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  • richardmitnick 5:10 pm on November 20, 2014 Permalink | Reply
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    From Caltech: “Caltech Geologists Discover Ancient Buried Canyon in South Tibet” 

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    Caltech

    11/20/2014
    Kimm Fesenmaier

    A team of researchers from Caltech and the China Earthquake Administration has discovered an ancient, deep canyon buried along the Yarlung Tsangpo River in south Tibet, north of the eastern end of the Himalayas. The geologists say that the ancient canyon—thousands of feet deep in places—effectively rules out a popular model used to explain how the massive and picturesque gorges of the Himalayas became so steep, so fast.

    h
    The general location of the Himalayan range

    v
    This photo shows the Yarlung Tsangpo Valley close to the Tsangpo Gorge, where it is rather narrow and underlain by only about 250 meters of sediments. The mountains in the upper left corner belong to the Namche Barwa massif. Previously, scientists had suspected that the debris deposited by a glacier in the foreground was responsible for the formation of the steep Tsangpo Gorge—the new discoveries falsify this hypothesis. Credit: Ping Wang

    r
    The wide valley floor of the Nyang River, a tributary of the Yarlung Tsangpo. Here, the valley floor of the paleocanyon lies at a depth of about 800 meters below the present-day river.
    Credit: Ping Wang

    g
    This Google Earth image looks down the Yarlung Tsangpo Valley towards the Namche Barwa (right) and Gyala Peri massifs (left). The confluence with the Nyang River (joining from the right) is shown in the foreground. Here, the valley floor is about 4 kilometers wide and the paleocanyon lies about 800-900 meters below the present-day river.
    Credit: Map data: Google, Mapabc.com, DigitalGlobe, and Cnes/Spot Image

    “I was extremely surprised when my colleagues, Jing Liu-Zeng and Dirk Scherler, showed me the evidence for this canyon in southern Tibet,” says Jean-Philippe Avouac, the Earle C. Anthony Professor of Geology at Caltech. “When I first saw the data, I said, ‘Wow!’ It was amazing to see that the river once cut quite deeply into the Tibetan Plateau because it does not today. That was a big discovery, in my opinion.”

    Geologists like Avouac and his colleagues, who are interested in tectonics—the study of the earth’s surface and the way it changes—can use tools such as GPS and seismology to study crustal deformation that is taking place today. But if they are interested in studying changes that occurred millions of years ago, such tools are not useful because the activity has already happened. In those cases, rivers become a main source of information because they leave behind geomorphic signatures that geologists can interrogate to learn about the way those rivers once interacted with the land—helping them to pin down when the land changed and by how much, for example.

    t
    World plate tectonics

    “In tectonics, we are always trying to use rivers to say something about uplift,” Avouac says. “In this case, we used a paleocanyon that was carved by a river. It’s a nice example where by recovering the geometry of the bottom of the canyon, we were able to say how much the range has moved up and when it started moving.”

    The team reports its findings in the current issue of Science.

    Last year, civil engineers from the China Earthquake Administration collected cores by drilling into the valley floor at five locations along the Yarlung Tsangpo River. Shortly after, former Caltech graduate student Jing Liu-Zeng, who now works for that administration, returned to Caltech as a visiting associate and shared the core data with Avouac and Dirk Scherler, then a postdoc in Avouac’s group. Scherler had previously worked in the far western Himalayas, where the Indus River has cut deeply into the Tibetan Plateau, and immediately recognized that the new data suggested the presence of a paleocanyon.

    Liu-Zeng and Scherler analyzed the core data and found that at several locations there were sedimentary conglomerates, rounded gravel and larger rocks cemented together, that are associated with flowing rivers, until a depth of 800 meters or so, at which point the record clearly indicated bedrock. This suggested that the river once carved deeply into the plateau.

    To establish when the river switched from incising bedrock to depositing sediments, they measured two isotopes, beryllium-10 and aluminum-26, in the lowest sediment layer. The isotopes are produced when rocks and sediment are exposed to cosmic rays at the surface and decay at different rates once buried, and so allowed the geologists to determine that the paleocanyon started to fill with sediment about 2.5 million years ago.

    The researchers’ reconstruction of the former valley floor showed that the slope of the river once increased gradually from the Gangetic Plain to the Tibetan Plateau, with no sudden changes, or knickpoints. Today, the river, like most others in the area, has a steep knickpoint where it meets the Himalayas, at a place known as the Namche Barwa massif. There, the uplift of the mountains is extremely rapid (on the order of 1 centimeter per year, whereas in other areas 5 millimeters per year is more typical) and the river drops by 2 kilometers in elevation as it flows through the famous Tsangpo Gorge, known by some as the Yarlung Tsangpo Grand Canyon because it is so deep and long.

    Combining the depth and age of the paleocanyon with the geometry of the valley, the geologists surmised that the river existed in this location prior to about 3 million years ago, but at that time, it was not affected by the Himalayas. However, as the Indian and Eurasian plates continued to collide and the mountain range pushed northward, it began impinging on the river. Suddenly, about 2.5 million years ago, a rapidly uplifting section of the mountain range got in the river’s way, damming it, and the canyon subsequently filled with sediment.

    “This is the time when the Namche Barwa massif started to rise, and the gorge developed,” says Scherler, one of two lead authors on the paper and now at the GFZ German Research Center for Geosciences in Potsdam, Germany.

    That picture of the river and the Tibetan Plateau, which involves the river incising deeply into the plateau millions of years ago, differs quite a bit from the typically accepted geologic vision. Typically, geologists believe that when rivers start to incise into a plateau, they eat at the edges, slowly making their way into the plateau over time. However, the rivers flowing across the Himalayas all have strong knickpoints and have not incised much at all into the Tibetan Plateau. Therefore, the thought has been that the rapid uplift of the Himalayas has pushed the rivers back, effectively pinning them, so that they have not been able to make their way into the plateau. But that explanation does not work with the newly discovered paleocanyon.

    The team’s new hypothesis also rules out a model that has been around for about 15 years, called tectonic aneurysm, which suggests that the rapid uplift seen at the Namche Barwa massif was triggered by intense river incision. In tectonic aneurysm, a river cuts down through the earth’s crust so fast that it causes the crust to heat up, making a nearby mountain range weaker and facilitating uplift.

    The model is popular among geologists, and indeed Avouac himself published a modeling paper in 1996 that showed the viability of the mechanism. “But now we have discovered that the river was able to cut into the plateau way before the uplift happened,” Avouac says, “and this shows that the tectonic aneurysm model was actually not at work here. The rapid uplift is not a response to river incision.”

