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  • richardmitnick 8:38 am on October 17, 2014 Permalink | Reply
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    From UC Berkeley: “New front in war on Alzheimer’s, other protein-folding diseases” 

    UC Berkeley

    UC Berkeley

    October 16, 2014
    Robert Sanders

    A surprise discovery that overturns decades of thinking about how the body fixes proteins that come unraveled greatly expands opportunities for therapies to prevent diseases such as Alzheimer’s and Parkinson’s, which have been linked to the accumulation of improperly folded proteins in the brain.

    “This finding provides a whole other outlook on protein-folding diseases; a new way to go after them,” said Andrew Dillin, the Thomas and Stacey Siebel Distinguished Chair of Stem Cell Research in the Department of Molecular and Cell Biology and Howard Hughes Medical Institute investigator at the University of California, Berkeley.

    br
    A cell suffering heat shock is like a country besieged, where attackers first sever lines of communications. The pat-10 gene helps repair communication to allow chaperones to treat misfolded proteins. (Andrew Dillin graphic)

    Dillin, UC Berkeley postdoctoral fellows Nathan A. Baird and Peter M. Douglas and their colleagues at the University of Michigan, The Scripps Research Institute and Genentech Inc., will publish their results in the Oct. 17 issue of the journal Science.

    Cells put a lot of effort into preventing proteins – which are like a string of beads arranged in a precise three-dimensional shape – from unraveling, since a protein’s activity as an enzyme or structural component depends on being properly shaped and folded. There are at least 350 separate molecular chaperones constantly patrolling the cell to refold misfolded proteins. Heat is one of the major threats to proteins, as can be demonstrated when frying an egg – the clear white albumen turns opaque as the proteins unfold and then tangle like spaghetti.

    Heat shock

    For 35 years, researchers have worked under the assumption that when cells undergo heat shock, as with a fever, they produce a protein that triggers a cascade of events that field even more chaperones to refold unraveling proteins that could kill the cell. The protein, HSF-1 (heat shock factor-1), does this by binding to promoters upstream of the 350-plus chaperone genes, upping the genes’ activity and launching the army of chaperones, which originally were called “heat shock proteins.”

    Injecting animals with HSF-1 has been shown not only to increase their tolerance of heat stress, but to increase lifespan.

    Because an accumulation of misfolded proteins has been implicated in aging and in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s diseases, scientists have sought ways to artificially boost HSF-1 in order to reduce the protein plaques and tangles that eventually kill brain cells. To date, such boosters have extended lifespan in lab animals, including mice, but greatly increased the incidence of cancer.

    Dillin’s team found in experiments on the nematode worm C. elegans that HSF-1 does a whole lot more than trigger release of chaperones. An equal if not more important function is to stabilize the cell’s cytoskeleton, which is the highway that transports essential supplies – healing chaperones included – around the cell.

    “We are suggesting that, rather than making more of HSF-1 to prevent diseases like Huntington’s, we should be looking for ways to make the actin cytoskeleton better,” Dillin said. Such tactics might avoid the carcinogenic side effects of upping HSF-1.

    Dillin is codirector of the Paul F. Glenn Center for Aging Research, a new collaboration between UC Berkeley and UC San Francisco supported by the Glenn Foundation for Medical Research. Center investigators will study the many ways that proteins malfunction within cells, ideally paving the way for novel treatments for neurodegenerative diseases.

    A cell at war

    Dillin compares a cell experiencing heat shock to a country under attack. In a war, an aggressor first cuts off all communications, such as roads, train and bridges, which prevents the doctors from treating the wounded. Similarly, heat shock disrupts the cytoskeletal highway, preventing the chaperone “doctors” from reaching the patients, the misfolded proteins.

    chap
    Chaperones help newborn proteins (polypeptides) fold properly, but also fix misfolded proteins.

    “We think HSF-1 not only makes more chaperones, more doctors, but also insures that the roadways stay intact to keep everything functional and make sure the chaperones can get to the sick and wounded warriors,” he said.

    The researchers found specifically that HSF-1 up-regulates another gene, pat-10, that produces a protein that stabilizes actin, the building blocks of the cytoskeleton.

    By boosting pat-10 activity, they were able to cure worms that had been altered to express the Huntington’s disease gene, and also extend the lifespan of normal worms.

    Dillin suspects that HSF-1’s main function is, in fact, to protect the actin cytoskeleton. He and his team mutated HSF-1 so that it no longer boosted chaperones, demonstrating, he said, that “you can survive heat shock with the normal level of heat shock proteins, as long as you make your cytoskeleton work better.”

