer timescales, sometimes decades. But it is not clear whether human causes play a role in that trend.

“We still lack a very clear understanding of the tropical natural variability, of what that dynamic is,” Ding said.

He said that in the next two or three decades it is quite possible that natural variability and forcing from human factors will play equivalent roles in temperature changes on the Antarctic Peninsula, but after that the forcing from human causes will likely play a larger role.

“If these trends continue, we will continue to see warming in the peninsular region, there is no doubt,” Ding said.

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 For more information, contact Ding at 206-685-8266 or qinghua@uw.edu.

Getty Images

Illustration of the Bull-leaping Fresco from the Great Palace at Knossos, Crete

DNA analysis is unearthing the origins of the Minoans, who some 5,000 years ago established the first advanced Bronze Age civilization in present-day Crete. The findings suggest they arose from an ancestral Neolithic population that had arrived in the region about 4,000 years earlier.

The British archeologist Sir Arthur Evans in the early 1900’s named the Minoans after a legendary Greek king, Minos. Based on similarities between Minoan artifacts and those from Egypt and Libya, Evans proposed that the Minoan civilization founders migrated into the area from North Africa. Since then, other archaeologists have suggested that the Minoans may have come from other regions, possibly Turkey, the Balkans, or the Middle East.

Now, a team of researchers in the United States and Greece has used mitochondrial DNA analysis of Minoan skeletal remains to determine the likely ancestors of these ancient people.

Mitochondria, the energy powerhouses of cells, contain their own DNA, or genetic code. Because mitochondrial DNA is passed down from mothers to their children via the human egg, it contains information about maternal ancestry.

Getty Images

One of the buildings in Knossos restored by British archeologist Sir Arthur Evans. Knossos was the major civil center of the Minoans.

Results published May 14 in Nature Communications suggest that the Minoan civilization arose from the population already living in Bronze Age Crete. The findings indicate that these people probably were descendents of the first humans to reach Crete about 9,000 years ago, and that they have the greatest genetic similarity with modern European populations.

Read the scientific paper.

Dr. George Stamatoyannopoulos, University of Washington professor of medicine and genome sciences, is the paper’s senior author. He believes that the data highlight the importance of DNA analysis as a tool for understanding human history.

“About 9,000 years ago,” he noted, “there was an extensive migration of Neolithic humans from the regions of Anatolia that today comprise parts of Turkey and the Middle East. At the same time, the first Neolithic inhabitants reached Crete.”

“Our mitochondrial DNA analysis shows that the Minoan’s strongest genetic relationships are with these Neolithic humans, as well as with ancient and modern Europeans,” he explained.

“These results suggest the Minoan civilization arose 5,000 years ago in Crete from an ancestral Neolithic population that had arrived in the region about 4,000 years earlier,” he said. “Our data suggest that the Neolithic population that gave rise to the Minoans also migrated into Europe and gave rise to modern European peoples.”

Stamatoyannopoulos, who directs the UW Markey Molecular Medicine Center and who formerly headed the UW Division of Medical Genetics in the Department of Medicine, added, “Genetic analyses are playing in increasingly important role and predicting and protecting human health. Our study underscores the importance of DNA not only in helping us to have healthier futures, but also to understand our past.”

Stamatoyannopoulos and his research team analyzed samples from 37 skeletons found in a cave in Crete’s Lassithi plateau and compared them with mitochondrial DNA sequences from 135 modern and ancient human populations. The Minoan samples revealed 21 distinct mitochondrial DNA variations, of which six were unique to the Minoans and 15 were shared with modern and ancient populations. None of the Minoans carried mitochondrial DNA variations characteristic of African populations.

Further analysis showed that the Minoans were only distantly related to Egyptian, Libyan, and other North African populations. The Minoan shared the greatest percentage of their mitochondrial DNA variation with European populations, especially those in Northern and Western Europe.

When plotted geographically, shared Minoan mitochondrial DNA variation was lowest in North Africa and increased progressively across the Middle East, Caucasus, Mediterranean islands, Southern Europe, and mainland Europe. The highest percentage of shared Minoan mitochondrial DNA variation was found with Neolithic populations from Southern Europe.

The analysis also showed a high degree of sharing with the current population of the Lassithi plateau and Greece. In fact, the maternal genetic information passed down through many generations of mitochondria is still present in modern-day residents of the Lassithi plateau.

Co-authors of the study are Jeffery R. Hughey of Hartnell College; Peristera Paschou of Democritus University of Thrace; Petros Drineas of the Rensselaer Polytechnic Institute; Manolis Michalodimitrakis of the University of Crete; and Donald Mastropaolo, Dimitra M. Lotakis, Patrick A. Navas, and John A. Stamatoyannopoulos of the University of Washington. The study was partially supported by a grant from the National Institutes of Health (5T32 GM007454), as well as from private funding.

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Expensive, state-of-the-art medical devices and surgeries often are thwarted by the body’s natural response to attack something in the tissue that appears foreign. Now, University of Washington engineers have demonstrated in mice a way to prevent this sort of response. Their findings were published online this week in the journal Nature Biotechnology.

Lei Zhang, UW

These images show differences in collagen build-up in two tissue samples. Collagen is labeled in blue. The left image shows a thick collagen wall forming in the presence of a material that’s widely used for implantable devices. In contrast, collagen in the right image is more evenly dispersed in the tissue after the UW-engineered hydrogel has been implanted.

The UW researchers created a synthetic substance that fully resists the body’s natural attack response to foreign objects. Medical devices such as artificial heart valves, prostheses and breast implants could be coated with this polymer to prevent the body from rejecting an implanted object.

“It has applications for so many different medical implants, because we literally put hundreds of devices into the body,” said Buddy Ratner, co-author and a UW professor of bioengineering and of chemical engineering. “We couldn’t achieve this level of excellence in healing before we had this synthetic hydrogel.”

The body’s biological response to implanted devices – medical technologies that often cost millions to develop – has frustrated experts for years. After an implant, the body usually creates a protein wall around the medical device, cutting it off from the rest of the body. Scientists call this barrier a collagen capsule. Collagen is a protein that’s naturally found in our bodies, particularly in connective tissues such as tendons and ligaments.

If a device such as an artificial valve or an electrode sensor is blocked off from the rest of the body, it usually fails to work. Physicians and scientists have tried to minimize this, but they haven’t been able to eliminate it, Ratner said.

Ratner’s collaborator and co-author Shaoyi Jiang, a UW professor of chemical engineering, and his team implanted the polymer substance into the bodies of mice. The substance is known as a hydrogel, a flexible biomedical material swollen with water. It’s made from a polymer that has both a positive and negative charge, which serves to deflect all proteins from sticking to its surface. Scientists have found that proteins appearing on the surface of a medical implant are the first signs that a larger collagen wall will form.

After three months, Jiang and his team found that collagen was loosely and evenly distributed in the tissue around the polymer, suggesting that the mice bodies didn’t even detect the polymer’s presence.

For humans, the first three weeks after an implant are the most critical, because by then the body will show signs of isolating the implant by building a collagen wall. If this hasn’t happened in the first several weeks, it’s likely the body won’t default to an attack response toward the object.

“Scientists have tried many materials, and with no exception, this is the first non-porous, synthetic substance demonstrating that no collagen capsule forms, which could have positive implications for implantable materials, tissue scaffolds and medical devices,” Jiang said.

UW researchers and others have worked for nearly 20 years to find a way to help the body accept implants. In 1996, the National Science Foundation-funded UW Engineered Biomaterials (UWEB) research center opened at the UW, with Ratner serving as director. Since that time, researchers have been trying to make a material that is invisible to the body’s immune response and could eliminate the body’s negative reaction to medical implants.

Now, nearly two decades years later, engineers have found the “perfect” substance, Ratner said.

“This hydrogel is not just pretty good, it’s exceptional,” he said.

The UW researchers plan to test this in humans, likely by working with manufacturers to coat an implantable device with the polymer, then measure its ability to ward off protein build-up.

The research was funded by the U.S. Office of Naval Research, UWEB and the UW Department of Chemical Engineering.

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For more information, contact Ratner at ratner@uw.edu or 206-685-1005 and Jiang at sjiang@uw.edu. Jiang is traveling this week and is available by email.

Aqqa Rosing-Asvid / Flickr

Fin whale surfacing in Greenland.

A carcass that washed up on a Seattle-area beach this spring provided a reminder that sleek fin whales, nicknamed “greyhounds of the sea,” are vulnerable to collision when they strike fast-moving ships. Knowing their swimming behaviors could help vessels avoid the animals. Understanding where and what they eat could also help support the fin whale’s slowly rebounding populations.

University of Washington oceanographers are addressing such questions using a growing number of seafloor seismometers, devices that record vibrations. A series of three papers published this winter in the Journal of the Acoustical Society of America interprets whale calls found in earthquake sensor data, an inexpensive and non-invasive way to monitor the whales. The studies are the first to match whale calls with fine-scale swimming behavior, providing new hints at the animals’ movement and communication patterns.

The research began a decade ago as a project to monitor tremors on the Juan de Fuca Ridge, a seismically active zone more than a mile deep off the Washington coast. That was the first time UW researchers had collected an entire year’s worth of seafloor seismic data.

John Delaney and Deborah Kelley, UW (taken with remotely operated vehicle Jason)

A seismometer inserted into a hole drilled in seafloor lava. Eight of these instruments were installed at an ocean spreading-center volcano 150 miles off Vancouver Island. A data recording device is enclosed in the yellow sphere. In three years of operation the network detected nearly 40,000 small earthquakes, and hundreds of thousands of fin-whale calls.

“Over the winter months we recorded a lot of earthquakes, but we also had an awful lot of fin-whale calls,” said principal investigator William Wilcock, a UW professor of oceanography. At first the fin whale calls, which at 17 to 35 vibrations per second overlap with the seismic data, “were kind of just a nuisance,” he said.

In 2008 Wilcock got funding from the Office of Naval Research to study the previously discarded whale calls.

Dax Soule, a UW doctoral student in oceanography, compared the calls recorded by eight different seismometers. Previous studies have done this for just two or three animals at a time, but the UW group automated the work to analyze more than 300,000 whale calls.

The method is similar to how a smartphone’s GPS measures a person’s location by comparing paths to different satellites. Researchers looked at the fin whale’s call at the eight seismometers to calculate a position. That technique let them follow the animal’s path through the instrument grid and within 10 miles of its boundaries.

Soule created 154 individual fin whale paths and discovered three categories of vocalizing whales that swam south in winter and early spring of 2003. He also found a category of rogue whales that traveled north in the early fall, moving faster than the other groups while emitting a slightly higher-pitched call.

“One idea is that these are juvenile males that don’t have any reason to head south for the breeding season,” Soule said. “We can’t say for sure because so little is known about fin whales. To give you an idea, people don’t even know how or why they make their sound.”

Luc Viatour

All varieties of peppers are in the same botanical family as tobacco. A new study shows that eating peppers may reduce the risk of Parkinson’s disease.

Eating peppers — which are in the same botanical family as tobacco — may reduce the risk of Parkinson’s disease. The findings are reported in the May 9 edition of the Annals of Neurology, a journal of the American Neurological Association and Child Neurology Society.

Nearly one million people in the United States are living with Parkinson’s disease, a neurodegenerative disorder that results from the loss of dopamine-producing brain cells. In early stages, Parkinson’s is characterized by difficulties in controlling movement. Initial symptoms include hand tremors, limb rigidity, and problems walking. As the disease progresses, cognitive problems may develop and advance into dementia.

Dietary sources of nicotine may prove protective.

“Eating peppers twice or more per week was consistently associated with at least 30 percent reduced risk of developing Parkinson’s disease,” said the study’s lead author, Dr. Susan Searles Nielsen, a research scientist in the Department of Environmental and Occupational Health Sciences at the UW School of Public Health.

The investigation of dietary sources of nicotine stems from the puzzling epidemiologic findings that repeatedly show that people who have regularly used tobacco have about half the risk of developing Parkinson’s disease, explained Searles Nielsen. In 2012, she published a study that suggested that second-hand smoke also might reduce risk of the disease.