    The other lead author on the paper, Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet, is Ping Wang of the State Key Laboratory of Earthquake Dynamics, in Beijing, China. Additional authors include Jürgen Mey, of the University of Potsdam, in Germany; and Yunda Zhang and Dingguo Shi of the Chengdu Engineering Corporation, in China. The work was supported by the National Natural Science Foundation of China, the State Key Laboratory for Earthquake Dynamics, and the Alexander von Humboldt Foundation.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 7:55 am on November 11, 2014 Permalink | Reply
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    From livescience: “Robot Gliders See How Antarctic Ice Melts From Below” 

    Livescience

    November 10, 2014
    Becky Oskin

    Scientists suspect Antarctica’s shrinking glaciers are melting from the bottom up, and a fleet of robot ocean gliders may help explain why.

    Beneath the icy Weddell Sea in West Antarctica, the gliders discovered turbulent warm currents near ice shelves, the huge floating platforms where continental glaciers extend icy tongues into the sea. The swirling eddies carry pulses of warm water to the shallow depths underneath the ice, scientists report today (Nov. 10) in the journal Nature Geoscience.

    boat
    The research ship James Clark Ross in the Weddell Sea, January 2012.
    Credit: Andrew Thompson/Caltech

    “What we’re looking at is delivery of heat right up to the ice shelf, where the ocean touches up against the ice,” said lead study author Andrew Thompson, a physical oceanographer at Caltech. “It’s almost like a blob of warm water, a little ocean storm.” [Album: Stunning Photos of Antarctic Ice]

    Previous work already pointed to warm water — rather than hotter air temperatures — as the reason for Antarctica’s retreating ice shelves. (The disappearing ice is part of the continental ice sheet, not the sea ice that freezes and melts each year.) But to confirm these suspicions, the researchers needed to get under the ice to see how the process works.

    In 2012, Thompson and colleagues from the University of East Anglia, in the United Kingdom, used remotely operated gliders to probe the ocean conditions near ice shelves in the Weddell Sea. The gliders rise and sink without propellers, relying instead on a battery-driven pump that changes their buoyancy via a fluid-filled bladder. Every few hours, the six-foot-long (1.8 meters) glider surfaces and uploads its data via a satellite phone network. The gliders collected temperature and salinity data for two months, exploring the upper 0.6 miles (1 kilometer) of the ocean.

    When the gliders hit an eddy, the sleek yellow robots were often caught up in the powerful vortices. “You could almost know by where it came up that it had hit this anomalous region,” Thompson told Live Science. “The glider would go down and end up in a quite different place.”

    shelf
    An illustration showing how warm ocean currents circulate beneath Antarctica’s floating ice shelves. The continental shelf and slope are brown and the glacier is white.
    Credit: Andrew Thompson/Caltech and Lance Hayashida/Caltech Marketing & Communications

    The findings are the first to explain how warm water rises from deeper levels to reach the floating ice shelves. The results suggest the stormlike currents bring up pulses of warm water, which flow under the ice at irregular intervals. Now, researchers need to find out what happens when this heat reaches the grounding line, the spot where glaciers transfer their weight from the continent to the ocean. This is where most of the melting takes place, Thompson said.

    “What we’re seeing from the gliders is that it’s not a steady circulation in and out,” Thompson said. “This is really the first step of understanding of what heat goes in, and how efficient that heat is in melting the ice shelves.”

    Alternating layers of cold and warm water surround Antarctica, and it only takes a few degrees of difference to dissolve a glacier. The warmer water is typically in the middle layer of the ocean. It arrives from the north, delivered on a giant current called the global conveyor belt. Colder water lies on the surface, often formed when cold wind blows over the ocean and sea ice freezes up. Dense, cold water is also on the ocean bottom.

    See the full article here.

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  • richardmitnick 1:09 pm on November 10, 2014 Permalink | Reply
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    From Caltech: “Heat Transfer Sets the Noise Floor for Ultrasensitive Electronics” 

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    Caltech

    11/10/2014
    Ker Than

    A team of engineers and scientists has identified a source of electronic noise that could affect the functioning of instruments operating at very low temperatures, such as devices used in radio telescopes and advanced physics experiments.

    The findings, detailed in the November 10 issue of the journal Nature Materials, could have implications for the future design of transistors and other electronic components.

    The electronic noise the team identified is related to the temperature of the electrons in a given device, which in turn is governed by heat transfer due to packets of vibrational energy, called phonons, that are present in all crystals. “A phonon is similar to a photon, which is a discrete packet of light,” says Austin Minnich, an assistant professor of mechanical engineering and applied physics in Caltech’s Division of Engineering and Applied Science and corresponding author of the new paper. “In many crystals, from ordinary table salt to the indium phosphide crystals used to make transistors, heat is carried mostly by phonons.”

    ph
    Cross-sectional image of ultra-low noise InP transistor. Electrons, accelerated in the high mobility channel under the 100-nanometer gate, collide and dissipate heat that fundamentally limits the noise performance of the transistor.
    Credit: Illustration courtesy of Lisa Kinnerud and Moa Carlsson, Krantz NanoArt/Chalmers University

    Phonons are important for electronics because they help carry away the thermal energy that is injected into devices in the form of electrons. How swiftly and efficiently phonons ferry away heat is partly dependent on the temperature at which the device is operated: at high temperatures, phonons collide with one another and with imperfections in the crystal in a phenomenon called scattering, and this creates phonon traffic jams that result in a temperature rise.

    One way that engineers have traditionally reduced phonon scattering is to use high-quality materials that contain as few defects as possible. “The fewer defects you have, the fewer ‘road blocks’ there are for the moving phonons,” Minnich says.

    A more common solution, however, is to operate electronics in extremely cold conditions because scattering drops off dramatically when the temperature dips below about 50 kelvins, or about –370 degrees Fahrenheit. “As a result, the main strategy for reducing noise is to operate the devices at colder and colder temperatures,” Minnich says.

    But the new findings by Minnich’s team suggest that while this strategy is effective, another phonon transfer mechanism comes into play at extremely low temperatures and severely restricts the heat transfer away from a device.

    Using a combination of computer simulations and real-world experiments, Minnich and his team showed that at around 20 kelvins, or –424 degrees Fahrenheit, the high-energy phonons that are most efficient at transporting heat away quickly are unlikely to be present in a crystal. “At 20 kelvins, many phonon modes become deactivated, and the crystal has only low-energy phonons that don’t have enough energy to carry away the heat,” Minnich says. “As a result, the transistor heats up until the temperature has increased enough that high-energy phonons become available again.”

    As an analogy, Minnich says to imagine an object that is heated until it is white hot. “When something is white hot, the full spectrum of photons, from red to blue, contribute to the heat transfer, and we know from everyday experience that something white hot is extremely hot,” he says. “When something is not as hot it glows red, and in this case heat is only carried by red photons with low energy. The physics for phonons is exactly the same—even the equations are the same.”