    He noted that the team’s results – that boosting chaperones is not essential to surviving heat stress – were so contradictory to current thinking that “I made my post-docs’ lives hell for three years” insisting on more experiments to rule out errors. Yet, when Dillin presented the results recently to members of the protein-folding community, he said the first reaction of many was, “That makes perfect sense.”

    Dillin’s colleagues include Milos S. Simic and Suzanne C. Wolff of UC Berkeley, Ana R. Grant of the University of Michigan in Ann Arbor, James J. Moresco and John R. Yates III of Scripps in La Jolla, Calif., and Gerard Manning of Genentech, South San Francisco, Calif. The work is funded by the Howard Hughes Medical Institute as well as by the National Institute of General Medical Sciences (8 P41 GM103533-17) and National Institute on Aging (R01AG027463-04) of the National Institutes of Health.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 3:51 pm on October 16, 2014 Permalink | Reply
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    From UC Berkeley: “Earth’s magnetic field could flip within a human lifetime” 

    UC Berkeley

    UC Berkeley

    October 14, 2014
    Robert Sanders

    Imagine the world waking up one morning to discover that all compasses pointed south instead of north.

    It’s not as bizarre as it sounds. Earth’s magnetic field has flipped – though not overnight – many times throughout the planet’s history. Its dipole magnetic field, like that of a bar magnet, remains about the same intensity for thousands to millions of years, but for incompletely known reasons it occasionally weakens and, presumably over a few thousand years, reverses direction.

    team
    Left to right, Biaggio Giaccio, Gianluca Sotilli, Courtney Sprain and Sebastien Nomade sitting next to an outcrop in the Sulmona basin of the Apennine Mountains that contains the Matuyama-Brunhes magnetic reversal. A layer of volcanic ash interbedded with the lake sediments can be seen above their heads. Sotilli and Sprain are pointing to the sediment layer in which the magnetic reversal occurred. (Photo by Paul Renne)

    Now, a new study by a team of scientists from Italy, France, Columbia University and the University of California, Berkeley, demonstrates that the last magnetic reversal 786,000 years ago actually happened very quickly, in less than 100 years – roughly a human lifetime.

    “It’s amazing how rapidly we see that reversal,” said UC Berkeley graduate student Courtney Sprain. “The paleomagnetic data are very well done. This is one of the best records we have so far of what happens during a reversal and how quickly these reversals can happen.”

    Sprain and Paul Renne, director of the Berkeley Geochronology Center and a UC Berkeley professor-in- residence of earth and planetary science, are coauthors of the study, which will be published in the November issue of Geophysical Journal International and is now available online.

    Flip could affect electrical grid, cancer rates

    The discovery comes as new evidence indicates that the intensity of Earth’s magnetic field is decreasing 10 times faster than normal, leading some geophysicists to predict a reversal within a few thousand years.

    Though a magnetic reversal is a major planet-wide event driven by convection in Earth’s iron core, there are no documented catastrophes associated with past reversals, despite much searching in the geologic and biologic record. Today, however, such a reversal could potentially wreak havoc with our electrical grid, generating currents that might take it down.

    And since Earth’s magnetic field protects life from energetic particles from the sun and cosmic rays, both of which can cause genetic mutations, a weakening or temporary loss of the field before a permanent reversal could increase cancer rates. The danger to life would be even greater if flips were preceded by long periods of unstable magnetic behavior.

    “We should be thinking more about what the biologic effects would be,” Renne said.

    Dating ash deposits from windward volcanoes

    The new finding is based on measurements of the magnetic field alignment in layers of ancient lake sediments now exposed in the Sulmona basin of the Apennine Mountains east of Rome, Italy. The lake sediments are interbedded with ash layers erupted from the Roman volcanic province, a large area of volcanoes upwind of the former lake that includes periodically erupting volcanoes near Sabatini, Vesuvius and the Alban Hills.

    two
    Leonardo Sagnotti, standing, and coauthor Giancarlo Scardia collecting a sample for paleomagnetic analysis.

    Italian researchers led by Leonardo Sagnotti of Rome’s National Institute of Geophysics and Volcanology measured the magnetic field directions frozen into the sediments as they accumulated at the bottom of the ancient lake.

    Sprain and Renne used argon-argon dating, a method widely used to determine the ages of rocks, whether they’re thousands or billions of years old, to determine the age of ash layers above and below the sediment layer recording the last reversal. These dates were confirmed by their colleague and former UC Berkeley postdoctoral fellow Sebastien Nomade of the Laboratory of Environmental and Climate Sciences in Gif-Sur-Yvette, France.