Sarah Fish

Dr. Susan Searles Nielsen, Department of Environmental and Occupational Health Sciences, researches the effects of dietary nicotine.

“It’s possible that people predisposed to Parkinson’s disease simply don’t respond well to tobacco smoke and therefore avoid it.  However, if tobacco is actually protective, and if the reason is nicotine as some experimental studies suggest,” said Searles Nielsen, “then our hypothesis was that other plants in the Solanaceae family that contain nicotine might also be protective.”

The subjects interviewed for the study included 490 Parkinson’s patients newly diagnosed at the UW Neurology Clinic or Group Health Cooperative between 1992-2008.  The control study subjects were 644 unrelated, neurologically normal people.

While she and the study co-authors investigated the association between Parkinson’s and the subjects’ dietary consumption of a variety of vegetables, including nicotine-containing peppers, tomatoes, and potatoes in the Solanaceae family, peppers showed the greatest protection.  The decreased risk of disease grew stronger with increasing pepper consumption and occurred mainly in people with little or no prior use of tobacco, which contains much more nicotine than the foods studied.

Searles Nielsen cautions that further studies are needed to confirm these findings and explore whether a similar but less toxic chemical shared by peppers and tobacco might be equally or more protective than nicotine.

Study co-authors included Dr. Harvey Checkoway and Dr. Gary Franklin from the UW Department of Environmental and Occupational Health Sciences and Dr. W.T. Longstreth and Dr. Phillip Swanson from the Department of Neurology in the UW School of Medicine.

Funding for the study was provided by the National Institute of Environmental Health Sciences, in part through the UW Superfund Research Program.

Northwestern University

Just as people take roads to gather in cities, some bacteria follow trails to congregate in colonies.

Bacteria may draw other bacteria to a site of infection by laying down trails of a “molecular glue” that lead free-swimming individuals to come together and organize into colonies.

In the study, researchers were looking at how a species of bacteria called Pseudomonas aeruginosa attach and move about on surfaces. P. aeruginosa is a common cause of serious, often difficult-to-treat infections.

One reason they are so difficult to treat is their ability to mass together and surround themselves with matrix of proteins, DNA and polysaccharides, called a biofilm, that protects them from antibiotics and the body’s immune attack.

The study was the result of a collaboration of researchers from the University of California, Los Angeles, the University of Washington in Seattle, and Northwestern University in Evanston, Illinois.

The findings were published May 8 in Nature in a paper titled, “Psl trails guide exploration and microcolony formation in Pseudomonas aeruginosa biofilms.”

Kun Zhao. from the UCLA Department of Bioengineering and Boo Shan Tseng from the UW Department of Microbiology are the paper’s lead authors. The senior authors are Gerald C. L. Wong, professor of bioengineering at the California Nanosystems Institute at UCLA;  Matthew R. Parsek,  UW  professor of microbiology, and Erik Luitjen, at Northwestern University.

In earlier studies, the researchers had noticed that when individual, free-swimming P. aeruginosa attached themselves to glass and began to crawl along the surface they left a trail of a polysaccharide called Psl.

“This was surprising because in the bacterial world this is somewhat unusual,” said Parsek,. “And it looked cool. But the question was whether it was biologically important.”

For this study, the researchers used a specially designed chamber that allowed them to watch how free-swimming P. aeruginosa attached to and moved about on a glass surface. They then used video microscopy to track and analyze the behavior the bacteria.

“Some of the bacteria remained fixed in position,” said Parsek. “But some moved around on the surface, apparently randomly but leaving a trail that influenced the surface behavior of other bacteria that encountered it.”

Once enough of the bacteria had gathered, about 50 or so, their behavior changed: they abandoned their wandering ways and began to organize into small structures called micro-colonies, the first step in biofilm formation.

If there are ways to inhibit the formation of these trails or block their effect, it may be possible to inhibit the formation of biofilms, Parsek said. This might help prevent infections or make them easier to treat.

The researchers are also interested to learn whether other bacterial species also take these polysaccharide trails as a signal to congregate. Pseudomonas infections often involve other bacterial species and this might explain how these polymicrobial infections get started.

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The UW portion of the study was supported by National Institutes of Health grants R01HL087920, R01AI077628, R01AI081983, R56AI061396 and National Science Foundation grant MCB0822405.

The University of Washington in collaboration with Washington State University is developing an “academic redshirt” program that will bring dozens of low-income Washington state high school graduates to the two universities to study engineering in a five-year bachelor’s program.

The first year will help incoming freshmen acclimate to university-level courses and workload and prepare to major in an engineering discipline. The students will receive extra advising and a detailed course plan to help lay a strong foundation in engineering. At the UW, they will earn a spot in one of the school’s 10 engineering departments starting their second year.

Dawn Wiggin

Math Academy students from 2012 are shown after a workshop. The summer program at UW could be a feeder program for the new “academic redshirt” initiative.

“Engineering education needs to adapt to the tortoises, not just the hares,” said Eve Riskin, UW associate dean of engineering and program lead for the UW. “We’re talking about investing an extra year in what will hopefully be a 30-year engineering career.”

The initiative, called the Washington State Academic RedShirt in Engineering Program –STARS, for short – is funded by a National Science Foundation grant awarded May 8. Eight other colleges and universities also will receive grants to help increase retention of undergraduates in engineering and computer sciences.

Under the five-year grant, the UW and WSU will enroll 32 freshmen from Washington high schools each year for a total of 320 students after five years. Both universities will hire a person to oversee the program, and they hope to keep it running indefinitely. The first 64 students will begin this fall.

“More and more, we’re seeing students who are bright, but they’ve gone to a high school where the college preparation isn’t good,” said Bob Olsen, a WSU associate dean of engineering and lead of the redshirt program at WSU.

The program specifically targets low-income, motivated high school students in Washington state who are eligible for federal Pell Grants – financial aid based on family income and the cost of attending a university – or go to high schools where a high percentage of the students are on free or reduced-price lunches. Such students usually have a lower retention rate at the university level and are more likely to struggle in the fields of science, technology, engineering and mathematics.

“Pell Grant students receive engineering degrees at significantly lower rates than non-Pell Grant students,” Riskin said. “This is unfortunate, because low-income students could most benefit from a lucrative engineering career.”

The Mathematics Academy, a summertime month-long intensive at the UW for high school students, could be a feeder for this new program in the state.

The UW will receive $970,000 over five years from the National Science Foundation to offer this program to incoming freshmen, and WSU will receive $700,000. Students in the UW cohort will get at least $2,000 in additional assistance from the College of Engineering as well as funding from traditional scholarship sources. These students will live in an engineering residential community.

The National Science Foundation partnered with Intel Corp. and General Electric Co. to fund the nine institutions for a total of $10 million in a grant called Graduate 10K+. Other funded schools include Cornell University, Syracuse University and California State University Monterey Bay. The Washington program is modeled after the Engineering GoldShirt Program at University of Colorado Boulder, now headed into its fifth year.

The UW will hire a full-time staff member to work with students in the five-year program. Dawn Wiggin and Scott Winter, associate directors in engineering’s student academic services, are collaborators.

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For more information, contact Riskin at riskin@uw.edu or 206-685-2313. She is traveling on Wednesday, May 8, but will be reachable by email.

Clare McLean

Family physician Dr. Alisa Hideg is checked by a UW Medical Center nurse after receiving her shots in a UW tumor vaccine trial. Hideg was diagnosed with an aggressive form of breast cancer in 2011.

In June 2011 Dr. Alisa Hideg was a 42-year-old mother and family physician in the prime of her career practicing at Group Health in Spokane when she was diagnosed with estrogen and progesterone receptor negative/HER 2 positive breast cancer.

Breast cancer in young, premenopausal women is usually aggressive. So even after chemotherapy, a double mastectomy, and radiation, with her cancer in remission, Hideg wasn’t ready to take it easy. Both the type of breast cancer and the fact that it happened at a young age made her chances of relapse higher. This knowledge led her to experimental trials, and to the UW’s Tumor Vaccine Group.

Hideg found the UW Tumor Vaccine Group on the National Institutes of Health clinical trials website, ClinicalTrials.gov. She had heard about a trial at the University of Pennsylvania’s Perelmen School of Medicine, where the use of gene-transfer therapy converted the patients’ own immune cells into weapons aimed at cancerous tumors. All 12 patients had advanced stage leukemia; nine of the 12 responded positively to the treatment, and two of the first three patients treated have been in remission for two full years.  The Perlelmen results encouraged her to seek out a UW study to see if she qualified.

The UW Tumor Vaccine Group currently offers clinical trials for patients with breast, ovarian or colon cancer. Hideg is in a very desirable trial with very specific criteria, and being approved to participate wasn’t easy. The goal of the clinical trial is to allow the patient to make and keep enough antibodies to quash any future HER-2 expressing breast cancer.

Dr. Nora Disis, UW professor of medicine and principal investigator of the study, explains how the vaccine may work.

“The vaccine is designed to stimulate a particular cell of the immune system, the T cell, to recognize the HER2 protein (that causes cancer),” Disis said. “If effective immunity is generated, the T cell activated by the vaccine should be able to hunt out tumor cells wherever they may be and destroy them.  This particular study is testing the use of an immune stimulator, ampligen, which may be able to activate the T cells more effectively than other agents we have used before.“

Clare McLean

The injection site for the tumor vaccine being tested raises four small dots on Dr. Hideg’s forearm.

Last month, Hideg received a vaccine dose at UW Medical Center. The process is gentle — a series of four small injections that make a little grid of dots on the upper arm — but the body’s response can be angry. Hideg experienced flu-like symptoms after the first visit. The reaction  may actually be a promising sign that her body is responding to the vaccine.

She’s positive and funny in the face of serious medicine. She tweets pictures of her experience to a network of fans and writes about her cancer in Spokane’s daily newspaper, the Spokesman-Review. In addition to being a doctor, patient and full-time mother, Hideg recently went through a series of intense interviews to add “teacher” to her resume. She has become a clinical faculty member to teach second-year UW medical students at the Spokane WWAMI site.  WWAMI is a regionalized medical education program that covers Washington, Wyoming, Alaska, Montana and Idaho.

“Teaching has always been a part of my clinical practice,” Hideg said. “I have taught medical students, residents and others in my clinic since I finished my own training. This experience has reminded me how important teaching can be and how much I enjoy passing on what I have learned as a physician, a parent, and as a patient. Whether the vaccine is effective for me or not, I am grateful for the opportunity to participate in the trial and help move the science forward. I believe in the potential of vaccine therapy for cancer and perhaps for other diseases also and I want a future with more options for my daughter and for others.”

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Kathy Newell / UW

The R/V Barnes during a research cruise.

It’s a landmark trip for the vessel that has spent almost 30 years taking people from the UW and elsewhere out to the Sound, the Olympic Peninsula and nearby coasts to make discoveries about chemistry, currents and marine life.

All this from a boat that even its biggest fans admit has serious drawbacks.

The boat was never built to go into open seas, and adding 10 tons of scientific equipment to the stern did nothing to help with stability issues.

“It’s safe; it’s just miserable,” said Ray McQuin, the ship’s captain and supervisor. “Everyone gets seasick.”

(McQuin has a naturally strong stomach, he said, and suffers from seasickness only a couple of times each year.)

The scientists’ berths, two sets of triple bunks that hang from chains, make the undergraduate dorms seem plush by comparison. There’s only one bathroom and shower. And a 100-square-foot room serves as kitchen, dining room, common area and recreational room for up to six researchers (15 for short trips) and a two-person crew.

But most noticeable are the small scientist quarters, which were squeezed on after the fact. The small room is jam-packed during cruises with people, laptops and science equipment.

“It’s very — personal,” said Ginger Armbrust, professor and director of the UW’s School of Oceanography. Others describe it as “crowded” or even “controlled chaos.”

Still, Armbrust has fond memories. “It’s fun working on the Barnes. It’s very hands-on. You can get to your first station in five minutes, in contrast to when you’re working offshore and it takes you a day to get to your first station.”

The vessel was built in 1966 as a U.S. Coast Guard inland harbor tug that spent years towing boats, quenching fires and doing light ice-breaking out of Bellingham and Alaska.

