Studying patterns in bacterial organization

credit to Gerard Wong, of the California NanoSystems Institute

Bacterial biofilms, at first glance, may seem to be spontaneous, random phenomena from which we have no power to protect our environment or ourselves.

They’re potentially useful as an aid to wastewater treatment, but they also cause infections that account for $6 billion a year in health care costs. Biofilms are also more resistant to antibiotic drugs, making them difficult to eradicate.

Dr. Kun Zhao, of the California NanoSystems Institute at UCLA, refuses to see biofilms as arbitrary: he emphasizes the fact that biofilms are communities of bacteria in self-produced polymeric matrices of polysaccharides, and using a biophysical approach, he studies the pattern behind their organization.

Central questions in Zhao’s research include how bacterial colonies transition from reversible to irreversible attachment, how they migrate, and how they ultimately disperse. Specifically, Zhao examines the polysaccharide Psl, which poses a positive feedback loop because it is both secreted by moving bacteria and serves as a chemo-attractant for future bacteria movement. The positive feedback creates an inherent pattern, as bacteria are more likely to visit a location they have been to before.

Zhao and colleagues have also discovered that bacterial mutants that cannot produce Psl exhibit more random and uniform movement.

To better quantify bacterial movement,Zhao has created a computer algorithm that shows the full movement history of each individual bacterium on a dish, and that provides a “search engine” allowing researchers to find every bacterium performing specific life cycle activities, like division.

Zhao has postulated a “rich get richer” mechanism for biofilms. He compares bacterial organization to Wall Street because concentrated movement ensures that some cells become extremely enriched. In the future, he hopes to model colloidal structures for biological problems, like the growth of the bacterial cell wall. Zhao currently uses colloids, which in physics are used as models for atomic systems, to observe how shapes affect self-assembly. He also would like to look at cell-substrate interactions, which are implicated in bacterial territoriality and social interactions.

by Olivia Zhu

Source: Duke University

Blue mussels not yet the bellwether of NE coastal environment

Marcy Cockrell installs cages to protect mussels from predators. In Maine, mussels inside cages faired as well as mussels in the wild. In Long Island Sound and Narragansett Bay it was a different story. Credit: Brown University

Ecologists sometimes look to mussel species, a well-studied and foundational genus in estuaries, as model organisms for assessing the condition of coastal habitats, which are crucial for people and well as the broader environment.

But a new study in the journal Ecosphere suggests that the seemingly simple blue mussel, when studied on regional scale from Maine to Connecticut, harbors at least three specific mysteries that must be solved if the mollusks are to serve as the "canaries in the coal mine" of the Northeast coast.

"Mussels could indeed be a good sentinel species for rocky shores, but what our work suggests is that we need to know a lot more about how they behave in these different estuarine settings to use them as an indicator of ecosystem health," said conservation scientist and study senior author Heather Leslie, the Peggy and Henry D. Sharpe Assistant Professor of Environmental Studies.

For the study, Leslie and former students Marcy Cockrell and Joanna Bernhardt monitored and experimented with mussels at 18 sites in the Casco Bay of Maine, the Narragansett Bay of Rhode Island, and the Long Island Sound of Connecticut and New York in 2010 and 2011 (a region spanning about 600 kilometers of coastline). They measured the abundance of mussels both at adult and larval stages, studied the populations of neighboring rocky shore animals and marine algae, and tracked data on ecosystem factors such as water salinity, temperature, nutrients, oxygen, and local human population density. In the experiments, the team protected some mussels with cages to expose the effect that birds, crabs and other predators have on their numbers.

In the end, the research uncovered three intriguing mysteries of mussel life across the region, particularly in Casco Bay:

Generation gaps: Adults were populous but "recruitment" of young mussels from surrounding waters was low in Long Island Sound and Narragansett Bay. The opposite was true in Casco Bay. There, juvenile recruitment was high but adult populations were low. Few Maine predators: The cage experiments showed a significant role for mussel predators in Long Island Sound and Narragansett Bay, but not in Casco Bay. There, unprotected mussels fared about as well as the protected ones. Inner vs. outer: In each estuary, Leslie's team made measurements at sites nestled well within the bay, as well as at sites closer to the open ocean. Prior research suggested that higher levels of food within the bay would promote growth and abundance for the filter-feeding mussels (due to higher levels of nutrients and phytoplankton at the inner estuary sites). The study results were notably mixed across the whole region, however, providing little support for that hypothesis.

Explanations await further research. Genetic studies could determine, for example, whether the young mussels that are so abundant in Casco Bay may be floating up from the more southerly shores. If so, that suggests that mussel population dynamics can only be understood on regional (or multi-estuary) geographic scale.

Meanwhile, understanding why predator activity seems low in Casco Bay might require learning more about the local predator populations there. The findings could shed light on whether the ecosystem is in balance or other factors are at play.

"We did this because we want to understand how these systems work," Leslie said. "Given their accessibility and how well-studied they have been in other locations, rocky shores are logical sentinel ecosystems. They provide an opportunity to investigate how climate change and other more local-scale human activities are affecting New England's coast."

It may take more work to crack open the mussels' mysteries, but the stakes are high enough to make it worthwhile, Leslie said.

Source: Brown University

Why do zebras have stripes?

A mother zebra with a foal in Tanzania’s Tarangire National Park. Credit: Brenda Larison/UCLA

One of nature’s fascinating questions is how zebras got their stripes.

A team of life scientists led by UCLA’s Brenda Larison has found at least part of the answer: The amount and intensity of striping can be best predicted by the temperature of the environment in which zebras live.

In the January cover story of the Royal Society’s online journal, Open Science, the researchers make the case that the association between striping and temperature likely points to multiple benefits — including controlling zebras’ body temperature and protecting them from diseases carried by biting flies.