    Because the lake sediments were deposited at a high and steady rate over a 10,000-year period, the team was able to interpolate the date of the layer showing the magnetic reversal, called the Matuyama-Brunhes transition, at approximately 786,000 years ago. This date is far more precise than that from previous studies, which placed the reversal between 770,000 and 795,000 years ago.

    “What’s incredible is that you go from reverse polarity to a field that is normal with essentially nothing in between, which means it had to have happened very quickly, probably in less than 100 years,” said Renne. “We don’t know whether the next reversal will occur as suddenly as this one did, but we also don’t know that it won’t.”

    Unstable magnetic field preceded 180-degree flip

    Whether or not the new finding spells trouble for modern civilization, it likely will help researchers understand how and why Earth’s magnetic field episodically reverses polarity, Renne said.
    the polar wanderingsThe ‘north pole’ — that is, the direction of magnetic north — was reversed a million years ago. This map shows how, starting about 789,000 years ago, the north pole wandered around Antarctica for several thousand years before flipping 786,000 years ago to the orientation we know today, with the pole somewhere in the Arctic.

    The magnetic record the Italian-led team obtained shows that the sudden 180-degree flip of the field was preceded by a period of instability that spanned more than 6,000 years. The instability included two intervals of low magnetic field strength that lasted about 2,000 years each. Rapid changes in field orientations may have occurred within the first interval of low strength. The full magnetic polarity reversal – that is, the final and very rapid flip to what the field is today – happened toward the end of the most recent interval of low field strength.

    Renne is continuing his collaboration with the Italian-French team to correlate the lake record with past climate change.

    Renne and Sprain’s work at the Berkeley Geochronology Center was supported by the Ann and Gordon Getty Foundation.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 9:59 am on March 7, 2014 Permalink | Reply
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    From UC Berkeley: “Colored diamonds are a superconductor’s best friend” 

    UC Berkeley

    March 6, 2014
    Robert Sanders

    Flawed but colorful diamonds are among the most sensitive detectors of magnetic fields known today, allowing physicists to explore the minuscule magnetic fields in metals, exotic materials and even human tissue.

    two
    Dmitry Budker and Ron Folman build ‘atom chips’ to probe the minuscule magnetic properties of high-temperature superconductors. Robert Sanders photo.

    University of California, Berkeley, physicist Dmitry Budker and his colleagues at Ben-Gurion University of the Negev in Israel and UCLA have now shown that these diamond sensors can measure the tiny magnetic fields in high-temperature superconductors, providing a new tool to probe these much ballyhooed but poorly understood materials.

    “Diamond sensors will give us measurements that will be useful in understanding the physics of high temperature superconductors, which, despite the fact that their discoverers won a 1987 Nobel Prize, are still not understood,” said Budker, a professor of physics and faculty scientist at Lawrence Berkeley National Laboratory.

    High-temperature superconductors are exotic mixes of materials like yttrium or bismuth that, when chilled to around 180 degrees Fahrenheit above absolute zero (-280ºF), lose all resistance to electricity, whereas low-temperature superconductors must be chilled to several degrees above absolute zero. When discovered 28 years ago, scientists predicted we would soon have room-temperature superconductors for lossless electrical transmission or magnetically levitated trains.

    It never happened.

    “The new probe may shed light on high-temperature superconductors and help theoreticians crack this open question,” said coauthor Ron Folman of Ben-Gurion University of the Negev, who is currently a Miller Visiting Professor at UC Berkeley. “With the help of this new sensor, we may be able to take a step forward.”

    Budker, Folman and their colleagues report their success in an article posted online Feb. 18 in the journal Physical Review B.

    Flawed but colorful

    Colorful diamonds, ranging from yellow and orange to purple, have been prized for millennia. Their color derives from flaws in the gem’s carbon structure: some of the carbon atoms have been replaced by an element, such as boron, that emits or absorbs a specific color of light.

    Once scientists learned how to create synthetic diamonds, they found that they could selectively alter a diamond’s optical properties by injecting impurities. In this experiment, Budker, Folman and their colleagues bombarded a synthetic diamond with nitrogen atoms to knock out carbon atoms, leaving holes in some places and nitrogen atoms in others. They then heated the crystal to force the holes, called vacancies, to move around and pair with nitrogen atoms, resulting in diamonds with so-called nitrogen-vacancy centers. For the negatively charged centers, the amount of light they re-emit when excited with light becomes very sensitive to magnetic fields, allowing them to be used as sensors that are read out by laser spectroscopy.