    The electronic noise that the team identified has been known about for many years, but until now it was not thought to play an important role at low temperatures. That discovery happened because of a chance encounter between Minnich and Joel Schleeh, a postdoctoral scholar from Chalmers University of Technology in Sweden and first author of the new study, who was at Caltech visiting the lab of Sander Weinreb, a senior faculty associate in electrical engineering.

    Schleeh had noticed that the noise he was measuring in an amplifier was higher than what theory predicted. Schleeh mentioned the problem to Weinreb, and Weinreb recommended he connect with Minnich, whose lab studies heat transfer by phonons. “At another university, I don’t think I would have had this chance,” Minnich says. “Neither of us would have had the chance to interact like we did here. Caltech is a small campus, so when you talk to someone, almost by definition they’re outside of your field.”

    The pair’s findings could have implications for numerous fields of science that rely on superchilled instruments to make sensitive measurements. “In radio astronomy, you’re trying to detect very weak electromagnetic waves from space, so you need the lowest noise possible,” Minnich says.

    Electronic noise poses a similar problem for quantum-physics experiments. “Here at Caltech, we have physicists trying to observe certain quantum-physics effects. The signal that they’re looking for is very tiny, and it’s essential to use the lowest-noise electronics possible,” Minnich says.

    The news is not all gloomy, however, because the team’s findings also suggest that it may be possible to develop engineering strategies to make phonon heat transfer more efficient at low temperatures. For example, one possibility might be to change the design of transistors so that phonon generation takes place over a broader volume. “If you can make the phonon generation more spread out, then in principle you could reduce the temperature rise that occurs,” Minnich says.

    “We don’t know what the precise strategy will be yet, but now we know the direction we should be going. That’s an improvement.”

    In addition to Minnich and Schleeh, the other coauthors of the paper, Phonon blackbody radiation limit for heat dissipation in electronics, are Javier Mateos and Ignacio Iñiguez-de-la-Torre of the Universidad de Salamanca in Salamanca, Spain; Niklas Wadefalk of the Low Noise Factory AB in Mölndal, Sweden; and Per A. Nilsson and Jan Grahn of Chalmers University of Technology. Minnich’s work on the project at Caltech was funded by a Caltech start-up fund and by the National Science Foundation.

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 2:23 pm on November 7, 2014 Permalink | Reply
    Tags: , Caltech, , Geochemistry,   

    From Caltech: “Unexpected Findings Change the Picture of Sulfur on the Early Earth” 

    Caltech Logo
    Caltech

    11/07/2014
    Kimm Fesenmaier

    Scientists believe that until about 2.4 billion years ago there was little oxygen in the atmosphere—an idea that has important implications for the evolution of life on Earth. Evidence in support of this hypothesis comes from studies of sulfur isotopes preserved in the rock record. But the sulfur isotope story has been uncertain because of the lack of key information that has now been provided by a new analytical technique developed by a team of Caltech geologists and geochemists. The story that new information reveals, however, is not what most scientists had expected.

    slope
    2.5 billion-year-old sedimentary strata exposed in the Northern Cape Province of South Africa. Credit: Jess Adkins/Caltech

    more
    Reef mounds formed of radiating calcium carbonate crystal fans on the Archean seafloor. Credit: Jess Adkins/Caltech

    and
    Cross-section view of calcium carbonate crystal fans that grew on the seafloor circa 2.6 billion years ago. Credit: Jess Adkins/Caltech

    “Our new technique is 1,000 times more sensitive for making sulfur isotope measurements,” says Jess Adkins, professor of geochemistry and global environmental science at Caltech. “We used it to make measurements of sulfate groups dissolved in carbonate minerals deposited in the ocean more than 2.4 billion years ago, and those measurements show that we have been thinking about this part of the sulfur cycle and sulfur isotopes incorrectly.”

    The team describes their results in the November 7 issue of the journal Science. The lead author on the paper is Guillaume Paris, an assistant research scientist at Caltech.

    Nearly 15 years ago, a team of geochemists led by researchers at UC San Diego discovered there was something peculiar about the sulfur isotope content of rocks from the Archean era, an interval that lasted from 3.8 billion to about 2.4 billion years ago. In those ancient rocks, the geologists were analyzing the abundances of stable isotopes of sulfur.

    When sulfur is involved in a reaction—such as microbial sulfate reduction, a way for microbes to eat organic compounds in the absence of oxygen—its isotopes are usually fractionated, or separated, from one another in proportion to their differences in mass. That is, 34S gets fractionated from 32S about twice as much as 33S gets fractionated from 32S. This process is called mass-dependent fractionation, and, scientists have found that it dominates in virtually all sulfur processes operating on Earth’s surface for the last 2.4 billion years.

    However, in older rocks from the Archean era (i.e., older than 2.4 billion years), the relative abundances of sulfur isotopes do not follow the same mass-related pattern, but instead show relative enrichments or deficiencies of 33S relative to 34S. They are said to be the product of mass-independent fractionation (MIF).

    The widely accepted explanation for the occurrence of MIF is as follows. Billions of years ago, volcanism was extremely active on Earth, and all those volcanoes spewed sulfur dioxide high into the atmosphere. At that time, oxygen existed at very low levels in the atmosphere, and therefore ozone, which is produced when ultraviolet radiation strikes oxygen, was also lacking. Today, ozone prevents ultraviolet light from reaching sulfur dioxide with the energy needed to fractionate sulfur, but on the early Earth, that was not the case, and MIF is the result. Researchers have been able to reproduce this effect in the lab by shining lasers onto sulfur dioxide and producing MIF.

    Geologists have also measured the sulfur isotopic composition of sedimentary rocks dating to the Archean era, and found that sulfides—sulfur-bearing compounds such as pyrite (FeS2)—include more 33S than would be expected based on normal mass-dependent processes. But if those minerals are enriched in 33S, other minerals must be correspondingly lacking in the isotope. According to the leading hypothesis, those 33S-deficient minerals should be sulfates—oxidized sulfur-bearing compounds—that were deposited in the Archean ocean.

    “That idea was put forward on the basis of experiment. To test the hypothesis, you’d need to check the isotope ratios in sulfate salts (minerals such as gypsum), but those don’t really exist in the Archean rock record since there was very little oxygen around,” explains Woody Fischer, professor of geobiology at Caltech and a coauthor on the new paper. “But there are trace amounts of sulfate that got trapped in carbonate minerals in seawater.”

    However, because those sulfates are present in such small amounts, no one has been able to measure well their isotopic composition. But using a device known as a multicollector inductively-coupled mass spectrometer to precisely measure multiple sulfur isotopes, Adkins and his colleague Alex Sessions, a professor of geobiology, developed a method that is sensitive enough to measure the isotopic composition of about 10 nanomoles of sulfate in just a few tens of milligrams of carbonate material.