“While past studies have typically focused their search for single mechanisms, we illustrate in this study how the cause of this extraordinary phenomenon is actually likely much more complex than previously appreciated, with temperature playing an important role,” said Thomas B. Smith, professor of ecology and evolutionary biology in the UCLA College and senior author of the research.

Larison, a researcher in UCLA’s department of ecology and evolutionary biology and the study’s lead author, and her colleagues examined the plains zebra, which is the most common of three zebra species and has a wide variety of stripe patterns. On zebras in warmer climes, the stripes are bold and cover the entire body. On others — particularly those in regions with colder winters such as South Africa and Namibia — the stripes are fewer in number and are lighter and narrower. In some cases, the legs or other body parts have virtually no striping.

Zebras evolved from horses more than 2 million years ago, biologists have found. Scientists have previously hypothesized that zebras’ stripes evolved for one, or a combination of, four main reasons: confusing predators, protecting against disease-carrying insects, controlling body temperature and social cohesion. And while numerous previous studies of the phenomenon focused on a single hypothesis, the Larison-led study was the first to fully test a large set of hypotheses against one another.

Analyzing zebras at 16 locations in Africa and considering more two dozen environmental factors, the researchers found that temperature was the strongest predictor of zebras’ striping. The finding provides the first evidence that controlling body temperature, or thermoregulation, is the main reason for the stripes and the patterns they form.
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Separate research by Daniel Rubenstein, a Princeton University professor of ecology and evolutionary biology and a co-author of the Open Science paper, and Princeton undergraduate Damaris Iriondo strongly suggests that boldly striped zebras have external body temperatures about five degrees Fahrenheit cooler than other animals of the same size — like antelopes — that do not have stripes but live in the same areas. The Rubenstein study is not yet published, but it is cited in the Open Science paper.

Larison has studied many zebras during her field work throughout Africa — including in Kenya, South Africa, Tanzania, Uganda and Zimbabwe. Using the fact that their stripes are unique like fingerprints, she is able to distinguish one zebra from another.

In addition to Rubenstein, arguably the world’s leading expert on zebras, the study’s co-authors were Alec Chan-Golston and Elizabeth Li, former UCLA undergraduates in mathematics; Ryan Harrigan, an assistant adjunct professor in UCLA’s Center for Tropical Research; and Henri Thomassen, a former UCLA postdoctoral scholar and current research associate at the Institute for Evolution and Ecology at Germany’s University of Tübingen.

The research was supported by the National Geographic Society Committee for Research and Exploration.

Larison and her research team have also collected zebra tissue samples and have used cutting-edge technology to sequence zebra DNA to try to identify which genes code for striping. The team is continuing to study the benefits stripes provide.

Source: UCLA

Smelly discovery challenges effectiveness of antimicrobial textiles

University of Alberta textiles scientist Rachel McQueen has found that anti-odor clothing may not be living up to its promise. Credit: University of Alberta

Anti-odour clothing may not be living up to its promise, and an ALES researcher is saying it could all be a matter of how the product was tested.

In two separate experiments, Human Ecology researcher Rachel McQueen and her team found that some antimicrobial textiles were far more effective at performing their advertised tasks in the lab than in testing on humans. In one experiment, the fabrics were designed to help lower the risk of infection; in the second, the fabric was treated with a silver compound, which can be marketed preventing odour in clothing.

"We aren't necessarily seeing the same results in the lab about antimicrobial activity translating into antimicrobial activity when we're wearing them next to our bodies in real life," she said.

The first experiment analyzed the effectiveness of three different textiles coated in antimicrobials triclosan, a zinc pyrithione derivative and a silver chloride-titanium dioxide compound. After putting the fabric on people's arms under plastic film for 24 hours, the silver-chloride titanium dioxide compound hardly eliminated any bacteria. Overall, they found the in vivo -- tested on humans -- results were not comparable with in vitro -- tested in the lab -- results in how they prevented microorganisms from surviving in the textile.

The second test had similar results, and tested whether polyester textiles treated with bioactive concentrations of an antimicrobial silver chloride compound reduced armpit odour and bacterial populations. Although lab testing showed antimicrobial activity, the treated fabrics did not lower odour or bacterial intensity in in vivo testing.

McQueen said that anything from sweat to the proteins in the human body can disrupt the antimicrobial properties of a fabric.

"In reality, when it goes to the point that it gets put on a textile... it may not have the same level of effectiveness as the ones they studied," she said.

McQueen said these findings highlight the importance of in vivo testing, which is less common than in vitro testing, in textile product development. But, because the textiles appear to be effective at reducing bacteria in the lab, she said they may be advertised as being anti-odourous, although they may not necessarily be so when actually worn.

So, for now, McQueen suggests thinking twice before trusting textile's advertised claims.

"It's just a real spectrum to how effective they may truly be. So I'd probably say, from a consumer's point of view, if you're actually buying something that says it's antimicrobial, it may not be," she said. "I think that's important to consider in relation to a lot of claims made about textiles, that is, to be skeptical about the claims marketers make."

McQueen's research was recently published in the International Journal of Clothing Science and Technology.

Source: University of Alberta

Plants return to Earth after growing in space

Astronaut Reid Wiseman injected a fixative solution onto the seedlings. Credit: NASA

Researchers at Simon Gilroy's lab in the Department of Botany at the University of Wisconsin-Madison this afternoon greeted a truck carrying small containers holding more than 1,000 frozen plants that germinated and grew aboard the International Space Station.

On Tuesday, when Gilroy's team inspected the plants at the Kennedy Space Center in Florida, they saw exactly what they wanted: Petri dishes holding seedlings that sprouted and grew in weightlessness.