    Folman noted that color centers in diamonds have the unique property of exhibiting quantum behavior, whereas most other solids at room temperature do not.

    “This is quite surprising, and is part of the reason that these new sensors have such a high potential,” Folman said.

    Applications in homeland security?

    Technology visionaries are thinking about using nitrogen-vacancy centers to probe for cracks in metals, such as bridge structures or jet engine blades, for homeland security applications, as sensitive rotation sensors, and perhaps even as building blocks for quantum computers.

    lattice
    The crystal lattice of a pure diamond is pure carbon (black balls), but when a nitrogen atom replaces one carbon and an adjacent carbon is kicked out, the ‘nitrogen-vacancy center’ becomes a sensitive magnetic field sensor.

    Budker, who works on sensitive magnetic field detectors, and Folman, who builds ‘atom chips’ to probe and manipulate atoms, focused in this work on using these magnetometers to study new materials.

    “These diamond sensors combine high sensitivity with the potential for high spatial resolution, and since they operate at higher temperatures than their competitors – superconducting quantum interference device, or SQUID, magnetometers – they turn out to be good for studying high temperature superconductors,” Budker said. “Although several techniques already exist for magnetic probing of superconducting materials, there is a need for new methods which will offer better performance.”

    The team used their diamond sensor to measure properties of a thin layer of yttrium barium copper oxide (YBCO), one of the two most popular types of high-temperatures superconductor. The Ben-Gurion group integrated the diamond sensor with the superconductor on one chip and used it to detect the transition from normal conductivity to superconductivity, when the material expels all magnetic fields. The sensor also detected tiny magnetic vortices, which appear and disappear as the material becomes superconducting and may be a key to understanding how these materials become superconducting at high temperatures.

    “Now that we have proved it is possible to probe high-temperatures superconductors, we plan to build more sensitive and higher-resolution sensors on a chip to study the structure of an individual magnetic vortex,” Folman said. “We hope to discover something new that cannot be seen with other technologies.”

    Researchers, including Budker and Folman, are attempting to solve other mysteries through magnetic sensing. For example, they are investigating networks of nerve cells by detecting the magnetic field each nerve cell pulse emits. In another project, they aim at detecting strange never-before-observed entities called axions through their effect on magnetic sensors.

    Coauthors include Amir Waxman, Yechezkel Schlussel and David Groswasser of Ben-Gurion University of the Negev, UC Berkeley Ph.D. graduate Victor Acosta, who is now at Google [x] in Mountain View, Calif., and former UC Berkeley post-doc Louis Bouchard, now a UCLA assistant professor of chemistry and biochemistry.

    The work was supported by the NATO Science for Peace program, AFOSR/DARPA QuASAR program, the National Science Foundation and UC Berkeley’s Miller Institute for Basic Research in Science.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 5:08 pm on March 5, 2014 Permalink | Reply
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    From UC Berkeley: “Using Carbon to Control the Light” 

    UC Berkeley

    The flip of a light switch – a nano-scale light switch – may some day dramatically boost the speed of data transmission, from streaming movies to accelerating the most data-intense computation. Today, information flow in a computer is based on electrical pulses. But if an electrical signal could instead control a light switch, the “ones and zeros” that give data meaning could race through computer circuits at ten times the current speed. A ten-fold increase in speed would mean a similar spike in the volume of information that can be processed.

    fw
    Feng Wang performing optoelectronic measurements in the lab. Photo: Peg Skorpinski.

    Of course, electrical signals are used to modulate light in the optical fibers that transmit massive amounts of data around the corner and around the world. But harnessing light to boost communication between chips within a computer circuit has proved an elusive goal. At the scale of computer circuitry, materials such as silicon can’t absorb light efficiently, and devices that can perform well are too bulky to integrate into a chip.

    So excitement runs high that graphene, a material under intense study for only a decade, might do the trick. Single atom-thick carbon graphene crystals absorb all wavelengths of light, and at certain voltages, electrical pulses can turn the material’s light absorption on and off – the key to data transmission. This trait and graphene’s nano-size “footprint” make it an ideal candidate for ultra-miniature optical devices that could be installed by the thousands on a chip to control traffic flow.

    “We’re not there yet,” says Feng Wang, assistant professor of physics and a Bakar Fellow, “but graphene’s remarkable combination of electrical and optical properties, and its potential for nanofabrication hold great promise for optoelectronics.”