    The authors used the method to measure the sulfate content of carbonates from an ancient carbonate platform preserved in present-day South Africa, an ancient version of the depositional environments found in the Bahamas today. Analyzing the samples, which spanned 70 million years and a variety of marine environments, the researchers found exactly the opposite of what had been predicted: the sulfates were actually enriched by 33S rather than lacking in it.

    “Now, finally, we’re looking at this sulfur cycle and the sulfur isotopes correctly,” Adkins says.

    What does this mean for the atmospheric conditions of the early Earth? “Our findings underscore that the oxygen concentrations in the early atmosphere could have been incredibly low,” Fischer says.

    Knowledge of sulfate isotopes changes how we understand the role of biology in the sulfur cycle, he adds. Indeed, the fact that the sulfates from this time period have the same isotopic composition as sulfide minerals suggests that the sulfides may be the product of microbial processes that reduced seawater sulfate to sulfide (which later precipitated in sediments in the form of pyrite). Previously, scientists thought that all of the isotope fractionation could be explained by inorganic processes alone.

    In a second paper also in the November 7 issue of Science, Paris, Adkins, Sessions, and colleagues from a number of institutions around the world report on related work in which they measured the sulfates in Indonesia’s Lake Matano, a low-sulfate analog of the Archean ocean.

    At about 100 meters depth, the bacterial communities in Lake Matano begin consuming sulfate rather than oxygen, as do most microbial communities, yielding sulfide. The researchers measured the sulfur isotopes within the sulfates and sulfides in the lake water and sediments and found that despite the low concentrations of sulfate, a lot of mass-dependent fractionation was taking place. The researchers used the data to build a model of the lake’s sulfur cycle that could produce the measured fractionation, and when they applied their model to constrain the range of concentrations of sulfate in the Archean ocean, they found that the concentration was likely less than 2.5 micromolar, 10,000 times lower than the modern ocean.

    “At such low concentration, all the isotopic variability starts to fit,” says Adkins. “With these two papers, we were able to come at the same problem in two ways—by measuring the rocks dating from the Archean and by looking at a model system today that doesn’t have much sulfate—and they point toward the same answer: the sulfate concentration was very low in the Archean ocean.”

    Samuel M. Webb of the Stanford Synchrotron Radiation Lightsource is also an author on the paper, “Neoarchean carbonate-associated sulfate records positive Δ33S anomalies.” The work was supported by funding from the National Science Foundation’s Division of Earth Sciences, the Henry and Camille Dreyfus Foundation’s Postdoctoral Program in Environmental Chemistry, and the David and Lucile Packard Foundation.

    Paris is also a co-lead author on the second paper, Sulfate was a trace constituent of Archean seawater. Additional authors on that paper are Sean Crowe and CarriAyne Jones of the University of British Columbia and the University of Southern Denmark; Sergei Katsev of the University of Minnesota Duluth; Sang-Tae Kim of McMaster University; Aubrey Zerkle of the University of St. Andrews; Sulung Nomosatryo of the Indonesian Institute of Sciences; David Fowle of the University of Kansas; James Farquhar of the University of Maryland, College Park; and Donald Canfield of the University of Southern Denmark. Funding was provided by an Agouron Institute Geobiology Fellowship and a Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship, as well as by the Danish National Research Foundation and the European Research Council.

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 9:58 pm on October 16, 2014 Permalink | Reply
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    From Caltech: “A Newborn Supernova Every Night” 

    Caltech Logo
    Caltech

    10/16/2014
    Douglas Smith

    Thanks to a $9 million grant from the National Science Foundation and matching funds from the Zwicky Transient Facility (ZTF) collaboration, a new camera is being built at Caltech’s Palomar Observatory that will be able to survey the entire Northern Hemisphere sky in a single night, searching for supernovas, black holes, near-Earth asteroids, and other objects. The digital camera will be mounted on the Samuel Oschin Telescope, a wide-field Schmidt telescope that began its first all-sky survey in 1949. That survey, done on glass plates, took nearly a decade to complete.

    Caltech Palomar Samuel Ochin Telescope
    Caltech Palomar Samuel Ochin Telescope Interior
    Samuel Ochin Telescope

    The ZTF camera’s field of view will encompass 47 square degrees, larger than 200 full moons. By contrast, the field of view of the Hubble Space Telescope is so small that a mosaic of 130 of its images of the moon would be needed to see it in its entirety. “The Hubble Space Telescope and the big ground-based telescopes see really deep but have small fields of view,” says astrophysicist Eric Bellm, a postdoctoral scholar at Caltech and ZTF’s project scientist. With its field of view, ZTF will be able to identify supernovas less than 24 hours old every single night. This quick response is critical, as the light emitted in the first few hours after a supernova explodes contains a wealth of information that cannot be retrieved later.

    “Discovery is only the first step,” says Shrinivas Kulkarni, ZTF’s principal investigator and Caltech’s John D. and Catherine T. MacArthur Professor of Astronomy and Planetary Science. “When something unusual is found, we will rapidly respond with some of the world’s most powerful telescopes,” including the Palomar Observatory’s 200-inch Hale.

    Caltech Palomar Hale Telescope
    Caltech Palomar Hale Telescope
    Caltech Palomar Hale Telescope

    In time, researchers hope, ZTF itself will be pointed at targets identified by the Laser Interferometer Gravitational-wave Observatory (LIGO), an NSF-funded project run by Caltech and MIT that is searching for gravitational waves. These ripples in the fabric of space and time are predicted to occur when neutron stars, black holes, or other massive objects collide. Currently, LIGO is offline undergoing a technical upgrade to Advanced LIGO, which is slated to begin operations in 2016. If and when Advanced LIGO registers a gravitational wave, it will command ZTF to scan the ribbon of sky from which the signal emanated, searching for any visible change that might mark the point of origin.

    ZTF—the successor to the intermediate Palomar Transient Factory (iPTF) survey and its predecessor, the Palomar Transient Factory—is a fully automated wide-field survey that uses the Oschin telescope to collect data that are then sent to the Infrared Processing and Analysis Center (IPAC) on the Caltech campus. At IPAC, software developed for PTF looks for anything that has changed between frames. ZTF will shoot one frame per minute at 18 gigabits per frame—the rough equivalent of watching eight hours of high-definition movies on Netflix every 60 seconds.

    “ZTF is really about celestial cinematography,” says Mansi Kasliwal (PhD ’11), currently a visiting associate in astronomy who will start as an assistant professor of astronomy at Caltech in September 2015. “Our new camera can make a movie of the entire sky. Moving solar-system bodies such as asteroids will just pop out at us, and we’ll be able to study catastrophic explosive transients such as supernovas and stars being torn apart by black holes.”