After their arrival in Madison, the plants went directly into a deep freeze. After being thawed in a few months, they will donate their RNA to an instrument that will measure the activity of all of their approximately 30,000 genes.

Half of the plants will become subjects in Gilroy's longstanding exploration of the genetic control of the proteins that enable plants to grow in zero gravity. "Gravity is a fantastically pervasive force that affects all biology," says Gilroy. "One astronaut observed that plants get lazy in a weightless environment; they grow long and thin, and don't lay down strong material, just like people lose bone mass in space because it isn't needed for supporting weight."

The other half of the experiment represents a departure for Gilroy, and for NASA, the agency supporting this area of space research. After these plants undergo a similar genetic analysis at UW-Madison's Biotech Center, the data will get an initial check-over from Gilroy's group. And then a treasure trove of digital data on plant genetic activity in microgravity will be made available to any researcher interested in mining it.

"Access to space is very rare," Gilroy says. "Traditionally, a research group will put an experiment in space, get the results and publish. But NASA is trying a new mode, called geneLAB, where the research group will put organisms in space, then, as soon as possible, release the raw data to anyone who wants to analyze it. They hope it will speed up major advances on these tiny samples that we can afford to place in space. I see this as open-source science."

Through the process called transcription, genes produce RNA that becomes the template for proteins, and in both sets of experiments, the RNA data will show which genes become more or less active in microgravity, when compared to an identical set of plants grown on Earth.

While Gilroy plans to focus on structural proteins, the geneLAB experiment compares four variants of Arabidopsis called ecotypes. "This data should provide a broad field of investigation -- far more than one lab can handle," Gilroy says. "We are going to end up with an enormous amount of transcription data. We will do some initial work to check the major genes which go up or down, but there's tremendous potential for further analysis by other labs around the world."

But while the geneLab approach sounds promising, Gilroy concedes that it carries no guarantees. "This may be a path forward in crowd-sourcing science. At the least, as a single lab we could never analyze this data as fully as many labs around the world all working with it."

The "Biological Research in Canister" containers that held these experiments on board the space station were designed, tested and operated according to NASA's rigorous approach, Gilroy says. "Each project represents an enormous investment, and you really want everything to go perfectly. You become one of the most careful scientists in the world. You test everything, make duplicates, and are always considering what may go wrong so you can do another test."

NASA is an unfamiliar world to most botanists, but Gilroy seems to be enjoying every step of the way, and has even learned the organization's peculiar parlance. "At first, talking in acronyms is very strange," he says, "and you can't understand anything when NASA people start going into NASA-speak. But once you get into it, you catch yourself doing the exact same thing."

In the microgravity experiments, Gilroy is exploring the genetic basis of a phenomenon known to gardeners and horticulturalists for many years. Plants that grow up without mechanical stresses -- due to wind, rain or other disturbances -- "are much more susceptible to pests, are not as robust," Gilroy says, "but if you go into a greenhouse and shake the plants, they grow up more compact, strong, and resistant to stress. They are even more resistant to plant diseases."

It turns out that the same signaling system used to detect mechanical stresses like gravity is also used to defend against pathogens. That may explain why plants in space appear more susceptible to disease.

That overlap raises the stakes for understanding the impact of gravity on plants beyond the notion of building stronger crops that can stand up in the field. Understanding the signals could help in the never ending battle against plant disease.

Likewise, NASA has its own practical interest in the research: Plants will supply food and oxygen for long-distance space travel, and keeping them healthy will be a matter of life and death. "If you are growing plants as part of a human life support system," Gilroy says, "you'd rather not have them suddenly die."

Source: University of Wisconsin-Madison

Breezy science, plant studies and more head to space station on SpaceX-4

This Artist's rendering of the ISS-RapidScat instrument (inset), will measure ocean surface wind speed and direction and help improve weather forecasts. It will be installed on the end of the station's Columbus laboratory. Credit: NASA/JPL-Caltech/Johnson Space Center

Imagine a dragon flying through the heavens on mighty, outstretched wings. The majestic beast knows the currents of winds and how to harness their power as it soars above the clouds. SpaceX's real Dragon -- the company's spacecraft that transports supplies and science to the International Space Station (ISS) -- will deliver, and later return, new technology, biology and biotechnology and Earth and space science research to the orbiting outpost.

One of the new Earth science investigations heading into orbit is the ISS-Rapid Scatterometer (ISS-RapidScat). ISS-RapidScat monitors ocean winds from the vantage point of the space station. This space-based scatterometer is a remote sensing instrument that uses radar pulses reflected from the ocean's surface at different angles to calculate surface wind speed and direction. This information will be useful for weather forecasting and hurricane monitoring.

"We'll be able to see how wind speed changes with the time of day," said Ernesto Rodríguez, principal investigator for ISS-RapidScat at NASA's Jet Propulsion Laboratory in Pasadena, California. "ISS-RapidScat will link together all previous and current scatterometer missions, providing us with a more complete picture of how ocean winds change. Combined with data from the European ASCAT scatterometer mission, we'll be able to observe 90 percent of Earth's surface at least once a day, and in many places, several times a day."

In addition to improving weather models, RapidScat enhances measurements from other international scatterometers by cross-checking their data. Due to its unique orbit, RapidScat will observe different parts of the planet at different times of day. This allows the instrument to track the effects of the sun on ocean winds as the day progresses. Because the instrument reuses leftover hardware originally built to test parts of the now inoperable NASA QuikScat scatterometer, this investigation demonstrates a unique way to replace an instrument aboard an aging satellite.