The UW acquired the 65-foot boat at a bargain price in 1983 and converted it, replacing the original transmission with one that will go at the slower speeds needed for research, attaching a winch to lower instruments into the water, and adding a science cabin.

“It’s not a purpose-built research boat. There are a lot of compromises, but we get the job done,” McQuin said. “It’s a work boat, and that’s what we need.”

Logbooks show that in recent years, the Barnes has been out studying nitrogen near Neah Bay, algal blooms, marine food webs, effects of the Elwha Dam removal, and oxygen levels in Hood Canal.

The 1000th cruise will be a series of half-day trips May 7-9 from Shilshole Marina for Oceanography 201, an introductory lab course that lets students take oceanographic measurements.

“For oceanography majors, getting out on the water early is really important,” said instructor Susan Hautala, a UW associate professor of oceanography. “It gives students an idea of both what oceanographers do, and of why oceanography is so challenging: It’s taking limited measurements in a highly variable environment, and trying to piece together bits of evidence.”

Doug Russell / UW

A recent photo of the Barnes in dry dock. The boat will be decommissioned in 2016.

The boat’s namesake, Clifford A. Barnes, was a UW alumnus and professor of oceanography from 1947 to 1973 whose publications include “Circulation near the Washington Coast” and “An Oceanographic Model of Puget Sound.”

The millennial cruise will be one of the last for the vessel, which is nearing the end of its lifetime. The National Science Foundation will decommission the boat in 2016.

“You reach a point – and we’re getting there with this boat – where you can’t afford to keep it running. There are too many repairs,” McQuin said.

Plans are already under way to find a replacement. The School of Oceanography is looking for grants and private donations to fund a new vessel. Jensen Maritime Consultants created a custom design for an 86-foot vessel that would have more than four times as much lab space, carry twice as many people, and include modern navigation capabilities.

“The Barnes has been an incredible resource both for monitoring and understanding Puget Sound, and for giving our students an opportunity to do hands-on research, which is a core part of our program,” Armbrust said. “We’re looking forward to getting a new ship that will allow us to do this and more.”

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For more information, contact Hautala at 206-543-0596 or susanh@ocean.washington.edu.

The new, deadly Human Coronavirus-Erasmus Medical Center was named for the Dutch hospital that identified the virus in a patient specimen.

A new virus that causes severe breathing distress and kidney failure elicits a distinctive airway cell response to allow it to multiply.  Scientists studying the Human Coronavirus-Erasmus Medical Center, which first appeared April 2012 in the Middle East, have discovered helpful details about its stronghold tactics.

Their findings predict that certain currently available compounds might treat the infection.  These could act not by killing the virus directly but by keeping lung cells from being forced to create a hospitable environment for the virus to reproduce.  The researchers caution that their lab and computer predictions would need to be tested to see if the drugs work clinically.

The results appear in the April 30 issue of mBio, the Journal of the American Society for Microbiology. University of Washington virologist Laurence Josset is lead author of the paper, “Cell host-response to infection with novel human coronavirus-Erasmus Medical Center predicts potential antivirals and important differences with SARS-coronavirus.” She conducted the research in the laboratory of senior author Michael G. Katze, UW professor of microbiology noted for pioneering systems biology approaches to host and pathogen interactions.

Eleven of the 17 reported human coronavirus-Erasmus Medical Center cases worldwide were fatal. The virus is named for the Dutch hospital that identified the specimen from a Saudi Arabia patient. So far the illness has not easily passed person to person.  The new disease agent belongs to the betacoronavirus family, as does the severe acute respiratory syndrome virus, SARS.  Both viruses attack the lungs.  The new virus, however, is more closely related to bat coronaviruses than to SARS.  The two viruses latch onto different receptors to infect cells.

Rose Howard

Systems biologist Michael Katze (left) and virologist Laurence Josset are developing rapid computational analyses of host/pathogen interactions to quickly predict possible treatments for emerging infectious diseases.

Josset, Katze and their team learned that, shortly after human coronavirus-Erasmus Medical Center enters lung cells, it, like the SARS virus, induces changes in how the cells’ genes are regulated.  But the newer virus does so sooner.   Later, and throughout infection, the human coronavirus-EMC incites a massive sabotage – much greater than that of the SARS virus – of many genetic controls of protein production in lung cells grown in the laboratory.

“We found that a set of 207 genes in the lung cells was dysregulated early and permanently throughout infection with human coronavirus-EMC,” Josset said.  Various RNA levels were turned up or down.  The new virus appears to specifically hamper the work of several genes that enable the body to sense the presence of viruses.   The scientists believe such gene re-tuning by the virus could significantly lower the ability of lung cells to mount an appropriate antiviral reaction.

While SARS and coronavirus-Erasmus Medical Center activated a few similar lung cell responses for their own benefit, overall, not much overlap occurred.  Each bad actor had its own modus operandi for interfering with lung cell gene activities.

“These differences in host gene-expression responses in the lab-grown lung cells,” the researchers said, “might affect how each virus causes illness in an infected individual.”

At present no proven treatment exists for human coronavirus-Erasmus Medical Center.  Because the virus succeeds in multiplying by hijacking cellular processes initiated in response to infection, the scientists searched for drugs that might target these cellular responses, and in so doing stop the virus from reproducing.  The researchers mentioned that this same approach is already being tested in influenza treatment. Drugs that reduce the body’s excessive inflammatory reaction to the flu virus have therapeutic benefit.

The scientists obtained a rapid, comprehensive assessment of the new coronavirus’s infective strategies by creating a global profile of how it disrupts gene transcription, the process by which DNA is copied into RNA for subsequent translation into proteins.  They analyzed this extensive data with computer programs that predict which current drugs might be re-purposed to correct the body’s virus-co-opted immune response.

The method could have widespread applications in fighting future dangerous viruses.

“Such an approach has the advantage of accelerating treatment availability, which could be crucial in case of an outbreak of an emerging pathogen,” Josset said.

Katze concurred, “Laurence and others in our group are developing new computational approaches to efficiently exploit information about the gene expression profiles induced by existing drugs and small molecules. Our goal is to quickly identify drugs that can modify specific host responses to virus infection.”

In the case of human coronavirus-Erasmus Medical Center, the approach yielded two promising possibilities.  The analysis suggested that the early and sustained changes in lung cell gene regulation could be reverted by four types of kinase inhibitor and one kind of glucocorticoid.  Additional studies are necessary, the researcher said, to determine the safety, effectiveness and required dosages of these drugs in treating human coronavirus-EMC.

What this study highlights, Josset said, is the advantages of fast, automated analysis of the transcriptome (all the messenger RNAs transcribed from the genome) of the infected cells.

“This method globally and efficiently characterizes the host response to emerging pathogens,” Josset said.  Data on the basic properties of a new virus and its interactions with host cells can usually be collected speedily.  It takes, on average, between two weeks to a month after the virus has been identified and isolated.

The gene expression data obtained from the analysis of human coronavirus-Erasmus Medical Center infection, she said, was so robust that it “provides a plethora of data to mine for further understanding and ideas to test about the new virus.”

“Because,” she added, “host response profiles also can be used to quickly identify possible treatment strategies, we anticipate that generating such profiles will become a general strategy for rapid characterization of future emerging viruses.”

Katze noted, “The emergence of new viruses, such as the H7N9 influenza virus in China, will continue to be a threat to public health. Devising new strategies to rapidly identify effective antiviral drugs is a high priority.”

In addition to Josset and Katze, the other researchers on the project were Vineet D. Menachery, Lisa E. Gralinski, Sudhakar Agnihothram, Boyd L. Yount,  Rachel L. Graham,  and Ralph S. Baric, all of the University of North Carolina at Chapel Hill, and Pavel Sova and Victoria S. Carter, both of the UW.

The project was funded in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, contract HHSN272200800060C and grant U54AI081680.

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The researchers screened 35 veterans with blast injuries. They found that 42 percent had irregular hormone levels indicative of hypopituitarism, a condition that can often be controlled by replacing the deficient hormones.

“This could be a largely missed opportunity for successful treatment,” said Charles W. Wilkinson, study leader and a UW research associate professor in psychiatry and behavioral sciences.

John McCall/U.S. Marine Corps

Marines assigned to a route clearance platoon destroy IEDs discovered near Sangin, Afghanistan.

He said up to 20 percent of veterans returning from Afghanistan and Iraq have experienced at least one blast concussion. He said many of these veterans have a problem so under-recognized that even military physicians may fail to look for it.

Results from the study, “Prevalence of chronic hypopituitarism after blast concussion” by Wilkinson, Elizabeth A. Colasurdo, Kathleen F. Pagulayan, Jane B. Shofer, and Elaine R. Peskind, were presented at the Experimental Biology 2013 Meeting April 22 in Boston. The results were published in Frontiers in Neurotrauma last year, but the presentation included new data as well and the results be published again.

Wilkinson said studies in the past few years have suggested that 25 to 50 percent of people who suffer traumatic brain injuries later have low pituitary hormone levels — a decrease in the concentrations of at least one of eight hormones produced by the pituitary, a gland beneath the base of the brain.

Wilkinson said these studies focused on head injuries that civilians are more likely to receive, such as an automobile accident. He and his team decided to investigate whether veterans returning from Afghanistan and Iraq who suffer blast injuries show a similar frequency of hypopituitarism.

They collected blood samples from 35 veterans diagnosed with a blast concussion about a year prior — enough time for hormone changes to become evident. They then did a screen to compare blood concentrations of the eight hormones produced by the pituitary with the documented normal levels of these hormones.

The researchers found that about 42 percent of these veterans showed abnormally low levels of at least one of these hormones. The most common low hormone was human growth hormone, which can cause behavioral and cognitive symptoms similar to PTSD and depression. Low levels can also cause increases in blood lipids and changes in metabolism and blood pressure that can raise the risk of heart attack and stroke. The second most common problem was hypogonadism, changes in sexual hormones that can affect body composition and sexual function.

The tiny, pendulous gland shown in blue is the pituitary.

The researchers saw that some veterans had abnormal levels of vasopressin and oxytocin. Low levels of these hormones make it harder for people to bond with others and are linked to other mental health issues. Problems with these hormone levels, in addition to growth hormone, could contribute to difficulties with personal relationships, Wilkinson said.

He said the prevalence of hypopituitarism in the general population is estimated at 0.03 percent, a value far lower than that found in veterans with blast concussions. Therefore, more research is needed into victims of blast concussions.

“We’re screening hormone levels, not diagnosing definite disorders in this study,” he said. “These individuals would still need a clinical evaluation.” But, he said, if even 10 percent of these veterans have hypopituitarism, it’s a problem that physicians should be aware of.

The Departments of Defense and Veterans Affairs supported the study.

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It turns out that scientists may have been looking for the starting line in the wrong places.

U of Texas at Austin/U of Washington

Newly discovered fossils, and those from existing collections, were considered from five basins in the south of what was once a single large land mass known as Pangea, and today are part of (from left to right) South Africa, Zambia, Malawi, Tanzania and Antarctica.

Newly discovered fossils from 10 million years after the mass extinction reveal a lineage of animals thought to have led to dinosaurs taking hold in Tanzania and Zambia in the mid-Triassic period, many millions of years before dinosaur relatives were seen in the fossil record elsewhere on Earth.

“The fossil record from the Karoo of South Africa remains a good representation of four-legged land animals across southern Pangea before the extinction event. But after the event animals weren’t as uniformly and widely distributed as before. We had to go looking in some fairly unorthodox places,” said Christian Sidor, University of Washington professor of biology. He’s lead author of a paper appearing the week of April 29 in the early edition of the Proceedings of the National Academy of Sciences.

The new insights come from seven fossil-hunting expeditions since 2003 in Tanzania, Zambia and Antarctica, funded by the National Geographic Society and National Science Foundation, along with work combing through existing fossil collections. The researchers created two “snapshots” of four legged-animals about 5 million years before and again about 10 million years after the extinction event at the end of the Permian period.

Marlene Donnelly/Field Museum of Natural History

The pig-size Dicynodon was part of a large, dominant group of plant eaters found across the southern hemisphere until the mass extinction event weakened their numbers so that newly emerging herbivores could compete.