    “Processing so many images in real time is a huge challenge,” says IPAC’s executive director, George Helou. “It takes imaginative programming and powerful computers.” ZTF will visit every corner of the sky some 900 times over the course of its three-year observing program; IPAC will compile the data into atlases of variable stars, active galactic nuclei, and other astronomically interesting objects.

    Part of the NSF grant will fund an annual summer institute, coordinated by Pomona College in Claremont, California, to train students from across the United States in the latest astronomy instrumentation skills, large sky surveys, and data-analysis software.

    “These undergraduates will be controlling some of the largest telescopes in the world and getting a taste of the excitement of the scientific process,” explains Bryan Penprase, a professor at Pomona College and a co-principal investigator on the project, and the organizer of the summer institute. “The technology is so advanced that discoveries will be common. In just one night, the ZTF can discover hundreds of new sources. It’s an incredible thing for a student to be able to say, ‘I discovered that thing in the sky that no one else has ever seen before.'”

    The Zwicky Transient Facility is named in memory of Caltech astronomer Fritz Zwicky, who pioneered the use of wide-field Schmidt-type telescopes for sky surveys. Zwicky was the prime mover behind the Oschin’s construction, using its survey plates to hunt for supernovas—a term that Zwicky and Walter Baade coined in 1931. Zwicky also predicted the existence of neutron stars, dark matter, and gravitational lensing.

    ZTF is a public-private partnership supported by the National Science Foundation, Caltech, IPAC, the Weizmann Institute of Science (Israel), the Oskar Klein Centre (Sweden), Humboldt University (Germany), Los Alamos National Laboratory, Lawrence Berkeley National Laboratory, the Jet Propulsion Laboratory, the TANGO consortium (Taiwan), the University of Wisconsin–Milwaukee, and Pomona College. The survey will begin in 2017

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 4:12 pm on October 16, 2014 Permalink | Reply
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    From Caltech: “Improving The View Through Tissues and Organs” 

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    Caltech

    10/16/2014
    Kimm Fesenmaier

    This summer, several undergraduate students at Caltech had the opportunity to help optimize a promising technique that can make tissues and organs—even entire organisms—transparent for study. As part of the Summer Undergraduate Research Fellowship (SURF) program, these students worked in the lab of Assistant Professor of Biology Viviana Gradinaru, where researchers are developing such so-called clearing techniques that make it possible to peer straight through normally opaque tissues rather than seeing them only as thinly sectioned slices that have been pieced back together.

    tissue
    Credit: iStock

    Gradinaru’s group recently published a paper in the journal Cell describing a new approach to tissue clearing. The method they have created builds on a technique called CLARITY that Gradinaru helped develop while she was a research associate at Stanford. CLARITY allowed researchers to, for the first time, create a transparent whole-brain specimen that could then be imaged with its structural and genetic information intact.

    CLARITY was specifically developed for studying the brain. But the new approach developed in Gradinaru’s lab, which the team has dubbed PARS (perfusion-assisted agent release in situ), can also clear other organs, such as the kidney, as well as tissue samples, such as tumor biopsies. It can even be applied to entire organisms.

    Like CLARITY, PARS involves removing the light-scattering lipids in the tissue to make samples transparent without losing the structural integrity that lipids typically provide. First the sample is infused with acrylamide monomers that are then polymerized into a hydrogel that provides structural support. Next, this tissue–hydrogel hybrid is immersed in a detergent that removes the lipids. Then the sample can be stained, often with antibodies that specifically mark cells of interest, and then immersed in RIMS (refractive index matching solution) for imaging using various optical techniques such as confocal or lightsheet microscopy.

    Over the summer, Sam Wie, a junior biology major at Caltech, spent 10 weeks in the Gradinaru lab working to find a polymer that would perform better than acrylamide, which has been used in the CLARITY hydrogel. “One of the limitations of CLARITY is that when you put the hydrogel tissue into the detergent, the higher solute concentration in the tissue causes liquid to rush into the cell. That causes the sample to swell, which could potentially damage the structure of the tissue,” Wie explains. “So I tried different polymers to try to limit that swelling.”

    Wie was able to identify a polymer that produces, over a similar amount of time, about one-sixth of the swelling in the tissue.

    “The SURF experience has been very rewarding,” Wie says. “I’ve learned a lot of new techniques, and it’s really exciting to be part of, and to try to improve, CLARITY, a method that will probably change the way that we image tissues from now on.”

    At another bench in Gradinaru’s lab, sophomore bioengineering major Andy Kim spent the summer focusing on a different aspect of the PARS technique. While antibodies have been the most common markers used to tag cells of interest within cleared tissues, they are too large for some studies—for example, those that aim to image deeper parts of the brain, requiring them to cross the blood–brain barrier. Kim’s project involved identifying smaller proteins, such as nanobodies, which target and bind to specific parts of proteins in tissues.

    “While PARS is a huge improvement over CLARITY, using antibodies to stain is very expensive,” Kim says. “However, some of these nanobodies can be produced easily, so if we can get them to work, it would not only help image the interior of the brain, it would also be a lot less costly.”

    During his SURF, Kim worked with others in the lab to identify about 30 of these smaller candidate binding proteins and tested them on PARS-cleared samples.

    While Wie and Kim worked on improving the PARS technique itself, Donghun Ryu, a third SURFer in Gradinaru’s lab, investigated different methods for imaging the cleared samples. Ryu is a senior electrical engineering and computer science major at the Gwangju Institute of Science and Technology (GIST) in the Republic of Korea.

    Last summer Ryu completed a SURF as part of the Caltech–GIST Summer Undergraduate Research Exchange Program in the lab of Changhuei Yang, professor of electrical engineering, bioengineering, and medical engineering at Caltech. While completing that project, Ryu became interested in optogenetics, the use of light to control genes. Since optogenetics is one of Gradinaru’s specialties, Yang suggested that he try a SURF in Gradinaru’s lab.

    This summer, Ryu was able to work with both Yang and Gradinaru, investigating a technique called Talbot microscopy to see whether it would be better for imaging thick, cleared tissues than more common techniques. Ryu was able to work on the optical system in Yang’s lab while testing the samples cleared in Gradinaru’s lab.

    “It was a wonderful experience,” Ryu says. “It was special to have the opportunity to work for two labs this summer. I remember one day when I had a meeting with both Professor Yang and Professor Gradinaru; it was really amazing to get to meet with two Caltech professors.”

    Gradinaru says that the SURF projects provided a learning opportunity not only for the participating students but also for her lab. “For example,” she says, “Ryu strengthened the collaboration that we have with the Yang group for the BRAIN Initiative. And my lab members benefited from the chance to serve as mentors—to see what works and what can be improved when transferring scientific knowledge. These are very important skills in addition to the experimental know-how that they master.”