New biomedical hardware launching on SpaceX's fourth commercial resupply mission to the space station will facilitate prolonged biological studies in microgravity. The Rodent Research Hardware and Operations Validation (Rodent Research-1) investigation provides a platform for long-duration rodent experiments in space. These experiments examine how microgravity affects animals, providing information relevant to human spaceflight, discoveries in basic biology and knowledge that may have direct impact toward human health on Earth. Rodent Research-1 tests the operational capabilities of the new hardware system, including the transporter, rodent habitat and access unit.

Because rodents experience developmental stages and aging processes more quickly than humans, they make ideal research model organisms to infer information about disease development and progression in humans. Model organisms are non-human species with characteristics that allow them easily to be maintained, reproduced and studied in a laboratory.

"In the coming years, rodent studies conducted aboard the space station will gather foundational data that will help advance human space exploration and provide new opportunities to improve quality of life on Earth," said Ruth Globus, Ph.D., Rodent Research Project scientist and researcher in the Space Biosciences Division at NASA's Ames Research Center in Moffett Field, California.

Another biological research investigation aboard Dragon includes a new plant study. The Biological Research in Canisters (BRIC) hardware has supported a variety of plant growth experiments aboard the space station. The BRIC-19 investigation, the first to collect data for the geneLAB research platform, will focus on the growth and development of Arabidopsis thaliana seedlings in microgravity. A. thaliana is a small flowering plant related to cabbage, and its genetic makeup is simple and well-understood by the plant biology community. This knowledge offers easy recognition of any changes that occur as a result of microgravity adaptation.

Plant development on Earth is impacted by mechanical forces such as wind or a plant's own weight. Researchers hope to get a better understanding of how the growth responses of plants are altered by the absence of these forces when grown in microgravity.

The BRIC hardware helps to maximize research and minimize space and crew time since it does not use power to operate and the canister is the size of a bread box. This study may add to the collective body of knowledge about basic plant growth phenomena and could help improve farming practices on Earth.

In addition to Earth and biological science studies, several new technology demonstrations are making their way to the space station. One of those, known as the Special Purpose Inexpensive Satellite, or SpinSat, will test how a small satellite moves and positions itself in space using new thruster technology. It will launch into orbit from the space station through the new Cyclops small satellite deployer, also known as the Space Station Integrated Kinetic Launcher for Orbital Payload Systems (SSIKLOPS).

SpinSat is a spherical satellite measuring 22 inches in diameter. It will test advanced thruster technology that uses a new class of non-pyrotechnic materials known as Electrically-Controlled Solid Propellants (ESP). ESPs are ignited only by electric current.

Researchers can use high-resolution atmospheric data captured by SpinSat to determine the density of the thermosphere, one of the uppermost layers of the atmosphere. With better knowledge of the thermosphere, engineers and scientists can refine satellite and telecommunications technology.

Another new technology demonstration catching a ride on the Dragon is the 3-D Printing In Zero-G Technology Demonstration (3-D Printing In Zero-G), which will be the first ever 3-D printer in space. Additive manufacturing could enable parts to be manufactured quickly and cheaply in space, instead of waiting for the next cargo resupply vehicle delivery. The research team also can gain valuable insight into improving 3-D printing technology on Earth by demonstrating it in microgravity.

With so many new investigations that directly impact human life, this Dragon's delivery is helping the space station make discoveries off the Earth, for the Earth.

Source: Nasa

Genes tell story of birdsong and human speech

The activity of genes related to singing shows a unique pattern in the brain of an Australian Budgerigar.
Credit: Duke University

His office is filled with all sorts of bird books, but Duke neuroscientist Erich Jarvis didn't become an expert on the avian family tree because of any particular interest in our feathered friends. Rather, it was his fascination with how the human brain understands and reproduces speech that brought him to the birds.

"We've known for many years that the singing behavior of birds is similar to speech in humans -- not identical, but similar -- and that the brain circuitry is similar, too," said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. "But we didn't know whether or not those features were the same because the genes were also the same."

Now scientists do know, and the answer is yes -- birds and humans use essentially the same genes to speak.

After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.

Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

The findings are part of a package of eight scientific papers in a Dec. 12 special issue of Science and 21 additional papers appearing nearly simultaneously in Genome Biology, GigaScience and other journals. Jarvis' name appears on 20 papers and he is a corresponding author for 8 of them.

Jarvis co-led the Avian Phylogenomics Consortium with Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen and M. Thomas P. Gilbert of the Natural History Museum of Denmark. His Duke lab contributed to preparing samples, sequencing and annotating the genomes, performing the analyses and coordinating the overall project.

The Jarvis lab in the Bryan Research Building prepared DNA of many of the species, pulling it from little chunks of frozen, pink bird flesh collected over the past 30 years by museums and other institutions around the world. To ensure the DNA being sequenced really belonged to the Golden-collared manakin and not an undergraduate lab assistant, the lab has been kept spotlessly clean and many of its tools are used only once, to avoid the possibility of subsequent contamination.

"We change gloves a lot," said Carole Parent, the lab research analyst who set up a DNA isolation pipeline for the next stage of the project to sequence still more birds and supervised sample prep with a team of Duke undergrads and a student from East Chapel Hill High School.

All of this meticulous and somewhat tedious work has given Jarvis and hundreds of colleagues around the world a crack at an unprecedented amount of genomic data generated by BGI in China. The whole-genome comparison of the 48 bird species required new algorithms written at the University of Illinois and University of Texas that ran for 400 years of CPU time on three supercomputers in the U.S.

Of the 29 papers covering everything from penguin evolution to color vision, eight are devoted to bird song.