Prior to the extinction event, for example, the pig-sized Dicynodon – said to resemble a fat lizard with a short tail and turtle’s head – was a dominant plant-eating species across southern Pangea. Pangea is the name given to the landmass when all the world’s continents were joined together. Southern Pangea was made up of  what is today Africa, South America, Antarctica, Australia and India. After the mass extinction at the end of the Permian, Dicynodon disappeared and other related species were so greatly decreased that newly emerging herbivores could suddenly compete with them.

“Groups that did well before the extinction didn’t necessarily do well afterward,” said Sidor, who also is the curator of vertebrate paleontology at the UW’s Burke Museum of Natural History and Culture. “What we call evolutionary incumbency was fundamentally reset.”

The snapshot 10 million years after the extinction event reveals, among other things, that archosaurs were in Tanzanian and Zambian basins, but not distributed across all of southern Pangea as had been the pattern for four-legged animals prior to the extinction.  Archosaurs are the group of reptiles that includes crocodiles, dinosaurs, birds and a variety of extinct forms. They are of interest because it is thought they led to animals like Asilisaurus, a dinosaur-like animal, and Nyasasaurus parringtoni, a dog-sized creature with a five-foot tail that scientists in December 2012 announced could be the earliest dinosaur, or else the closest relative found so far.

Marlene Donnelly/Field Museum of Natural History

Ten million years after the mass extinction, members of the archosaur reptiles – such as the 10-foot (3 meter) long Asilisaurus pictured – had more restricted geographic ranges compared to the communities of four-legged animals that existed before the extinction.

“Early archosaurs being found mainly in Tanzania is an example of how fragmented communities became after the extinction event,” Sidor said. And the co-authors write: “These findings suggest that . . . archosaur diversification was more intimately related to recovery from the end-Permian mass extinction than previously suspected.”

A new framework for analyzing biogeographic patterns from species distributions, developed by co-author Daril Vilhena, a UW biology graduate student, provided a way to discern the complex recovery, Sidor said.

It revealed that before the extinction event 35 percent of four-legged species were found in two or more of the five areas studied, with some species having ranges that stretched 1,600 miles (2,600 kilometers), encompassing the Tanzanian and South African basins. Ten million years after the extinction event, the authors say there was clear geographic clustering and just 7 percent of species were found in two or more regions.

The techniques – new ways to statistically consider how connected or isolated species are from each other – could be useful for other paleontologists and modern day biogeographers, Sidor said.

In the early 2000s Sidor and some of his co-authors started putting together expeditions to collect fossils from sites in Tanzania that hadn’t been visited since the 1960s and in Zambia where there’d been little work since the ’80s. Two expeditions to Antarctica provided additional materials, as did long-term efforts to examine museum-held fossils that had not been fully documented or named.

Other co-authors from the UW are graduate students Adam Huttenlocker and Brandon Peecook, post-doctoral researcher Sterling Nesbitt and research associate Linda Tsuji; Kenneth Angielczyk of the Field Museum of Natural History in Chicago; Roger Smith, of the Iziko South African Museum in Cape Town; and Sébastien Steyer from the National Museum of Natural History in Paris.

Funding was also received from the Evolving Earth Foundation, the Grainger Foundation, the Field Museum/IDP Inc. African Partners Program and the National Research Council of South Africa.

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For more information:

• Sidor, on sabbatical from UW, spending year at the Field Museum of Natural History in Chicago, office: 312-665-7637, casidor@uw.edu
• Angielczyk, phone: 312-665-7639,  kangielczyk@fieldmuseum.org
• Smith, phone: +27 0 21 481 3879, rsmith@iziko.org.za
• Steyer, phone: +33 662 697 643, steyer@mnhn.fr

***********************************

The following fact sheet was developed by the co-authors.

 FAQ : Provincialization of terrestrial faunas following the end-Permian mass extinction

 Major Findings

• The end-Permian mass extinction permitted a significant reorganization of the land-living animal communities living in southern part of the supercontinent of Pangea.
• In addition to causing high levels of extinction, the mass extinction brought about an emptying of ecological niches, which then promoted the diversification of various groups at different places.
• Mass extinctions can have unpredictable long-term effects (e.g., on the makeup of communities and biogeographic provinces).
• Traditional sources of data regarding the effects of the end-Permian extinction on land (viz. Russia and especially South Africa) might not provide as complete a picture of the extinction and subsequent recovery as previously thought.
• The radiation of archosaurs, including dinosaurs, was probably more closely tied to the recovery from the end-Permian extinction than previously realized.

 Facts about the end-Permian mass extinction (AKA Permo-Triassic mass extinction)

• The end-Permian extinction was the largest in Earth History. Nearly 90% of life disappeared.
• The end-Permian mass extinction event is poorly known on land. Most of the data available today come from the marine realm.
• The end-Permian mass extinction is dated to 252.3 Ma (based on radiometric dates from marine beds in China).
• On land, many diverse groups of Permian animals went extinct. The groups that radiated after the extinction in the Triassic include recognizable members of many of the groups of land vertebrates we still have today: mammals, crocodilians, turtles, lizards, and dinosaurs (which include birds).

 Species involved in the analysis

• Archosaurs.  Archosaurs are a group including modern crocodiles, modern birds, their common ancestor and all of its descendants, including the dinosaurs. Many of the oldest known archosaurs, including the oldest close relatives of dinosaurs and possibly the oldest true dinosaur, are known from the Middle Triassic of Tanzania and Zambia.
• Cynodonts.  Cynodonts are the group from which mammals later evolved.  If this group had perished at the end-Permian extinction, mammals wouldn’t be around today.
• Dicynodonts.  These were the dominant herbivores of the Permian. They were cat- to hippo-sized and distantly related to mammals. They survived the extinction and re-diversified in the Triassic, before becoming extinct at the end of the Triassic.
• Temnospondyls.  These amphibians, which could reach giant sizes, were mostly freshwater top predators like crocodiles today. They survived the extinction but underwent a drastic faunal turnover in the Triassic, with many species going extinct and new species originating.
• Pareiasaurs and other reptiles. Pareiasaurs were mostly large-bodied terrestrial herbivores with robust skulls ornamented by bosses or horns. They were victims of the end-Permian extinction. However, other reptiles like procolophonids survived the extinction and went on to diversify in the Triassic.

 Age

• The Permian Period lasted from 300 to 252 million years ago.  The Permian fossils in this study are about 257 Ma (i.e., Late Permian).
• The Triassic Period lasted from 252 to 201 million years ago. The Triassic fossils in this study are about 242 Ma (i.e., Middle Triassic).

 Geography

• During most of the Permian and Triassic, the continents were coalesced into a single landmass named Pangea.
• The southern portion of Pangea is called Gondwana, and included what is now Africa, Madagascar, South America, Antarctica, Australia, and India.
• The areas in which we collected fossils in Africa were much farther south in the Permian and Triassic than they are today. For example, the Ruhuhu Basin of southern Tanzania is currently ~10.5° S latitude, but in the Late Permian it was about ~50° S.

 Fossils and fieldwork leading to this paper

• Tanzanian fossils were collected in the Ruhuhu valley of southern Tanzania in 2007, 2008, and 2012. They are temporarily on loan to our team for research but will eventually return to be housed at the National Museum of Tanzania in Dar es Salaam.
• Zambian fossils were collected in the Luangwa valley of northeastern Zambia in 2009 and 2011. They are temporarily on loan to our team for research but will eventually return to the National Heritage Conservation Commission in Lusaka.
• Antarctic fossils were most recently collected in 2003 and 2010 are housed at the Burke Museum (Univ. Washington).
• South African fossils are the product of long-term fieldwork projects and are stored at a variety of museums in Cape Town, Johannesburg, Pretoria, etc.

Our paper DOES NOT say:

• Anything about the causes of end-Permian mass extinction.
• Anything about the extinction in the marine realm.
• Anything about global climate change at the end of the Permian.

Funding:
National Geographic Society (to C.A.S.)
National Geographic Society (to J.S.S.)
National Science Foundation (to C.A.S.)
Evolving Earth Foundation (to S.J.N.)
The Grainger Foundation (to K.D.A.)
Field Museum/IDP, Inc. African Partners Program (to K.D.A.)
NSF Graduate Research Fellowships (to B.R.P.)
National Research Council (to R.M.H.S.)

Potential Commentators (not affiliated with this research):
Robert Reisz, University of Toronto (robert.reisz@utoronto.ca)
David Jablonski, University of Chicago (djablons@uchicago.edu)
Paul Olsen, Columbia University (polsen@ldeo.columbia.edu)
Randy Irmis, University of Utah (irmis@umnh.utah.edu)
Hans Sues, Smithsonian Institution (suesh@si.edu)

Co-author emails:
USA
Christian Sidor (Univ. Washington): casidor@uw.edu
Daril Vilhena (Univ. Washington): daril@uw.edu
Kenneth Angielczyk (Field Museum): kangielczyk@fieldmuseum.org
Sterling Nesbitt (formerly UW, now Field Museum):
Adam Huttenlocker (Univ. Washington): huttenla@uw.edu
Brandon Peecook (Univ. Washington): bpeecook@uw.edu
Linda Tsuji (Univ. Washington): latsuji@uw.edu

South Africa
Roger Smith (Iziko South African Museum, Cape Town): rsmith@iziko.org.za

France
J.Sébastien Steyer (CNRS and Muséum national d’Histoire naturelle, Paris): steyer@mnhn.fr

Goodchild/Wygonik

This diagram shows how a delivery truck can save on mileage when compared with personal vehicles driving to and from a store.

University of Washington engineers have found that using a grocery delivery service can cut carbon dioxide emissions by at least half when compared with individual household trips to the store. Trucks filled to capacity that deliver to customers clustered in neighborhoods produced the most savings in carbon dioxide emissions.

“A lot of times people think they have to inconvenience themselves to be greener, and that actually isn’t the case here,” said Anne Goodchild, UW associate professor of civil and environmental engineering. “From an environmental perspective, grocery delivery services overwhelmingly can provide emissions reductions.”

Consumers have increasingly more grocery delivery services to choose from. AmazonFresh operates in the Seattle area, while Safeway’s service is offered in many U.S. cities. FreshDirect delivers to residences and offices in the New York City area. Last month, Google unveiled a shopping delivery service experiment in the San Francisco Bay Area, and UW alumni recently launched the grocery service Geniusdelivery in Seattle.

Goodchild/Wygonik

A comparison of carbon dioxide produced per customer for personal vehicles and delivery vehicles. The bars on the left represent a system in which customers choose their delivery times. The right side shows a more efficient system whereby the delivery service sets delivery times.

As companies continue to weigh the costs and benefits of offering a delivery service, Goodchild and Erica Wygonik, a UW doctoral candidate in civil and environmental engineering, looked at whether using a grocery delivery service was better for the environment, with Seattle as a test case. In their analysis, they found delivery service trucks produced 20 to 75 percent less carbon dioxide than the corresponding personal vehicles driven to and from a grocery store.

They also discovered significant savings for companies – 80 to 90 percent less carbon dioxide emitted – if they delivered based on routes that clustered customers together, instead of catering to individual household requests for specific delivery times.

“What’s good for the bottom line of the delivery service provider is generally going to be good for the environment, because fuel is such a big contributor to operating costs and greenhouse gas emissions,” Wygonik said. “Saving fuel saves money, which also saves on emissions.”

The research was funded by the Oregon Department of Transportation and published in the Journal of the Transportation Research Forum.

The UW researchers compiled Seattle and King County data, assuming that every household was a possible delivery-service customer. Then, they randomly drew a portion of those households from that data to identify customers and assign them to their closest grocery store. This allowed them to reach across the entire city, without bias toward factors such as demographics and income level.

They used an Environmental Protection Agency modeling tool to calculate emissions at a much more detailed level than previous studies have done. Using factors such as vehicle type, speed and roadway type, they calculated the carbon dioxide produced for every mile for every vehicle.

Emissions reductions were seen across both the densest parts and more suburban areas of Seattle. This suggests that grocery delivery in rural areas could lower carbon dioxide production quite dramatically.