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 4:00 pm on October 10, 2014 Permalink | Reply
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    From Caltech: “Sensors to Simplify Diabetes Management” 

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    Caltech

    10/10/2014
    Jessica Stoller-Conrad

    For many patients diagnosed with diabetes, treating the disease can mean a burdensome and uncomfortable lifelong routine of monitoring blood sugar levels and injecting the insulin that their bodies don’t naturally produce. But, as part of their Summer Undergraduate Research Fellowship (SURF) projects at Caltech, several engineering students have contributed to the development of tiny biosensors that could one day eliminate the need for these manual blood sugar tests.

    two
    From left to right: Sagar Vaidyanathan, a visiting undergraduate researcher from UCLA, and Caltech sophomore Sophia Chen. Chen spent her summer in the laboratory of Hyuck Choo, assistant professor of electrical engineering, studying new ways to power tiny health-monitoring sensors and devices.
    Credit: Lance Hayashida/Caltech Marketing and Communications

    Because certain patients with diabetes are unable to make their own insulin—a hormone that helps transfer glucose, or sugar, from the blood into muscle and other tissues—they need to monitor frequently their blood glucose, manually injecting insulin when sugar levels surge after a meal. Most glucose monitors require that patients prick their fingertips to collect a drop of blood, sometimes up to 10 times a day for the rest of their lives.

    In their SURF projects, the students, all from Caltech’s Division of Engineering and Applied Science, looked for different ways to do these same tests but painlessly and automatically.

    man
    Senior applied physics major Mehmet Sencan has approached the problem with a tiny chip that can be implanted under the skin. The sensor, a square just 1.4 millimeters on each side, is designed to detect glucose levels from the interstitial fluid (fluid found in the spaces between cells) that is just under the skin. The glucose levels in this fluid directly relate to the blood glucose concentration.

    Sencan has been involved in optimizing the electrochemical method that the chip will use to detect glucose levels. Much like a traditional finger-stick glucose meter, the chip uses glucose oxidase, an enzyme that reacts in the presence of glucose, to create an electrical current. Higher levels of glucose result in a stronger current, allowing the device to measure glucose levels based on the charge that passes through the fluid.

    Once the glucose level is detected, the information is wirelessly transmitted via a radio wave frequency to a reader that uses the same frequency to power the device itself. Ultimately an external display will let the patient know if their levels are within range.

    Sencan, who works in the laboratory of Axel Scherer, the Bernard Neches Professor of Electrical Engineering, Applied Physics, and Physics, and who is co-mentored by postdoctoral researcher Muhammad Mujeeb-U-Rahman, started this project three years ago during his very first SURF.

    “When I started, we were just thinking about what kind of chemistry the sensor would use, and now we have a sensor that is actually designed to do that,” he says. Over the summer, he implanted the sensors in rat models, and he will continue the study over the fall and spring terms using both rat and mouse models—a first step in determining if the design is a clinically viable option.

    jun
    Junior electrical engineering major Sith Domrongkitchaiporn from the Scherer laboratory, also co-mentored by Mujeeb-U-Rahman, took a different approach to glucose detection, making tiny biosensors that are inconspicuously wearable on the surface of a contact lens. “It’s an interesting concept because instead of having to do a procedure to place something under the skin, you can use a less invasive method, placing a sensor on the eye to get the same information,” he says.

    He used the method optimized by Mehmet to determine blood glucose levels from interstitial fluid and adapted the chemistry to measure glucose in the eyes’ tears. This summer, he will be attempting to fabricate the lens itself and improve upon the process whereby radio waves are used to power the sensor and then transmit data from the sensor to an external computer.

    girl
    SURF student and sophomore electrical engineering major Jennifer Chih-Wen Lin wanted to incorporate a different kind of glucose sensor into a contact lens. “The concept—determining glucose readings from tears—is very similar to Sith’s, but the method is very different,” she says.

    Instead of determining the glucose level based on the amount of electrical current that passes through a sample, Lin, who works in the laboratory of Hyuck Choo, assistant professor of electrical engineering, worked on a sensor that detects glucose levels from the interaction between light and molecules.

    In her SURF project, she began optimizing the characterization of glucose molecules in a sample of glucose solution using a technique called Raman spectroscopy. When molecules encounter light, they vibrate differently based on their symmetry and the types of bonds that hold their atoms together. This vibrational information provides a unique fingerprint for each type of molecule, which is represented as peaks on the Raman spectrum—and the intensity of these peaks correlates to the concentration of that molecule within the sample.

    “This step is important because once I can determine the relationship between peak intensities and glucose concentrations, our sensor can just compare that known spectrum to the reading from a sample of tears to determine the amount of glucose in the sample,” she says.

    Lin’s project is in the very beginning stages, but if it is successful, it could provide a more accurate glucose measurement, and from a smaller volume of liquid, than is possible with the finger-stick method. Perhaps more importantly for patients, it can provide that measurement painlessly.

    girl12
    Also in Choo’s laboratory, sophomore electrical engineering major Sophia Chen’s SURF project involves a new way to power devices like these tiny sensors and other medical implants, using the vibrations from a patient’s vocal cords. These vibrations produce the sound of our voice, and also create vibrations in the skull.

    “We’re using these devices called energy harvesters that can extract energy from vibrations at specific frequencies. When the vibrations go from the vocal folds to the skull, a structure in the energy harvester vibrates at the same frequency, generating energy—energy that can be used to power batteries or charge things,” Chen says.

    Chen’s goal is to determine the frequency of these vibrations—and if the energy that they produce is actually enough to power a tiny device. The hope is that one day these vibrations could power, or at least supplement the power of, medical devices that need to be implanted near the head and that presently run on batteries with finite lifetimes.

    Chen and the other students acknowledge that health-monitoring sensors powered by the human body might be years away from entering the clinic. However, this opportunity to apply classroom knowledge to a real-life challenge—such as diabetes treatment—is an important part of their training as tomorrow’s scientists and engineers.

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 3:50 pm on September 22, 2014 Permalink | Reply
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    From Caltech: “Variability Keeps The Body In Balance” 

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    Caltech

    09/22/2014
    Jessica Stoller-Conrad

    Although the heart beats out a very familiar “lub-dub” pattern that speeds up or slows down as our activity increases or decreases, the pattern itself isn’t as regular as you might think. In fact, the amount of time between heartbeats can vary even at a “constant” heart rate—and that variability, doctors have found, is a good thing.

    runner

    Reduced heart rate variability (HRV) has been found to be predictive of a number of illnesses, such as congestive heart failure and inflammation. For athletes, a drop in HRV has also been linked to fatigue and overtraining. However, the underlying physiological mechanisms that control HRV—and exactly why this variation is important for good health—are still a bit of a mystery.