One of the Dec. 12 papers in Science found there is a consistent set of just over 50 genes that show higher or lower activity in the brains of vocal learning birds and humans. These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak, according to this Duke team, which was led by Jarvis; Andreas Pfenning, a graduate of the Ph.D. program in computational biology and bioinformatics (CBB); and Alexander Hartemink, professor of computer science, statistical science and biology.

"This means that vocal learning birds and humans are more similar to each other for these genes in song and speech brain areas than other birds and primates are to them," Jarvis said.

These genes are involved in forming new connections between neurons of the motor cortex and neurons that control the muscles that produce sound.

A companion study by another CBB doctorate, Rui Wang, looked at the specialized activity of a pair of genes involved in the regions of the brain that control song and speech. This study, appearing in the Journal of Comparative Neurology, found that these genes are down- and up-regulated in one brain region of song-learning birds during the juvenile period of their vocal learning , changes that last into adulthood. This study, and that of Pfenning, hypothesize that changes in these genes could be critical for the evolution of song in birds and speech in humans.

"You can find those same genes in the genomes of all species, but they're active at much higher or lower levels in the specialized song or speech brain regions of vocal learning birds and humans," Jarvis said. "What this suggests to me is that when vocal learning evolves, there may be a limited way in which the brain circuits can evolve."

Another paper in Science from Duke, led by post-doc Osceola Whitney, Pfenning, Hartemink and Anne West, an associate professor of neurobiology, looked at gene activation in different areas of the brain during singing. This team found activation of 10 percent of the expressed genome during singing, with diverse activation patterns in different song-learning regions of the brain. The diverse gene patterns are best explained by epigenetic differences in the genomes of the different brain regions, meaning that individual cells in different brain regions can regulate genes at a moment's notice when the birds sing.

Among the three main groups of vocal learning birds, parrots are clearly different in their ability to mimic human speech. Mukta Chakraborty, a postdoc in the Jarvis lab, led a project that used the activity of some of the specialized genes to discover that the parrot's speech center is organized somewhat differently. It has what the researchers call a "song-system-within-a-song-system" in which the area of the brain with different gene activity for producing song has an outer ring of still more differences in gene expression.

Parrots are very social animals, Chakraborty said, and having the ability to quickly pick up "dialects" of parrot speech may account for their super-charged speech center. The "shell" or outer regions were found to be proportionally larger in the parrot species, which are believed to have the highest vocal, cognitive and social abilities. These species include Amazon parrots, the African Grey and the Blue and Gold Macaw.

Jarvis was also part of a team with Claudio Mello and his Ph.D. student Morgan Wirthlin at Oregon Health & Science University that found ten more genes that are unique to song-control regions of songbirds. This paper appears in BMC Genomics.

A paper in Science led by Zhang, Gilbert and Jarvis found the genomes of vocal learners are more rapidly evolving and have more chromosomal rearrangements compared to other bird species. This genomic comparison also found similar changes occurred independently in in the song-learning area of different birds' brains.

Jarvis said knowing more of this history of how speech evolved in birds makes vocal learning birds even more valuable model organisms for helping to answer the questions he and other researchers are addressing about human speech.

"Speech is difficult to study in human brains," he said. "Whales and elephants learn speech and songs, but they're too big to house in the lab. Now that we have a deeper understanding of how similar birdsong brain regions are to human speech regions at the genetic level, I think they'll be a better model than ever."

Jarvis' general exploration of the bird brain over his 16 years at Duke has also led to several unexpected discoveries unrelated to song.

In 2005, he and colleagues found a center of the brain in migratory birds that apparently enables sensing of magnetic fields through "night vision." That year he also led a revision of the understanding of bird brain organization and vertebrate brain evolution. Last year, he led a re-drawing of the geography of the bird brain based on analysis of 52 genes that are active in 23 areas of the brains of eight species of birds. This new map shows neuron groupings in the birds' brains to be organized in columns like the brains of humans and other mammals.

He also branched out a bit and learned about the brain structures that enable mice to "sing" in ultrasonic ranges beyond human hearing.

Jarvis said this first wave of findings from the Avian Phylogenomics Consortium is just the beginning of an exciting new era of genomic analysis. The international group is already sequencing more birds at the whole-genome level.

"This is an exciting moment," said Jarvis, who is also a member of the Duke Institute for Brain Sciences. "Lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution."

Source: Duke University

John Lennon commemorated by naming a new tarantula species from South America after him

A newly described tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon, a founder member of the legendary band the Beatles. Credit: Doi: 10.3897/zookeys.448.7920, Image courtesy of Pensoft Publishers

A newly described tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon, a founder member of the legendary band the Beatles. The new species is part of the tarantula family Theraphosidae which comprises the largest spider species in the world. The study was published in the open access journal ZooKeys.

The name of the new species came across when the authors of the study Fernando Pérez-Miles, from the University of the Republic, Uruguay, and Alexandre Bonaldo and Laura Miglio, both from the Museu Paraense Emilio Goeldi, Brazil, found out that they are all great fans of the Beatles music.

The genus, Bumba, which is proposed as replacement of the old one Maraca, already taken and used for Orthoptera, also has a story behind the choice of name. The new name is taken from Brazilian theatrical folk tradition of the popular festival called Boi-bumbá (hit my bull), which takes place annually in North and Northeastern Brazil.

The new species, as other tarantulas, has defensive urticating hairs on the abdomen which produce irritation upon contact with the skin or sensible tissues.

The specimens used in the study were captured manually or in traps during the night in Caxiuaná, Pará, Brasil, which suggest they could be mainly nocturnal animals.

Source: Pensoft Publishers

Female frogs modify offspring development depending on reproduction date

Breeding male of Rana arvalis from the study area. Credit: Germán Orizaola

Global warming is altering the reproduction of plants and animals, notably accelerating the date when reproduction and other life processes occur. A study by the University of Uppsala (Sweden), including the participation of Spanish researcher Germán Orizaola, has discovered that some amphibians are capable of making their offspring grow at a faster rate if they have been born later due to the climate.