“We tend to think of grocery delivery services as benefiting urban areas, but they have really significant potential to offset the environmental impacts of personal shopping in rural areas as well,” Wygonik said.

Work commuters are offered a number of incentives to reduce traffic on the roads through discounted transit fares, vanpools and carpooling options. Given the emissions reductions possible through grocery delivery services, the research raises the question of whether government or industry leaders should consider incentives for consumers to order their groceries online and save on trips to the store, Goodchild said.

In the future, Goodchild and Wygonik plan to look at the influence of customers combining their grocery shopping with a work commute trip and the impact of the delivery service’s home-base location on emissions.

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For more information, contact Goodchild at annegood@uw.edu or 206-543-3747.

“Characterization by proxy” is the technique used by Sarah Ballard, a post-doctoral researcher at the UW, to infer the properties of small, relatively cool stars too distant for measurement, by comparing them to closer stars that now can be directly observed.

Ballard is lead author of a study accepted for publication in The Astrophysical Journal that used this method and observations from the Kepler Space Telescope to learn the nature of the distant star Kepler-61.

Our understanding of the size and temperature of planets depends crucially on the size and temperature of the stars they orbit. Astronomers already have a robust way to discern the physical properties of solar-type stars — those like the sun — by measuring the light they emit at different wavelengths and matching that to synthetically created spectra.

“The challenge is that small stars are incredibly difficult to characterize,” Ballard said. Those theoretical methods don’t work well for what are called M-dwarf stars, lower-mass stars about half the size of the sun and smaller — which is too bad, because such stars make up about three-quarters of the universe.

Ballard is using the characterization by proxy method to try to fill this knowledge gap. She is building on what she calls “truly remarkable” work by astronomer Tabetha Boyajian, now at Yale University, who uses a near-infrared interferometer — an array of telescopes working in unison studying light wavelengths a bit longer than visible light — to resolve the physical size of relatively nearby stars.

Ballard said her characterization by proxy method takes “full advantage that there now exists this precious sample” of relatively nearby stars that have been directly measured. You could say the method borrows a bit from Greek mathematician Euclid, whose first “common notion” held that things that equal the same thing must necessarily also equal each other.

In the new paper, Ballard and co-authors used this reasoning to learn about Kepler-61b, a planet orbiting near the inner edge of the habitable zone of the distant, low-mass star Kepler-61, about 900 light-years away in the Cygnus Constellation. A star’s habitable zone is that swath of space just right for an orbiting planet’s surface water to be in liquid form, thus giving life a chance.

She did this by comparing it to temperature size averages from four spectroscopically similar stars between 12 and 25 light-years away in the Ursa Major and Cygnus constellations. A light-year is about 6 trillion miles.

A funny thing also happened along the way: Kepler-61 turned out to be bigger and hotter than expected, which in turn recalibrated planet Kepler-61b’s relative size upward as well — meaning it, too, would be hotter than previously thought and no longer a resident of the star’s habitable zone.

All of this caused Ballard to informally subtitle the paper, “How Nearby Stars Bumped a Planet out of the Habitable Zone.”

Funding for the research came from NASA and its Jet Propulsion Laboratory at the California Institute of Technology.

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For more information, contact Ballard at 617-249-3081 sarahba@uw.edu.

It turns out that in sultry weather condensation on the outside of a canned beverage doesn’t just make it slippery: those drops can provide more heat than the surrounding air, meaning your drink would warm more than twice as much in humid weather compared to in dry heat. In typical summer weather in New Orleans, heat released by condensation warms the drink by 6 degrees Fahrenheit in five minutes.

“Probably the most important thing a beer koozie does is not simply insulate the can, but keep condensation from forming on the outside of it,” said Dale Durran, a UW professor of atmospheric sciences.

He’s co-author of results published in the April issue of Physics Today that give the exact warming for a range of plausible summer temperatures and humidity levels. For example, on the hottest, most humid day in Dhahran, Saudi Arabia, condensation alone would warm a can from near-freezing temperature to 48 degrees Fahrenheit in just five minutes.

The investigation began a couple of years ago when Durran was teaching UW Atmospheric Sciences 101 and trying to come up with a good example for the heat generated by condensation. Plenty of examples exist for evaporative cooling, but few for the reverse phenomenon. Durran thought droplets that form on a cold canned beverage might be just the example he was looking for.

A quick back-of-the-napkin calculation showed the heat released by water just four thousandths of an inch thick covering the can would heat its contents by 9 degrees Fahrenheit.

“I was surprised to think that such a tiny film of water could cause that much warming,” Durran said.

Though he’s normally more of a theoretician, Durran decided this result required experimental validation. He recruited co-author Dargan Frierson, a UW associate professor of atmospheric sciences, and they ran an initial test in Frierson’s little-used basement bathroom, using a space heater and hot shower to vary the temperature and humidity.

The findings corroborated the initial result, and they embarked on a larger-scale test.

“You can’t write an article for Physics Today where the data has come from a setup on the top of the toilet tank in one of the author’s bathrooms,” Durran said.

Univ. of Washington

A test subject being weighed to measure the amount of condensation. The cap prevents air from moving through the opening on top.

First they recruited colleagues in Frierson’s beachside hometown of Wilmington, North Carolina, to duplicate the experiment and compare results with those taken on a hot, dry Seattle day. But they decided they needed to test a wider range of conditions.

Finally, last summer undergraduates Stella Choi and Steven Brey joined the project to run a proper experiment in the UW Atmospheric Sciences building. They unearthed an experimental machine with styling that looks to be from the 1950s, last used decades ago to simulate cloud formation.

With funding for educational outreach from the National Science Foundation, the students first cooled a can in a bucket of ice water then dried it and placed it in the experimental chamber dialed up to the appropriate conditions. After five minutes they removed the can, weighed it to measure the amount of condensation, and recorded the final temperature of the water inside.

The phenomenon at work – latent heat of condensation – is central to Frierson’s research on water vapor, heat transfer and global climate change.

“We expect a much moister atmosphere with global warming because warmer air can hold a lot more water vapor,” Frierson said. Because heat is transferred when water evaporates or condenses, this change affects wind circulation, weather patterns and storm formation.

Durran’s research includes studies of thunderstorms, which are powered by heat released from condensation in rising moist air.

As for his demonstration of the heat released during this process, he and Frierson are now working with the National Center for Atmospheric Research to develop an educational tool that will let students around the world try the experiment and post their results online for comparison.

The example promises to become as classic as a cold drink on a hot summer day.

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For more information, contact Durran at 206-543-7440 or durrand@atmos.washington.edu and Frierson at 206-685-7364 or dargan@atmos.washington.edu.

• Engineering Discovery Days
• Fri., April 26, 9 a.m. – 2 p.m.
• Sat., April 27, 9 a.m. – 2 p.m.

Which is better for electrical storage: A potato, a lemon, an AA battery or a car battery?

If you’re curious, the answer to this question and more will be scattered around the University of Washington campus on Friday and Saturday, April 26-27, during the 2013 Engineering Discovery Days.

College of Engineering Dean's Office

A student gets a hug from the next-generation personal robot at last year’s event.

Friday’s events geared toward school-aged children are at capacity, but families and members of the UW community can stop by on Saturday to see the hands-on exhibits, meet research teams and visit various engineering labs.

Saturday’s program also includes presentations for high school students about each engineering department, admissions and financial aid, and women in science and engineering.

The promenade along Rainier Vista and Drumheller Fountain will be filled with outdoor exhibits, and many of the engineering buildings will house the indoor displays. Look for old favorites such as the glowing pickle exhibit, homemade silly putty and flame movement demonstrations. You may also spot a water rocket, human-powered submarine and a life-sized robot.

Some new exhibits on this year’s program are wool dying, game demonstrations from the Center for Game Science and solar cell-powered toy car races. There will also be a scavenger hunt in which students visit various stations to find answers to baffling and quirky science questions.

Both days are free and open to everyone, but organizers ask that attendees register online. Close to 10,000 visitors are expected over the two days to this nearly century-old UW event.

Organizers recommend avoiding driving on campus during the event. Public transit and parking are available.

Photos from this year’s event will be posted on the Engineering Discovery Days Facebook page.

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Planetery Habitability Laboratory

The newly discovered Kepler 62e and 62f compared with the Earth. UW astronomer Eric Agol found 62f.

A University of Washington astronomer has discovered perhaps the most Earth-like planet yet found outside the solar system by the Kepler Space Telescope.

Eric Agol, a UW associate professor of astronomy, has identified Kepler 62f, a small, probably rocky planet orbiting a sunlike star in the Lyra constellation. The planet is about 1.4 times the size of Earth, receives about half as much solar flux, or heat and radiation, as Earth and circles its star in 267.3 (Earth) days.

It’s one of two “super-Earth” planets discovered in the star Kepler 62′s habitable zone, that swath of space the right distance from the star to potentially allow liquid water to exist on a planet’s surface, thus giving life a chance. A super-Earth is a planet greater in mass than our own but still smaller than gas giants such as Neptune.

Kepler 62′s other super-Earth, nearby 62e, is 1.61 times Earth’s size, circles the star in 122.4 days and gets about 20 percent more stellar flux than the Earth. The two are the smallest exoplanets — planets outside the solar system — yet found in a host star’s habitable zone.

“The planets this small that we have found until now have been very close to their stars and much too hot to be possibly habitable. This is the first one Kepler has found in the habitable zone that satisfies this small size,” Agol said. “Kepler 62f is the smallest size and the most promising distance from its star, which by these measures makes it the most similar exoplanet to Earth that has been found by Kepler.”

Agol is the second author of a paper documenting the discovery published April 18 by Science Express, the online edition of the journal Science.

While the sizes of Kepler 62e and 62f are known, Agol said, their mass and densities are not — but every planet found in their size range so far has been rocky, like Earth.

“Based on its size, our best guess is that it’s rocky and has some atmosphere, but not a thick gaseous envelope, like Neptune,” Agol said.

The Kepler telescope was launched in 2009 with the aim of finding Earth-like planets beyond the solar system. It detects planets by “transits” that cause their host stars to appear fainter when the planets pass in front as they orbit.

Kepler 62f was a late-arrival in terms of its discovery. Its planetary siblings were found by a team of researchers led by William Borucki of the NASA Ames Research Center, principal investigator for the Kepler Space Telescope. Kepler 62 b, c and d are 1.31, 0.54 and 1.95 times the size of the Earth, respectively, but orbit the star too close to be in the habitable zone.

Borucki and some 45 co-authors were preparing to publish their findings in August 2012 when Agol contacted them that he had found an additional planet orbiting Kepler 62 that he identified in work with UW postdoctoral researcher Brian Lee.

Despite the extraordinary number of planets found by the Kepler team, they had overlooked 62f due to a sort of coincidence. Three transits are usually necessary to confirm a planet’s existence, but the Kepler software recognized only two. Agol pinpointed three transits for 62f with a process developed with Lee that takes into account the slight variation of stellar brightness in the vicinity of a transit. That enabled him to confirm 62f as an actual planet — and made him a leading author of the paper.

Though the mass and densities of Kepler 62e and f are not yet known, Agol has pioneered a process called transit timing variations that may in the future show the mass of such planets by the gravitational effect they have on each other.

“This type of discovery is the reason we launched the Kepler spacecraft — to find small, Earth-sized, potentially Earth-temperature planets,” Agol said. “At the same time,  though, it isn’t exactly the same as Earth. It is slightly larger and cooler than Earth. It tells me how special the Earth is and how it may take some time — hopefully not too long — to find its exact twin.”

The work was funded by the National Science Foundation.

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For more information, contact Agol at agol@astro.washington.edu or 206-543-7106.

Frederick Dooley

A bean plant treated with hydrogen sulfide (top) is substantially bigger at two weeks after gestation than the control plant (bottom) that was untreated.

But in low doses, hydrogen sulfide could greatly enhance plant growth, leading to a sharp increase in global food supplies and plentiful stock for biofuel production, new University of Washington research shows.

“We found some very interesting things, including that at the very lowest levels plant health improves. But that’s not what we were looking for,” said Frederick Dooley, a UW doctoral student in biology who led the research.