    By combining heart rate data from real athletes with a branch of mathematics called control theory, a collaborative team of physicians and Caltech researchers from the Division of Engineering and Applied Sciences have now devised a way to better understand the relationship between HRV and health—a step that could soon inform better monitoring technologies for athletes and medical professionals.

    The work was published in the August 19 print issue of the Proceedings of the National Academy of Sciences.

    To run smoothly, complex systems, such as computer networks, cars, and even the human body, rely upon give-and-take connections and relationships among a large number of variables; if one variable must remain stable to maintain a healthy system, another variable must be able to flex to maintain that stability. Because it would be too difficult to map each individual variable, the mathematics and software tools used in control theory allow engineers to summarize the ups and downs in a system and pinpoint the source of a possible problem.

    Researchers who study control theory are increasingly discovering that these concepts can also be extremely useful in studies of the human body. In order for a body to work optimally, it must operate in an environment of stability called homeostasis. When the body experiences stress—for example, from exercise or extreme temperatures—it can maintain a stable blood pressure and constant body temperature in part by dialing the heart rate up or down. And HRV plays an important role in maintaining this balance, says study author John Doyle, the Jean-Lou Chameau Professor of Control and Dynamical Systems, Electrical Engineering, and Bioengineering.

    “A familiar related problem is in driving,” Doyle says. “To get to a destination despite varying weather and traffic conditions, any driver—even a robotic one—will change factors such as acceleration, braking, steering, and wipers. If these factors suddenly became frozen and unchangeable while the car was still moving, it would be a nearly certain predictor that a crash was imminent. Similarly, loss of heart rate variability predicts some kind of malfunction or ‘crash,’ often before there are any other indications,” he says.

    To study how HRV helps maintain this version of “cruise control” in the human body, Doyle and his colleagues measured the heart rate, respiration rate, oxygen consumption, and carbon dioxide generation of five healthy young athletes as they completed experimental exercise routines on stationary bicycles.

    By combining the data from these experiments with standard models of the physiological control mechanisms in the human body, the researchers were able to determine the essential tradeoffs that are necessary for athletes to produce enough power to maintain an exercise workload while also maintaining the internal homeostasis of their vital signs.

    Because monitors in hospitals can already provide HRV levels and dozens of other signals and readings, the integration of such mathematical analyses of control theory into HRV monitors could, in the future, provide a way to link a drop in HRV to a more specific and treatable diagnosis. In fact, one of Doyle’s students has used an HRV application of control theory to better interpret traditional EKG signals.

    Control theory could also be incorporated into the HRV monitors used by athletes to prevent fatigue and injury from overtraining, he says.

    “Physicians who work in very data-intensive settings like the operating room or ICU are in urgent need of ways to rapidly and acutely interpret the data deluge,” says Marie Csete, MD (PhD, ’00), chief scientific officer at the Huntington Medical Research Institutes and a coauthor on the paper. “We hope this work is a first step in a larger research program that helps physicians make better use of data to care for patients.”

    “For example, the heart, lungs, and circulation must deliver sufficient oxygenated blood to the muscles and other organs while not raising blood pressure so much as to damage the brain,” Doyle says. “This is done in concert with control of blood vessel dilation in the muscles and brain, and control of breathing. As the physical demands of the exercise change, the muscles must produce fluctuating power outputs, and the heart, blood vessels, and lungs must then respond to keep blood pressure and oxygenation within narrow ranges.”

    Once these trade-offs were defined, the researchers then used control theory to analyze the exercise data and found that a healthy heart must maintain certain patterns of variability during exercise to keep this complicated system in balance. Loss of this variability is a precursor of fatigue, the stress induced by exercise. Today, some HRV monitors in the clinic can let a doctor know when variability is high or low, but they provide little in the way of an actionable diagnosis.

    Because monitors in hospitals can already provide HRV levels and dozens of other signals and readings, the integration of such mathematical analyses of control theory into HRV monitors could, in the future, provide a way to link a drop in HRV to a more specific and treatable diagnosis. In fact, one of Doyle’s students has used an HRV application of control theory to better interpret traditional EKG signals.

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 8:15 pm on September 14, 2014 Permalink | Reply
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    From Caltech: “Slimy Fish and the Origins of Brain Development” 

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    Caltech

    09/14/2014
    Jessica Stoller-Conrad

    Lamprey—slimy, eel-like parasitic fish with tooth-riddled, jawless sucking mouths—are rather disgusting to look at, but thanks to their important position on the vertebrate family tree, they can offer important insights about the evolutionary history of our own brain development, a recent study suggests.

    eel
    A sea lamprey held by postdoctoral scholar Stephen Green in the Caltech Zebrafish/Xenopus/Lamprey Facility. Credit: Lance Hayashida/Caltech Marketing and Communications

    The work appears in a paper in the September 14 advance online issue of the journal Nature.

    “Lamprey are one of the most primitive vertebrates alive on Earth today, and by closely studying their genes and developmental characteristics, researchers can learn more about the evolutionary origins of modern vertebrates—like jawed fishes, frogs, and even humans,” says paper coauthor Marianne Bronner, the Albert Billings Ruddock Professor of Biology and director of Caltech’s unique Zebrafish/Xenopus/Lamprey facility, where the study was done.

    mb
    Marianne Bronner, the Albert Billings Ruddock Professor of Biology, with the tanks where the sea lamprey are kept during their time at Caltech.
    Credit: Lance Hayashida/Caltech Marketing and Communications

    The facility is one of the few places in the world where lampreys can be studied in captivity. Although the parasitic lamprey are an invasive pest in the Great Lakes, they are difficult to study under controlled conditions; their lifecycle takes up to 10 years and they only spawn for a few short weeks in the summer before they die.

    Each summer, Bronner and her colleagues receive shipments of wild lamprey from Michigan just before the prime of breeding season. When the lamprey arrive, they are placed in tanks where the temperature of the water is adjusted to extend the breeding season from around three weeks to up to two months. In those extra weeks, the lamprey produce tens of thousands of additional eggs and sperm, which, via in vitro fertilization, generate tens of thousands of additional embryos for study. During this time, scientists from all over the world come to Caltech to perform experiments with the developing lamprey embryos.

    tank
    Lamprey embryos are sorted for observation at a microscope in the Caltech Zebrafish/Xenopus/Lamprey facility.
    Credit: Lance Hayashida/Caltech Marketing and Communications

    In the current study, Bronner and her collaborators—who traveled to Caltech from Stower’s Institute for Medical Research in Kansas City, Missouri—studied the origins of the vertebrate hindbrain.