Over recent decades many organisms, both plants and animals, have experienced a notable advance in the date when many of their life processes (like reproduction, migration or flowering) occur, attributed to the impact of climate change. An article published in the journal Ecology examines the effects that these changes in the reproduction date have on the life cycles of the amphibians.

"We specifically examined whether changes in the reproduction date of a common amphibian species in the north of Europe, Rana arvalis, can condition the growth and development of their offspring," the Spanish researcher Germán Orizaola, from the University of Uppsala (Sweden) and co-author of the study, said.

Results revealed that female frogs have the ability to influence both the growth rate and the development of their offspring, and they adjust it depending on the date of reproduction.

According to Orizaola, "the mechanism by which the female frogs can condition the growth of their larvae could be due to the genes associated with the maintenance of their biological clock being transferred to the embryos and becoming active even before fertilisation. This would provide the larvae with the exact information regarding the progression of the growing season."

The later the birth, the faster the growth

One of the characteristics associated with climate change is an increase in the interannual variability of climatic conditions, so organisms are also exposed to greater uncertainty when it comes to determining the right time to reproduce. This explains why the existence of mechanisms adjusting growth and development rates depending on the variation in the start of breeding is highly advantageous for many species.

In particular, as part of this study they observed that by delaying the date of reproduction (which simulated a time of environmental instability), the result was an equivalent reduction in the growth period for the larvae. "That means the later this species of frog breeds, the faster the larvae develop," explains the scientist.

An interesting aspect of the study is that the acceleration in growth is produced under constant lab conditions. "The larvae were not exposed to any outside sign that would indicate the progression of the growing season," adds Orizaola.

"This result is very novel and demonstrates that the acceleration in the development of the larvae is conditioned by the breeding females, which reveals the existence of a 'transgenerational effect' in which the breeding adults are capable of altering key aspects of the life cycle for the following generations, to better prepare them to survive the environmental conditions that they are going to experience," concludes the expert.

Source: Plataforma SINC.

Global consumption an increasingly significant driver of tropical deforestation

The EU and China are the largest importers of carbon dioxide emissions linked to deforestation for the production of beef, soy, palm oil and timber between 2000-2009. The researchers have focused on seven countries (Argentina, Bolivia, Brazil, Paraguay, Indonesia, Malaysia and Papua New Guinea), all of which are major exporters of goods that contribute to deforestation. Credit: Center for Global Development

International trade with agricultural and wood products is an increasingly important driver of tropical deforestation. More than a third of recent deforestation can be tied to production of beef, soy, palm oil and timber. "The trend is clear, the drivers of deforestation have been globalized and commercialized," says assistant professor Martin Persson, Chalmers University of Technology.

In a report commissioned by US think-tank Center for Global Development (CGD) Martin Persson and colleagues in Linköping, Sweden, and Vienna, Austria, have investigated to which extent international trade in agricultural and silvicultural products drives deforestation in seven case countries: Argentina, Bolivia, Brazil, Paraguay, Indonesia, Malaysia and Papua New Guinea.

"From having been caused mainly by smallholders and production for local markets, an increasing share of deforestation today is driven by large-scale agricultural production for international markets. More than a third of global deforestation can be tied to rising production of beef, soy, palm oil and wood products," says Martin Persson.

"If we exclude Brazilian beef production, which is mainly destined for domestic markets, more than half of deforestation in our case countries is driven by international demand."

The research group has also analyzed the magnitude of the associated carbon dioxide emissions embodied in these trade flows. In total 1.7 billion tons of carbon dioxide emissions can be linked to the production of the analyzed commodities, with one third being embodied in commodity exports. The biggest recipients of these embodied carbon emissions are China and the EU. By elucidating the links between consumption and environmental impacts, the aim is to identify more effective measures to address tropical forest loss by targeting key commodities and countries.

"Another key trend is that more and more corporations have pledged to rid their supply chains from deforestation. Pushed by environmental organizations and seeing the risks of being associated with environmental destruction, companies like Unilever and McDonalds are pressuring their suppliers to stop expanding production on forest land," says Martin Persson.

It is no longer enough to just focus on the countries where deforestation happens and the potential policy measures available there, he adds.

"Today both public and private consumers, be it individuals or corporations, have the possibility to contribute to the protection of tropical forests by holding suppliers accountable for the environmental impacts of their production," Martin Persson concludes.

Source: Chalmers University of Technology

Cats and humans have shared the same households for at least 9,000 years, but we still know very little about how our feline friends became domesticated.

The scientists fitted GPS collars and motion sensors on 38 free-ranging lynx for the study. Credit: Image courtesy of Albert-Ludwigs-Universität Freiburg

An international research team recorded and analyzed the activity patterns of 38 wild cats over the course of months Whether a lynx hunts by day or by night and how active it is overall depend primarily on the behavior of the wild cat's most important prey and its individual traits -- lighting conditions, on the other hand, do not play a major role in its basic behavioral patterns. This is the key finding of a study published in the journal PLOS ONE by an international research team led by forest scientist Dr. Marco Heurich.

The scientists fitted GPS collars and motion sensors on 38 free-ranging lynx for the study. Since the study sites were located across a wide latitudinal range from Central Europe to northern Scandinavia, the length of days and nights varied greatly between them. The team recorded and analyzed the activity patterns of the wild cats on a total of more than 11,000 days. The results reveal that lynx in more southerly regions are most active at dawn and dusk and that they move more by night than by day. They take their longest break in the middle of the day, and this break is extended as daylight duration increases. However, the cats exhibit this basic behavioral pattern independently of lighting conditions: "Lynx keep to a 24-hour rhythm with an active and a resting phase even on the polar day and the polar night," reports Heurich.