Dooley started off to examine the toxic effects of hydrogen sulfide on plants but mistakenly used only one-tenth the amount of the toxin he had intended. The results were so unbelievable that he repeated the experiment. Still unconvinced, he repeated it again – and again, and again. In fact, the results have been replicated so often that they are now “a near certainty,” he said.

“Everything else that’s ever been done on plants was looking at hydrogen sulfide in high concentrations,” he said.

The research is published online April 17 in PLOS ONE, a Public Library of Science journal.

At high concentrations – levels of 30 to 100 parts per million in water – hydrogen sulfide can be lethal to humans. At one part per million it emits a telltale rotten-egg smell. Dooley used a concentration of 1 part per billion or less to water seeds of peas, beans and wheat on a weekly basis. Treating the seeds less often reduced the effect, and watering more often typically killed them.

A time-lapse video shows how a seed of dwarf wheat treated with a low dose of hydrogen sulfide begins growing at an accelerated rate compared with an untreated seed.

With wheat, all the seeds germinated in one to two days instead of four or five, and with peas and beans the typical 40 percent rate of germination rose to 60 to 70 percent.

“They germinate faster and they produce roots and leaves faster. Basically what we’ve done is accelerate the entire plant process,” he said.

Crop yields nearly doubled, said Peter Ward, Dooley’s doctoral adviser, a UW professor of biology and of Earth and space sciences and an authority on Earth’s mass extinctions.

Hydrogen sulfide, probably produced when sulfates in the oceans were decomposed by sulfur bacteria, is believed to have played a significant role in several extinction events, in particular the “Great Dying” at the end of the Permian period. Ward suggests that the rapid plant growth could be the result of genetic signaling passed down in the wake of mass extinctions.

Frederick Dooley

Bean seeds treated with hydrogen sulfide showed substantially more development at 96 hours after germination (top photo) than did the untreated control seeds (bottom).

At high concentrations, hydrogen sulfide killed small plants very easily while larger plants had a better chance at survival, he said, so it is likely that plants carry a defense mechanism that spurs their growth when they sense hydrogen sulfide.

“Mass extinctions kill a lot of stuff, but here’s a legacy that promotes life,” Ward said.

Dooley recently has applied hydrogen sulfide treatment to corn, carrots and soybeans with results that appear to be similar to earlier tests. But it is likely to be some time before he, and the general public, are comfortable with the level of testing to make sure there are no unforeseen consequences of treating food crops with hydrogen sulfide.

The most significant near-term promise, he believes, is in growing algae and other stock for biofuels. Plant lipids are the key to biofuel production, and preliminary tests show that the composition of lipids in hydrogen sulfide-treated plants is the same as in untreated plants, he said.

When plants grow to larger-than-normal size, they typically do not produce more cells but rather elongate their existing cells, Dooley said. However, in the treatment with hydrogen sulfide, he found that the cells actually got smaller and there were vastly more of them. That means the plants contain significantly more biomass for fuel production, he said.

“If you look at a slide of the cells under a microscope, anyone can understand it. It is that big of a difference,” he said.

Ward and Suven Nair, a UW biology undergraduate, are coauthors of the PLOS ONE paper. The work was funded by the UW Astrobiology Program.

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 For more information, contact Dooley at fdd@uw.edu, or Ward at 206-543-2962 or ward.biology.uw@gmail.com.

The paper is available at http://dx.plos.org/10.1371/journal.pone.0062048

• U.S. Ocean Observatories Initiative
• UW-led regional cabled observatory
• UW Applied Physics Laboratory work building the observatory

The basement lab near the University of Washington campus is, literally, buzzing. High-voltage machines produce energy that will soon run through cables snaking along the seafloor. A dozen engineers hunch over electronics, making alterations or running checks. In one corner, a nitride-coated titanium shaft has been sitting in a bucket of saltwater for four months to test the coating for corrosion. A glass-walled cleanroom prevents contaminants from interfering with seals on housings designed to keep out seawater pressing in at 4,200 pounds per square inch.

This is crunch time for University of Washington preparations to build the world’s largest underwater observatory. The National Science Foundation in 2009 launched the $239 million effort, pending availability of funds and Congressional approval. John Delaney, UW professor of oceanography, leads the project to create a cabled observatory that will bring power and Internet to the ocean floor. This new concept will use remote-controlled instruments and high-bandwidth video to create an enduring, real-time presence in the deep ocean.

Researchers in the UW’s Applied Physics Laboratory were tasked by Delaney to build and test the equipment that will make up the observatory. Much of that equipment will be installed this summer. This is the biggest project the 70-year-old marine engineering institute has ever undertaken, said project lead Gary Harkins, a principal engineer with the lab.

“This concept of a real-time observatory will change what we do as ocean engineers, what we will learn how to do, and what ocean scientists can do with these systems now and in the future,” Harkins said.

The cabled observatory, known as the Regional Scale Nodes project, is part of the national Ocean Observatories Initiative, an effort to integrate U.S. measurements of the ocean and seafloor. Other partners will build coastal and global observing networks, manage the data and conduct educational outreach. The Pacific Northwest observatory will span the Juan de Fuca tectonic plate off the Washington and Oregon coasts, the likely source of the next large regional earthquake.

Most of the regional network’s components will be built from aircraft-grade titanium because the material is strong and resists corrosion, which is crucial for electronics that will spend decades in saltwater.

“We are having a notable impact on the non-aircraft market for titanium,” remarked Applied Physics Laboratory engineer Geoff Cram.

Even so, most components must be designed to be switched out for possible repairs or upgrades during the observatory’s projected 25-year lifespan.

Over the past two summers, the backbone cable and high-voltage junction boxes were laid by telecommunications contractors. This summer’s deployments venture into uncharted territories. The team has booked 60 days of ship time on the UW’s Thomas G. Thompson research vessel for three cruises in July and August. Researchers will install lower-voltage cables that run from high-voltage nodes closer to the areas of scientific interest: deep-ocean volcanoes, seismically active plates, and an underwater ridge that seeps energy-rich methane gas.

While the engineering team readies the components, the science team is mapping out the science plan and finalizing the cruise details.

“The timeline isn’t forgiving on this one,” Cram noted.

In design work over the past four years, the engineers have considered how to protect the infrastructure from a possible failure by any of the components – some of which are experimental, and none of which has operated for this long at these pressures. They also have created a common time stamp for all the data, since scientists might want to make precise comparisons of measurements taken by different instruments at opposite ends of the network. They will do their best to protect all the instruments from ships, waves, marine animals and corrosion.

As the team finalizes the design, engineers have to ensure the sensors don’t interfere with each other. They also have to dissipate heat from the electronics, which give off about as much heat as a 60-watt light bulb but, in a tightly sealed housing, could still fry instruments.

“This is a highly integrated system operating in a very challenging environment,” said Applied Physics Laboratory engineer Dana Manalang, who oversees the sensor group. “From an engineering perspective, that makes this a challenging project.”

The team this summer will install about 40 sensors, of 13 different types, now being assembled and tested at the UW. The instruments include:

• A high-definition video and still camera that will provide live footage, starting this summer, to researchers and the public.
• Seismometers to provide early warning of earthquakes or volcanic eruptions.
• Commercial oceanographic sensors, including three precision pressure sensors built by Sea-Bird Electronics of Bellevue, Wash.
• Water samplers built by UW oceanographer David Butterfield. Some samples will be stored until researchers collect them; others will be analyzed in place to detect the seawater’s chemical and genetic contents.
• A deep-water mass spectrometer, developed by Harvard University oceanographer Peter Girguis, that will be installed near the volcano’s caldera
• Chemical sensors, developed by UW oceanographer Marv Lilley, that will go inside the hydrothermal vents. These will be inserted slowly so fragile ceramic parts survive the transition from near-freezing water to 570 ºF (300 ºC) temperatures inside the vent.
• Seafloor pressure and tilt sensors, developed by Bill Chadwick at Oregon State University, that detect pressure buildup below the ocean floor.

UW engineers have designed the system to digitize all this data and send it back to land via the cables in a few thousandths of a second.

Miles of underwater cable will arrive during coming weeks to a UW storage facility on Lake Washington. The engineering team will expand there as it builds components and outgrows its campus lab space.

The next few months will be hectic, said Harkins. Some of the UW researchers will join the telecommunications contractor to run a month-long final check of the backbone cable system from the Newport, Ore. shore station. UW engineers will build and test 10 secondary nodes to drive the instruments that will be installed this summer. Members of the engineering team will work with contractors and scientists to run pressure tests and perform final checks on their instruments.

Yet another team is developing a profiling system that records data in the upper 650 feet (200 m) of the ocean. That system is perhaps the most technically challenging aspect of the whole observatory, researchers said, and won’t be installed until summer of 2014, but initial testing will begin this summer at the UW’s Friday Harbor Laboratories.

Forty-six UW faculty and staff members are putting in long hours on the cabled observatory, including 15 on the science team and 31 on the engineering side.

Whoever you talk to, there’s one common refrain: “This is going to be a very busy summer.”

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For more information, contact Nancy Penrose, UW’s OOI Communications Coordinator, at 206-221-5781 or penrose@ocean.washington.edu.

Researchers at the University of Washington and Boston University led by Jiangyu Li and Yanhang Zhang have discovered that a certain type of protein found in organs that repeatedly stretch and retract – such as the heart and lungs – is the source for a favorable electrical property that could help build and support healthy connective tissues. But when exposed to sugar, some of the proteins no longer could perform their function, according to findings published online April 15 in the journal Physical Review Letters.

Jiangyu Li, UW

The blue spots in this image show where glucose has halted ferroelectric switching in an elastin protein.

The property, called ferroelectricity, is a response to an electric field in which a molecule switches from having a positive to a negative charge. Only recently discovered in animal tissues, researchers have traced this property to elastin and found that when exposed to sugar, the elastin protein sometimes slows or stops its ferroelectric switching. This could lead to the hardening of those tissues and, ultimately, degrade an artery or ligament.

“This finding is important because it tells us the origin of the ferroelectric switching phenomenon and also suggests it’s not an isolated occurrence in one type of tissue as we thought,” said co-corresponding author Li, a UW associate professor of mechanical engineering. “This could be associated with aging and diabetes, which I think gives more importance to the phenomenon.”

About a year ago, Li and collaborators discovered ferroelectric switching in mammalian tissues, a surprising first for the field. Ferroelectricity is common in synthetic materials and is used for displays, memory storage and sensors. Li’s research team found that the wall of a pig’s aorta, the largest blood vessel carrying blood to the heart, exhibits ferroelectric switching properties.

Li said that discovery left researchers with a lot of questions, including whether this property is found in other soft tissues and the health implications of its presence. Observing differences in ferroelectric behavior at the protein level has helped to answer some of those questions.

The research team separated the aortic tissue into two types of proteins, collagen and elastin. Fibrous collagen is widespread in biological tissues, while elastin has only been found in animals with a backbone. Elastin, as its name suggests, is springy and helps the heart and lungs stretch and contract. Ferroelectric switching gives elastin the flexibility needed to perform repeated pulses as with an artery.

When researchers treated the elastin with sugar, they found that glucose suppressed ferroelectric switching by up to 50 percent. This interaction between sugar and protein mimics a natural process called glycation, in which sugar molecules attach to proteins, degrading their structure and function. Glycation happens naturally when we age and is associated with a number of diseases such as diabetes, high blood pressure and arteriosclerosis, a thickening and hardening of the arteries.

The research team has focused solely on the aortic tissues, but this finding likely applies to other biological tissues that have the protein elastin, such as the lungs and skin.

“I would expect the same phenomena will be observed in those tissues and organs as well,” Li said. “It will be more common than what we originally thought.”

Researchers next will drill down even more to look at the molecular mechanics of ferroelectric switching and further try to connect the process with disease onset.

Co-authors are Yuanming Liu, Nataly Q. Chen and Feiyue Ma at the UW, and Zhang, Yunjie Wang and Ming-Jay Chow at Boston University.

The research was funded by the National Science Foundation, the National Institutes of Health, the UW and a NASA Space Technology Research Fellowship.

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For more information, contact Li at 206-543-6226 or jjli@uw.edu.