    The hindbrain is a part of the central nervous system common to chordates—or organisms that have a nerve cord like our spinal cord. During the development of vertebrates—a subtype of chordates that have backbones—the hindbrain is compartmentalized into eight segments, each of which becomes uniquely patterned to establish networks of neuronal circuits. These segments eventually give rise to adult brain regions like the cerebellum, which is important for motor control, and the medulla oblongata, which is necessary for breathing and other involuntary functions.

    br
    A lamprey embryo expressing the Hox gene Hoxb3 (green). In the study, Bronner and her colleagues found that Hox genes are important for hindbrain segmentation during lamprey development.
    Credit: Hugo Parker

    However, this segmentation is not present in so-called “invertebrate chordates”—a grouping of chordates that lack a backbone, such as sea squirts and lancelets.

    “The interesting thing about lampreys is that they occupy an intermediate evolutionary position between the invertebrate chordates and the jawed vertebrates,” says Hugo Parker, a postdoc at Stower’s Institute and first author on the study. “By investigating aspects of lamprey embryology, we can get a picture of how vertebrate traits might have evolved.”

    hp
    Hugo Parker, a postdoctoral scholar from the Stowers Institute for Medical Research, works with lamprey embryos at a microscope in the Caltech Zebrafish/Xenopus/Lamprey facility.
    Credit: Lance Hayashida/Caltech Marketing and Communications

    In the vertebrates, segmental patterning genes called Hox genes help to determine the animal’s head-to-tail body plan—and those same Hox genes also control the segmentation of the hindbrain. Although invertebrate chordates also have Hox genes, these animals don’t have segmented hindbrains. Because lampreys are centered between these two types of organisms on the evolutionary tree, the researchers wanted to know whether or not Hox genes are involved in patterning of the lamprey hindbrain.

    To their surprise, the researchers discovered that the lamprey hindbrain was not only segmented during development but the process also involved Hox genes—just like in its jawed vertebrate cousins.

    “When we started, we thought that the situation was different, and the Hox genes were not really integrated into the process of segmentation as they are in jawed vertebrates,” Parker says. “But in actually doing this project, we discovered the way that lamprey Hox genes are expressed and regulated is very similar to what we see in jawed vertebrates.” This means that hindbrain segmentation—and the role of Hox genes in this segmentation—happened earlier on in evolution than was once thought, he says.

    Parker, who has been spending his summers at Caltech studying lampreys since 2008, is next hoping to pinpoint other aspects of the lamprey hindbrain that may be conserved in modern vertebrate information that will help contribute to a fundamental understanding of vertebrate development. And although those investigations will probably mean following the lamprey for a few more summers at Caltech, Parker says his time in the lamprey facility continually offers a one-of-a-kind experience.

    “The lamprey system here is unique in the world—and it’s not just the water tanks and how we’ve learned to maintain the animals. It’s the small nucleus of people who have particular skills, people who come in from all over the world to work together, share protocols, and develop the field together,” he says. “That’s one of the things I’ve liked ever since I first came here. I really felt like I was a part of something very special.

    These results were published in a paper titled A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates. Robb Krumlauf, a scientific director at the Stower’s Institute and professor at the Kansas University Medical Center, was also a coauthor on the study. The Zebrafish/Xenopus/Lamprey facility at Caltech is a Beckman Institute facility.

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 2:41 pm on August 20, 2014 Permalink | Reply
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    From Caltech: “Programmed to Fold: RNA Origami” 

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    Caltech

    08/20/2014
    Katie Neith

    Researchers from Aarhus University in Denmark and Caltech have developed a new method for organizing molecules on the nanoscale. Inspired by techniques used for folding DNA origami—first invented by Paul Rothemund, a senior research associate in computation and neural systems in the Division of Engineering and Applied Science at Caltech—the team, which includes Rothemund, has fabricated complicated shapes from DNA’s close chemical cousin, RNA.

    Unlike DNA origami, whose components are chemically synthesized and then folded in an artificial heating and cooling process, RNA origami are synthesized enzymatically and fold up as they are being synthesized, which takes place under more natural conditions compatible with living cells. These features of RNA origami may allow designer RNA structures to be grown within living cells, where they might be used to organize cellular enzymes into biochemical factories.

    “The parts for a DNA origami cannot easily be written into the genome of an organism. An RNA origami, on the other hand, can be represented as a DNA gene, which in cells is transcribed into RNA by a protein machine called RNA polymerase,” explains Rothemund.

    So far, the researchers have demonstrated their method by designing RNA molecules that fold into rectangles and then further assemble themselves into larger honeycomb patterns. This approach was taken to make the shapes recognizable using an atomic force microscope, but many other shapes should be realizable.

    fold
    This illustration is an artist’s impression of RNA nanostructures that fold up while they are being synthesized by polymerase enzymes, which read instructions from DNA templates. Once formed, the RNAs assemble into honeycomb-shaped lattices on the mica surface below. Credit: Cody Geary

    A paper describing the research appears in the August 15 issue of the journal Science.

    “What is unique about the method is that the folding recipe is encoded into the molecule itself, through its sequence.” explains first author Cody Geary, a postdoctoral scholar at Aarhus University.

    In other words, the sequence of the RNAs defines both the final shape, and the order in which different parts of the shape fold. The particular RNA sequences that were folded in the experiment were designed using software called NUPACK, created in the laboratory of Caltech professor Niles Pierce. Both the Rothemund and Pierce labs are funded by a National Science Foundation. Molecular Programming Project (MPP) Expeditions in Computing grant.

    “Our latest research is an excellent example of how tools developed by one part of the MPP are being used by another,” says Rothemund.

    “RNA has a richer structural and functional repertoire than DNA, and so I am especially interested in how complex biological motifs with special 3-D geometries or protein-binding regions can be added to the basic architecture of RNA origami,” says Geary, who completed his BS in chemistry at Caltech in 2003.

    The project began with an extended visit by Geary and corresponding author Ebbe Andersen, also from Aarhus University, to Rothemund’s Caltech lab.

    “RNA origami is still in its infancy,” says Rothemund. “Nevertheless, I believe that RNA origami, because of their potential to be manufactured by cells, and because of the extra functionality possible with RNA, will have at least as big an impact as DNA origami.”

    Rothemund (BS ’94) reported the original method for DNA origami in 2006 in the journal Nature. Since then, the work has been cited over 6,000 times and DNA origami have been made in over 50 labs worldwide for potential applications such as drug delivery vehicles and molecular computing.

    “The payoff is that unlike DNA origami, which are expensive and have to be made outside of cells, RNA origami should be able to be grown cheaply in large quantities, simply by growing bacteria with genes for them,” he adds. “Genes and bacteria cost essentially nothing to share, and so RNA origami will be easily exchanged between scientists.”

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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