What the study found to be more important for explaining the wild cats' activity patterns are their individual traits: Young lynx are more active than adult lynx, and male adults are more active than female adults. In addition, they move more in spring and summer than in fall and winter, and the farther north they live, the larger the territory they cover -- and this of course results in higher activity. Lynx adapt their hunting schedule to the behavior of their prey. In polar regions, the height of their activity at dusk is less pronounced. 

This corresponds to the behavioral pattern of reindeer, which exhibit a steady movement profile outside of their sleeping phases.. In Central Europe, by contrast, the team found a maximum amount of activity at dusk -- in lynx as well as in deer. "The findings of this study make an important contribution to our understanding of the habits of predatory animals in our landscape," says Heurich. "They also show that human activities in the areas included in the study do not have a general influence on the activity pattern of the animals."

Study of mountain lion energetics shows the power of the pounce

The SMART wildlife collar is equipped with GPS, accelerometers, and a magnetometer to provide detailed data on where the animal is and what it is doing.

Scientists at UC Santa Cruz, using a new wildlife tracking collar they developed, were able to continuously monitor the movements of mountain lions in the wild and determine how much energy the big cats use to stalk, pounce, and overpower their prey.

The research team's findings, published October 3 in Science, help explain why most cats use a "stalk and pounce" hunting strategy. The new "SMART" wildlife collar--equipped with GPS, accelerometers, and other high-tech features--tells researchers not just where an animal is but what it is doing and how much its activities "cost" in terms of energy expenditure.

"What's really exciting is that we can now say, here's the cost of being a mountain lion in the wild and what they need in terms of calories to live in this environment," said first author Terrie Williams, a professor of ecology and evolutionary biology at UC Santa Cruz. "Understanding the energetics of wild animals moving in complex environments is valuable information for developing better wildlife management plans."

The researchers were able to quantify, for example, the high energetic costs of traveling over rugged terrain compared to the low cost of "cryptic" hunting behaviors such as sit-and-wait or stalk-and-ambush movements. During the actual pounce and kill, the cats invest a lot of energy in a short time to overpower their prey. Data from the collars showed that mountain lions adjust the amount of energy they put into the initial pounce to account for the size of their prey.

"They know how big a pounce they need to bring down prey that are much bigger than themselves, like a full-grown buck, and they'll use a much smaller pounce for a fawn," Williams said.

Cats on treadmills

Before Williams and her team could interpret the data from collars deployed on wild mountain lions, however, they first had to perform calibration studies with mountain lions in captivity. This meant, among other things, training mountain lions to walk and run on a treadmill and measuring their oxygen consumption at different activity levels. Those studies took a bit longer than planned.

"People just didn't believe you could get a mountain lion on a treadmill, and it took me three years to find a facility that was willing to try," Williams said.

Finally, she met Lisa Wolfe, a veterinarian with Colorado Parks and Wildlife, who had three captive mountain lions (siblings whose mother had been killed by a hunter) at a research facility near Fort Collins, Colorado. After eight months of training by Wolfe, the mountain lions were comfortable on the treadmill and Williams started collecting data.

Power animals

According to Williams, the treadmill data showed that mountain lions do not have the aerobic capacity for sustained, high-energy activity. "They are power animals. They have a slow routine walking speed and use a burst of speed and the force of the pounce to knock down or overpower their prey," she said.

In addition to the treadmill studies, the captive cats were videotaped wearing the collars while doing a wide range of activities in a large outdoor enclosure. This provided a library of collar acceleration signatures specific for different behaviors, from resting and grooming to running and pouncing. "We got all the different behaviors videotaped and analyzed with the corresponding accelerometer traces," Williams said.

Meanwhile, coauthor Chris Wilmers led a team that deployed the collars on wild cats in the Santa Cruz mountains. Wilmers, an associate professor of environmental studies at UC Santa Cruz, leads the Santa Cruz Puma Project, which has been tracking mountain lions in the area to study the effects of habitat fragmentation and developing new technology for understanding the animals' behavior and energetics.

"Because mountain lions are a cryptic animal, we can't really observe them hunting and killing prey. With the SMART collars, we can see how they go about doing that, what their strategies are, and how many calories they are expending to do it," Wilmers said. "The ability to estimate the field energetics of animals in the wild opens up a whole new suite of questions we can ask about the ecology of these animals, which ultimately informs not only our basic understanding of them but also their conservation and management."

State-of-the-art collars

Coauthor Gabriel Elkaim, professor of computer engineering at UCSC's Baskin School of Engineering, worked on signal processing of the accelerometer data and is continuing to develop the state-of-the-art tracking collars. The prototype used in this study, called the Species Movement, Acceleration, and Radio Tracking (SMART) wildlife collar, was developed by computer engineering graduate student Matthew Rutishauser. The collars include a GPS unit, accelerometers, and a magnetometer to provide detailed data on where an animal is and what it is doing. "We hope this will be an enabling technology to allow a much greater depth of understanding of animals in the wild," Elkaim said.

The researchers now want to look at mountain lion energetics in a range of different habitat types. In particular, Wilmers said, he is interested in how human land use and habitat fragmentation may be influencing the energetic demands on mountain lions in the wild. Williams and her students also have projects using the new collar technology to study other large carnivores, including wolves, polar bears, and Weddell seals.

"A lot of these large carnivore species are threatened or endangered, and understanding their physiological limitations has been a big missing piece in conservation planning," Williams said. "This technology gives us a whole new level understanding of what these animals are doing and what it costs them to live in the wild, and that can really help move the science of conservation forward."