New ice core research suggests that, while the changes are dramatic, they cannot be attributed with confidence to human-caused global warming, said Eric Steig, a University of Washington professor of Earth and space sciences.

Heidi Roop

This photo from December 2010 shows a one-meter long section of the West Antarctic Ice Sheet Divide core, with a dark layer of volcanic ash visible.

Previous work by Steig has shown that rapid thinning of Antarctic glaciers was accompanied by rapid warming and changes in atmospheric circulation near the coast. His research with Qinghua Ding, a UW research associate, showed that the majority of Antarctic warming came during the 1990s in response to El Niño conditions in the tropical Pacific Ocean.

Their new research suggests the ’90s were not greatly different from some other decades – such as the 1830s and 1940s – that also showed marked temperature spikes.

“If we could look back at this region of Antarctica in the 1940s and 1830s, we would find that the regional climate would look a lot like it does today, and I think we also would find the glaciers retreating much as they are today,” said Steig, lead author of a paper on the findings published online April 14 in Nature Geoscience.

The researchers’ results are based on their analysis of a new ice core from the West Antarctic Ice Sheet Divide that goes back 2,000 years, along with a number of other ice core records going back about 200 years. They found that during that time there were several decades that exhibited similar climate patterns as the 1990s.

The most prominent of these in the last 200 years – the 1940s and the 1830s – were also periods of unusual El Niño activity like the 1990s. The implication, Steig said, is that rapid ice loss from Antarctica observed in the last few decades, particularly the ’90s, “may not be all that unusual.”

The same is not true for the Antarctic Peninsula, the part of the continent closer to South America, where rapid ice loss has been even more dramatic and where the changes are almost certainly a result of human-caused warming, Steig said.

But in the area where the new research was focused, the West Antarctic Ice Sheet, it is more difficult to detect the evidence of human-caused climate change. While changes in recent decades have been unusual and at the “upper bound of normal,” Steig said, they cannot be considered exceptional.

“The magnitude of unforced natural variability is very big in this area,” Steig said, “and that actually prevents us from answering the questions, ‘Is what we have been observing exceptional? Is this going to continue?’”

He said what happens to the West Antarctic Ice Sheet in the next few decades will depend greatly on what happens in the tropics.

The West Antarctic Ice Sheet is made up of layers of ice, greatly compressed, that correspond with a given year’s precipitation. Similar to tree rings, evidence preserved in each layer of ice can provide climate information for a specific time in the past at the site where the ice core was taken.

In this case, the researchers detected elevated levels of the isotope oxygen 18 in comparison with the more commonly found oxygen 16. Higher levels of oxygen 18 generally indicate higher air temperatures.

Levels of oxygen 18 in ice core samples from the 1990s were more elevated than for any other time in the last 200 years, but were very similar to levels reached during some earlier decades.

The work was funded by the National Science Foundation Office of Polar Programs.

For more information, contact Steig at 206-685-3715, 206-543-6327 or steig@uw.edu.

Co-authors are Qinghua Ding, Marcell Küttel, Peter Neff, Ailie Gallant, Spruce Schoenemann, Bradley Markle, Tyler Fudge, Andrew Schauer and Rebecca Teel of the University of Washington; James White and Bruce Vaughn of the University of Colorado; Summer Rupper, Landon Burgener and Jessica Williams of Brigham Young University; Thomas Neumann of NASA’s Goddard Space Flight Center; Paul Mayewski, Daniel Dixon and Elena Korotkikh of the University of Maine; Kendrick Taylor of Desert Research Institute, Reno, Nev.; Georg Hoffmann of the Centre d’Etudes de Saclay in France and Utrecht University in The Netherlands; and David Schneider of the National Center for Atmospheric Research, Boulder, Colo.

A new procedure that thickens and thins fluid at the micron level could save consumers and manufacturers money, particularly for soap products that depend on certain molecules to effectively deal with grease and dirt. Researchers at the University of Washington published their findings online April 9 in the Proceedings of the National Academy of Sciences.

Read the back of most shampoos and dishwashing detergents and you’ll find the word “surfactant” in the list of active ingredients. Surfactant molecules are tiny, yet they are the reason dish soap can attack an oily spot and shampoo can rid the scalp of grease.

Surfactant molecules are made up of two main parts, a head and a tail. Heads are attracted to water, while the tails are oil-soluble. This unique structure helps them break down and penetrate grease and oil while immersed in water. It also makes the soaps, shampoos and detergents thicker, or more viscous.

Environmental Molecular Sciences Laboratory and UW

A web-like, gel structure is formed after fluid passes through the flow device. The unit of measurement is 1 micron.

Soap manufacturers add organic and synthetic surfactants – and often a slew of other ingredients – to their products to achieve a desired thickness and to help remove grease and dirt. These extra ingredients add volume to the soap products, which then cost more to manufacture, package and ship, ultimately shifting more costs to consumers, said Amy Shen, a UW associate professor of mechanical engineering and lead author of the paper.

The research team’s design could create the same thickening results without having to add extra ingredients.

“Our flow procedure can potentially help companies and consumers save a lot of money,” Shen said. “This way, companies don’t have to add too many surfactants to their products.”

Researchers found that when they manipulated the flow of a liquid through microscopic channels, the resulting substance became thicker. Now, scientists add a lot of salt, or alter the temperature and level of acidity to induce this change, but these methods can be expensive and more toxic, Shen said.

The team built a palm-sized tool called a microfluidics device that lets researchers pump water mixed with a little detergent and salt through a series of vertical posts. The distance between posts is about one-tenth the size of a single human hair. That micron-sized gap squeezes the liquid as it flows, causing it to quickly deform. The end result is a gel-like substance that’s more viscous and elastic.

University of Washington

A diagram showing how the microfluidics device works. Water mixed with salt and soap is injected into a spout (left back). The fluid travels through a series of posts (see enlarged segment) that cause the fluid to thicken.

When researchers looked at high-resolution images of the end product, they saw a series of wormlike rods attaching and intermingling with each other, creating an entangled web. This structure stayed intact after the procedure was complete, which suggests this process can create a permanent, scaffold-like network that could prove useful for biological applications, Shen said. She is collaborating with other UW researchers to try to create stable structures that could house enzymes and other biomarkers for detecting certain diseases.

Shen and her team also discovered that when they pumped a thicker, more elastic fluid through the device, the opposite effect happened – the gel became thinner and more porous. This could be useful in biomedical applications, Shen said, though it hasn’t yet been tested. In theory, a semi-solid gel could be injected into veins, then transform into a thinner liquid, delivering drugs throughout the body.

Researchers hope one eventual outcome will be a scaled-up industrial design of their microfluidics device that could help manufacturers churn out soap products that aren’t filled with an excess of added materials. Shen has presented her initial findings at Procter & Gamble Co.

“What we can provide are all of the important parameters for operating conditions so companies can have an industrial design to achieve their goals,” Shen said.

Research collaborators are Joshua Cardiel and Ya Zhao, UW doctoral students in mechanical engineering; Alice Dohnalkova, senior research scientist at Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory in Richland, Wash.; and Neville Dubash and Perry Cheung, former post-doctoral researchers in mechanical engineering.

The research was funded by the National Science Foundation.

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For more information, contact Shen at amyshen@uw.edu or 206-708-3411.

WA Dept. of Fish and Wildlife

A dock washed away by the tsunami that made landfall in December in Olympic National Park.

Remnants of the wreckage continue to reach the Pacific Northwest: A 65-foot Japanese dock washed up in December on a beach near Forks, Wash., a fish hitched a ride on a 20-foot boat that washed up in March in Long Beach, Wash., and pieces of a Japanese shrine washed ashore in March and April in Oregon. Japanese sports balls, foam insulation and other flotsam regularly wash up on the coast to provide a reminder of the lasting effects of the disastrous earthquake and tsunami.

Ian Miller, a coastal hazards specialist with Washington Sea Grant, a UW-based center that’s part of the national Sea Grant network, co-authored a report on possible scenarios for debris accumulation in Washington state and has recently given public talks about the debris found to date.

“So far there still hasn’t been a big wash-up significantly above and beyond our normal debris load,” he said. He and hundreds of volunteers will comb the beach April 20 to see if that remains true after the largest annual beach cleanup of Washington’s coast.

Immediately after the March 11, 2011, tsunami, one of the concerns was that huge amounts of garbage would wash up on the U.S. coastline.

“What became obvious early on was that nobody had a clue,” Miller said. “There was a lot of uncertainty, a lot of contradictory information, and that caused anxiety.

“That tells me we need to focus on what is happening now, so that next time we have a more factual basis to make projections.”

To officially be designated as tsunami debris, an item must have an identifying marker and get verification of its origin from the Japanese government. However, pieces of plastic foam believed to have probably come from Japan are common, as are pieces of lumber that observers say are unlike their American counterparts.

A widely reported pulse of suspected tsunami material washed ashore in early summer, Miller said, and then things quieted down. Winter storms in recent months have been bringing more items.

Miller’s review of oceanographic literature, published in the fall, predicted that most of the debris would wash up in Alaska, and that most would land within four years of the tsunami. Anecdotal reports and media coverage suggest that most material so far is in fact hitting Alaska, Miller said.

Computer models from the University of Hawaii suggest that most of the tsunami material has washed ashore by now. Models from the National Oceanographic and Atmospheric Administration show a large patch still offshore. But those are probably items that don’t catch the wind, such as plastic bags or pieces of wood, that likely will follow currents to what’s known as the garbage patch in the center of the North Pacific Gyre, Miller said.

He is studying the actual debris accumulation and working with colleagues at the National Park Service, NOAA and other agencies to monitor the beaches and dispose of the dock and other large items.

It’s not until the big annual cleanup that many of the more remote sections of beach are combed for litter. To document possible tsunami debris, a team from Western Washington University will be sorting and weighing collected material.

That cataloging effort is a step in the right direction, Miller said.

“We know that we get debris on our coast, but we don’t know what is a quote-unquote ‘normal’ load,” Miller said.

He hopes documentation will broaden awareness and knowledge of washed-up ocean garbage.

“The tsunami has highlighted the issue. On a global scale, it’s a drop in the bucket compared to the amount of trash that’s out in the ocean and the amount that’s added to the ocean every year,” Miller said. “If this gives us more information about where it washes ashore we can focus [cleanup] investment accordingly.”

If you plan to spend the lead-up to Earth Day cleaning up the Washington coast, register online and arrive early Saturday. No special tools are required, but volunteers may want to bring a sharp knife, hacksaw or small shovel to deal with tenacious debris items. Cleanup takes place at beaches along the coast, and some organizing groups host volunteer barbecues or chowder lunches afterward.

The annual event is a chance to help clean the coast and experience a connection with other nations around the Pacific Rim.

“Last year I can remember sitting down with a bag of plastic bottles, and I think I ended up counting eight different languages,” Miller said. “You find things from all over the world.”

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For more information, contact Miller at 360-417-6460 or immiller@uw.edu.

A University of Washington class is using the nation’s first controlled-ocean research tool to study the effects of increased acidity on marine ecosystems.

“The goal is to study the impact of ocean acidification on biological community structure in seawater from the San Juan Islands,” said James Murray, a UW oceanography professor.

On the main dock at the UW’s Friday Harbor Laboratories until April 29 the team will start at 8:30 each morning by lowering bottles six feet (two meters) into each reservoir to collect water samples. Students enrolled in a research apprenticeship class then analyze the seawater to see how acidity affects chemistry, bacterial communities, and marine animal and plant life.

“The biological impacts of ocean acidification are the big unknowns,” Murray said. “We know that CO₂ is going up, and we know that the oceans are going to be more acidic, but what we don’t know, and everyone is concerned about, is the possible impact on the biology.”

Jim Murray / UW

The nine test tanks, on the left, attach to the main dock at the UW’s Friday Harbor Laboratories on San Juan Island.

Murray led development of the experimental facility over the past five years with funding from the Educational Foundation of America and the National Science Foundation. In recent years the group has worked out some tweaks – adding floats to each reservoir to keep from straining the dock, and shading the covers to slow down biological blooms in the reservoirs.

This is the first spring that the reservoirs will be used to carry out experiments, launched April 9, to simulate more acidic oceans. Four faculty members, four technicians and two teaching assistants will help the students perform chemical tests, conduct microscope analyses and do simple genetic tests of biological diversity on the seawater.

The reservoirs, called mesocosms, are water enclosures that provide a controllable section of the natural ocean. They allow researchers to conduct studies that are midway between a controlled lab test and an open-ocean experiment.

Jim Murray / UW

Students prepare the frames for the April 9 start of the experiment.

The Friday Harbor structures are 18-foot-tall plastic bags that hang from metal rings. For two days seawater near the dock was coarsely filtered to remove jellyfish and other large pieces of marine life before gradually filling the bags. Each bag holds 3,000 liters (790 gallons), enough water to fill more than 35 bathtubs. Three of the bags stay at the natural acidity, the other six have carbon dioxide pumped inside to increase acidity to the levels projected under climate change.

“This experiment is a way to look at all interactions between the components of the food web, including some of the more complex biological interactions that happen in the real ocean,” Murray said.

The acrylic domes are actually loose covers that prevent seagulls or other debris from landing in the tank.

The UW aquatic mesocosm was modeled after similar structures to study ocean acidification in Bergen, Norway, and Pohang, South Korea. Researchers from both countries are also involved in the experiments this spring at the Friday Harbor facility.

Korean scientists are interested in dimethyl sulfide, the chemical that helps give ocean air its characteristic smell. The concentrations of this gas may differ under climate change, and some scientists believe it plays a role in cloud formation.

“This year’s experiment has gone really smoothly so far, and I think we’re on track to have some interesting results,” Murray said.

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For more information, contact Murray in Friday Harbor at 206-251-5220 or jmurray@uw.edu. Sampling will take place on the dock each day from 8:30-10 a.m. Visitors are welcome.

Francisco Jose Roca Soler

Exuberant mycobacterial growth showing chains of fluorescent microbes in an infected zebrafish larva which had an excess of tumor necrosis factor.

Tumor necrosis factor – normally an infection-fighting substance produced by the body – can actually heighten susceptibility to tuberculosis if its levels are too high.

University of Washington TB researchers unravel this conundrum in a report this week in Cell.

Their study shows how excess production of this disease-cell destroyer at first acts as a TB germ killer. But later the opposite occurs: too much tumor necrosis factor encourages TB pathogens to multiply in the body.

In addition to figuring out some reasons behind this back-pedaling, the scientists learned that certain combinations of drugs already available for other conditions can curtail the shift from anti-TB to pro-TB.

The drug combination revealed in this study, the authors noted, “has the potential to revert some cases of hypersusceptibility to hyperresistance.”

The scientists were Francisco Jose Roca Soler, of the UW Department of Microbiology, and Lalita Ramakrishnan, UW professor of microbiology, medicine and immunology. A recipient of the National Institutes of Health Director’s Pioneer Award, Ramakrishnan is recognized for her work on how the TB pathogen and its hosts’ cells interact to cause disease.

These studies are conducted in zebrafish, an animal model for tuberculosis. The fish’s embryos and small fry are transparent. Researchers can see through their skin to observe their organs, tissues and cells and the internal appearance of some infections, for example, the bacterial cording of TB.

Roca and Ramakrishnan explained that TB had traditionally been thought of as a disease of failed immunity. However, more recent studies from their lab and other labs, both in zebrafish and in humans, have suggested that it also can result from too strong of a defensive inflammatory response.

“While tumor necrosis factor is a critical host defense against tuberculosis,” Roca and Ramakrishnan noted, “an excess of this factor is also implicated in the development of the disease in zebrafish and in humans.”

Variations in a specific location of the zebrafish genome can cause either too much or too little tumor necrosis factor to be produced, depending on the type of variation. In either case, deficiency or overabundance, zebrafish become prone to tuberculosis.

In both cases the scavenger cells, or macrophages, that are trying to clear away the TB pathogens by ingesting them, die and burst open. They are like torn vacuum cleaner bags spilling their dirty contents.

When the TB bacteria escape the confines of the scavenger cells, “they grow exuberantly in the extracellular environment,” Roca and Ramakrishnan said.

Researchers needed to work out the differences between TB susceptibility caused by too high or too low tumor necrosis factors because the distinction is vital to treatment decisions. Only patients whose genetics made them launch a pro-inflammatory response, benefited from steroid treatment, previous studies have shown. Steroids can increase the chance of death among TB patients with a weak inflammatory response.

In the present study, Roca and Ramakrishnan elucidated the molecular pathways by which too much tumor necrosis factor at first rapidly promotes macrophages to go after TB bacteria, and then turns around and forces the hard-working macrophages to die and expel their captives.

They found that both the microbiocidal activity, and the death of the macrophages, resulted from upping the production of reactive oxygen species by the mitochondria inside the macrophages. Mitochondria are the energy-generating power plants of living cells.

Tumor necrosis factor inside of infected macrophages induces reactive oxygen species from the mitochondria. These are the chemicals responsible for cell damage from oxidative stress.

Early on, reactive oxygen species can be beneficial. Initially their presence encourages the macrophages to destroy pathogens. As they accumulate, however, they promote self-harm.

Suddenly the macrophage is programmed to self-destruct. The reactive oxygen species carry out the death sentence by modulating a pathway for a substance called cyclophilin D, which sets the stage for the demolition of mitochondria.

Reactive oxygen species also play a role in acid sphingomyelinase-mediated ceramide production. This waxy substance occurs in cell membranes. One of its many roles is regulating signals for cell death.

The researchers were able to convert the high tumor necrosis factor state to become resistant to tuberculosis. They did so by genetically blockading both cyclophilin D and acid sphingomyelinase in previously susceptible zebrafish.

Similarly, they discovered that the drug combination of alisporivir, a cyclophilin D-inhibiting drug, and desipramine, an antidepressant that inactivates acid sphingomyelinase, also reverses susceptibility to TB in zebrafish prone to tumor necrosis factor excess.

Essentially, the experiments suggest that preventing cell death in TB infected macrophages can prolong their capacity to attack TB pathogens.

A longer-living army of macrophages, filled with the microbiocidal reactive oxygen species, will destroy the TB pathogens inside them and make the host highly resistant to tuberculosis.

Because excessive amounts of tumor necrosis factor are implicated in several inflammatory diseases such as rheumatoid arthritis, ankylosing spondylitis, sarcoidosis, and Crohn’s, the authors noted, “The findings may be useful for understanding diseases in addition to tuberculosis.”

Grants from the National Institutes of Health and the Northwest Research Center of Excellence for Biodefense and Emerging Diseases, and a postdoctoral fellowship from the educational ministry of Spain, funded this research project.

The Cell paper is titled, “Tumor necrosis factor dually mediates resistance and susceptibility to mycobacteria through induction of mitochondrial reactive oxygen species.”

Dean Forbes

Brain surgeon and cancer researcher Eric Holland has been recruited to UW Medicine and Fred Hutchinson Cancer Research Institute. He will arrive this summer.

UW Medicine and the Fred Hutchinson Cancer Research Center have recruited world renowned neurosurgeon and brain cancer researcher Eric Holland to establish world-class research programs on brain and other solid-tumor cancers. He will leave Memorial Sloan-Kettering Cancer Center in New York City and arrive in Seattle this summer.

At UW Medicine, Holland will be a professor of neurological surgery, hold the Chap and Eve Alvord and Elias Alvord Chair in Neuro-oncology, and direct the Nancy and Buster Alvord Brain Tumor Center, established in 2009 to promote, develop and coordinate interdisciplinary brain tumor care and research among physicians and scientists in a variety of fields.

One of Holland’s priorities will be to recruit a team of internationally recognized brain cancer investigators to implement the vision of the late Ellsworth “Buster” Alvord, former head of neuropathology in the UW Department of Pathology and a Seattle philanthropist. Alvord and his family funded five endowed chairs in five different UW Medicine departments to create a multidisciplinary brain cancer research center.

“Eric Holland is exceptionally well qualified to lead the Alvord Brain Tumor Center, and I am confident that he will recruit outstanding researchers and clinicians to establish the Alvord Center as the best in the world,” said Paul G. Ramsey, CEO of UW Medicine and dean of the UW School of Medicine. “Under Dr. Holland’s leadership, we will be able to fulfill the vision for brain cancer research and clinical care established by Buster Alvord when he and his family made their extraordinarily generous commitment to establish the Alvord Center. I am delighted to welcome Eric Holland to UW Medicine.”

At Fred Hutch, where Holland’s research laboratory will be based, he will be senior vice president and director of the Human Biology Division, an interdisciplinary program that encourages collaboration among faculty with a broad range of expertise – from molecular and cellular biology to genetics and clinical research. The division’s structure fosters laboratory, computational and clinical research that yields discoveries which can be rapidly translated into cancer treatments. Holland will oversee the recruitment of new scientists who are at the forefront of solid-tumor translational research in such areas as breast, prostate, gastrointestinal and other cancers.

With advances in genomics increasingly playing an important role in solid-tumor oncology, Holland’s expertise in this area will provide strong leadership to strengthen Seattle’s reputation in translational, solid-tumor research.

“I am thrilled at the prospect of working with the world’s leading experts in genome sciences, computational biology and those involved in the development of novel platforms for delivering innovative therapies to cancer patients,” Holland said. “The highly collaborative, multidisciplinary nature of cancer research at Fred Hutch and UW Medicine provides a solid foundation to build on.”

Now, armed with more sophisticated data from a satellite mission observing the cosmic microwave background – a faint glow in the universe that acts as sort of a fossilized fingerprint of the Big Bang – Cramer has produced new recordings that fill in higher frequencies to create a fuller and richer sound. (The sound files run from 20 seconds to a little longer than 8 minutes.)

The effect is similar to what seismologists describe as a magnitude 9 earthquake causing the entire planet to actually ring. In this case, however, the ringing covered the entire universe – before it grew to such gargantuan proportions.

“Space-time itself is ringing when the universe is sufficiently small,” Cramer said.

European Space Agency/Planck Collaboration

The Planck satellite mission mapped light temperature differences on the oldest surface known — the background sky left billions of years ago when our universe first became transparent to light. Those differences helped to recreate the sound of the Big Bang.

In 2001, Cramer wrote a science-based column for Analog Science Fiction & Fact magazine describing the likely sound of the Big Bang based on cosmic microwave background radiation observations taken from balloon experiments and satellites.

A couple of years later that article prompted a question from a mother in Pennsylvania whose 11-year-old son was working on a project about the Big Bang: Is the sound of the Big Bang actually recorded anywhere?

Cramer answered that it wasn’t – but then began thinking that it could be. He used data from the cosmic microwave background on temperature fluctuations in the very early universe. The data on those wavelength changes were fed into a computer program called Mathematica, which converted them to sound. A 100-second recording represents the sound from about 380,000 years after the Big Bang until until about 760,000 years after the Big Bang.

“The original sound waves were not temperature variations, though, but were real sound waves propagating around the universe,” he said.

Cramer noted, however, that the 2003 data lacked high-frequency structure. More complete data were recently gathered by an international collaboration using the European Space Agency’s Planck satellite mission, which has detectors so sensitive that they can distinguish temperature variations of a few millionths of a degree in the cosmic microwave background. That data were released in late March and led to the new recordings.

As the universe cooled and expanded, it stretched the wavelengths to create “more of a bass instrument,” Cramer said. The sound gets lower as the wavelengths are stretched farther, and at first it gets louder but then gradually fades. The sound was, in fact, so “bass” that he had to boost the frequency 100 septillion times (that’s a 100 followed by 24 more zeroes) just to get the recordings into a range where they can be heard by humans.

Cramer is a UW physics professor who has been part of a large collaboration studying what the universe might have been like moments after the Big Bang by causing collisions between heavy ions such as gold in the Relativistic Heavy Ion Collider at Brookhaven National Laboratory in New York.

Creating a sound profile for the Big Bang was something to do on the side, Cramer said.

“It was an interesting thing to do that I wanted to share. It’s another way to look at the work these people are doing,” he said.

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For more information, contact Cramer at jcramer@uw.edu.