In addition to Williams, Wilmers, Wolfe, and Elkaim, the coauthors of the paper include Tracy Davis at Colorado Parks and Wildlife; program manager Traci Kendall and head trainer Beau Richter in Williams's lab at UC Santa Cruz; and UCSC graduate students Yiwei Wang and Caleb Bryce. This research was funded by the National Science Foundation.

Source: University of California - Santa Cruz

Hunter-gatherer past shows our fragile bones result from inactivity since invention of farming

Hunter-gatherer bone mass compared to agriculturalist bone mass. Credit: Timothy Ryan

New research across thousands of years of human evolution shows that our skeletons have become much lighter and more fragile since the invention of agriculture -- a result of our increasingly sedentary lifestyles as we shifted from foraging to farming.

The new study, published today in the journal PNAS, shows that, while human hunter-gatherers from around 7,000 years ago had bones comparable in strength to modern orangutans, farmers from the same area over 6,000 years later had significantly lighter and weaker bones that would have been more susceptible to breaking.

Bone mass was around 20% higher in the foragers -- the equivalent to what an average person would lose after three months of weightlessness in space.

After ruling out diet differences and changes in body size as possible causes, researchers have concluded that reductions in physical activity are the root cause of degradation in human bone strength across millennia. It is a trend that is reaching dangerous levels, they say, as people do less with their bodies today than ever before.

Researchers believe the findings support the idea that exercise rather than diet is the key to preventing heightened fracture risk and conditions such as osteoporosis in later life: more exercise in early life results in a higher peak of bone strength around the age of 30, meaning the inevitable weakening of bones with age is less detrimental.

There is, in fact, no anatomical reason why a person born today could not achieve the bone strength of an orangutan or early human forager, say researchers; but even the most physically active people alive are unlikely to be loading bones with enough frequent and intense stress to allow for the increased bone strength seen in the 'peak point' of traditional hunter-gatherers and non-human primate bones.

"Contemporary humans live in a cultural and technological milieu incompatible with our evolutionary adaptations. There's seven million years of hominid evolution geared towards action and physical activity for survival, but it's only in the last say 50 to 100 years that we've been so sedentary -- dangerously so," said co-author Dr Colin Shaw from the University of Cambridge's Phenotypic Adaptability, Variation and Evolution (PAVE) Research Group.

"Sitting in a car or in front of a desk is not what we have evolved to do."

The researchers x-rayed samples of human femur bones from the archaeological record, along with femora from other primate species, focusing on the inside of the femoral head: the ball at the top of the femur which fits into the pelvis to form the hip joint, one of the most load-bearing bone connections in the body.

Two types of tissue form bone: the cortical or 'hard' bone shell coating the outside, and the trabecular or 'spongy' bone: the honeycomb-like mesh encased within cortical shell that allows flexibility but is also vulnerable to fracture.

The researchers analysed the trabecular bone from the femoral head of four distinct archaeological human populations representing mobile hunter-gatherers and sedentary agriculturalists, all found in the same area of the US state of Illinois (and likely to be genetically similar as a consequence).

The trabecular structure is very similar in all populations, with one notable exception: within the mesh, hunter-gatherers have a much higher amount of actual bone relative to air.

"Trabecular bone has much greater plasticity than other bone, changing shape and direction depending on the loads imposed on it; it can change structure from being pin or rod-like to much thicker, almost plate-like. In the hunter-gatherer bones, everything was thickened," said Shaw.

This thickening is the result of constant loading on the bone from physical activity as hunter-gatherers roamed the landscape seeking sustenance. This fierce exertion would result in minor damage that caused the bone mesh to grow back ever stronger and thicker throughout life -- building to a 'peak point' of bone strength which counter-balanced the deterioration of bones with age.

Shaw believes there are valuable lessons to be learnt from the skeletons of our prehistoric predecessors. "You can absolutely morph even your bones so that they deal with stress and strain more effectively. Hip fractures, for example, don't have to happen simply because you get older if you build your bone strength up earlier in life, so that as you age it never drops below that level where fractures can easily occur."

Other theories for humans evolving a lighter, more fragile skeleton include changes in diet or selection for a more efficient, lighter skeleton, which was never reversed.

While the initial switch to farming did cause a dip in human health due to monoculture diets that lacked variety, the populations tested were unaffected by this window in history. "Of course we need a level of calcium to maintain bone heath, but beyond that level excess calcium isn't necessary," said Shaw.

The research also counters the theory that, at some point in human evolution, our bones just became lighter -- perhaps because there wasn't enough food to support a denser skeleton. "If that was true, human skeletons would be entirely distinct from other living primates. We've shown that hunter-gatherers fall right in line with primates of a similar body size. Modern human skeletons are not systemically fragile; we are not constrained by our anatomy."

"The fact is, we're human, we can be as strong as an orangutan -- we're just not, because we are not challenging our bones with enough loading, predisposing us to have weaker bones so that, as we age, situations arise where bones are breaking when, previously, they would not have" Shaw said.

While the 7,000-year-old foragers had vastly stronger bones than the 700-year-old farmers, Shaw says that neither competes with even earlier hominids from around 150,000 years ago. 

"Something is going on in the distant past to create bone strength that outguns anything in the last 10,000 years."

The next step for Shaw's research team will be to look at how different types of loading and mobility shape bodies and bones by cross-referencing archaeological records with testing on modern ultra-marathon runners, who cover punishing distances over a range of terrains -- from the Himalayas to the Namibian desert. He hopes this future work will provide insight into the kind of mobility that gave our ancient ancestors such powerful physical strength.

Source: University of Cambridge