    Wang’s lab studies how electrical fields modulate the optical properties of a number of materials. The Bakar Fellows Program supports his efforts to develop graphene modulators for chip-to-chip communication. Because he’s manipulating photons, he can do much of the research under an optical microscope. At this relatively low magnification, a graphene layer looks like a continuous thin sheet. But under the power of a scanning tunneling microscope that can resolve individual atoms, the material’s chicken wire-like atomic configuration appears.

    Wang grew up in Nanchang in the south of China and went to college in Shanghai. He received his PhD in physics at Columbia and was a postdoc at Berkeley before joining the physics faculty. His focus on graphene’s potential to boost chip-to-chip performance in computers circuits began about six years ago. Before that, he studied carbon nanotubes, a one dimensional carbon material.

    fw2
    Feng Wang began to focus on graphene’s potential to boost chip-to-chip performance in computer circuits about six years ago. Photo: Peg Skorpinski.

    “Our lab mainly focuses on the fundamental physics of how light interacts with materials at the nano-scale, and what novel properties emerge,” Wang says. This holds a lot of fascination for me.

    “But exploring ways to exploit some of these novel behaviors in microelectronics is just as exciting. The basic research can reveal real-world applications. It’s a great combination.”

    Out on the horizon, Wang can see graphene integrated into infrared imagers and optical sensors, and possibly being used to detect telltale changes in diseased cells. Metabolism changes the pH, or acidity, of cells, and fast-metabolizing cancer cells have distinct metabolic signatures. Local pH variations, in turn, alter the optical absorption properties of graphene. This could be measured to aid in diagnosis.

    Similarly, graphene may one day aid detection of neurological disease. Neurons communicate with pulses of ions – their so-called “action potential” – and the release of ions modified the optical absorption of graphene. Such a change in graphene could potentially be used detect neuron activity.

    These applications are well down the line, Wang says, though not at all out of the question. For now, he seems fully absorbed by the physics of this truly absorbing nano-material.
    ____________________________

    The Bakar Fellows Program supports innovative research by early career faculty at UC Berkeley with a special focus on projects that hold commercial promise. For more information, see http://bakarfellows.berkeley.edu.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 2:16 pm on February 25, 2014 Permalink | Reply
    Tags: UC Berkeley, Wikipedia   

    From UC Berkeley: “Berkeley’s Wikipedian-in-residence is a first” 

    UC Berkeley

    February 25, 2014
    Cathy Cockrell

    With guidance from a Wikipedian-in-residence — the first at a U.S. college or university — scores of Berkeley undergraduates will soon be publishing their academic work on one of the world’s most widely read websites.

    An aficionado of the free, collaboratively edited online encyclopedia, Kevin Gorman, 24, has been hired by the campus’s American Cultures program to facilitate Wikipedia-based research and writing assignments.

    kg
    Wikipedian-in-Residence Kevin Gorman

    Until now, Wikipedians-in-residence have been assigned to cultural institutions, more than 50 in all, such as the British Museum, the Gerald Ford Presidential Library and the U.S. National Archives.

    A hardcore Wikipedian since his undergrad days at Berkeley, Gorman was a natural candidate to bring the role to academia. By the time he graduated last year, he had edited scores of Wikipedia articles — on personal interests ranging from mushrooms to men’s rights — and had helped to design and facilitate a Wikipedia-based assignment for Berkeley course on prisons.

    According to Gorman, the combined page views for the articles they produced for Wikipedia (see, for instance, their entry for the Latina activist group Mothers of East Los Angeles) have been in the hundreds of thousands, if not millions.

    Many students initially resist Wikipedia project, he says, because they don’t want their work subjected to public view. But once they realize the potential impact of their efforts, “they start to get excited. They go from ‘you can’t make me’ to enthusiastic participants.”

    From food deserts to urban ag

    One of the first Berkeley instructors to tap the expertise of the new Wikipedian-in-residence is Associate Professor Dara O’Rourke, whose popular course on environmental justice combines classroom instruction with “engaged scholarship” through collaboration with non-profit organizations.

    “I’m not interested in students writing term papers that only I and the graduate-student instructor read,” O’Rourke says. “That’s not utilizing students’ potential to the fullest.”

    This semester, he offered students a choice for the community-service component of the course. They could collaborate directly with local groups focused on environmental justice-related issues, or they could work in teams to improve Wikipedia content on some of those same topics.

    “You can imagine building a Wikipedia page [on each topic] that is really comprehensive,” says O’Rourke.” It’s compelling that the site gets 550 million unique visitors per month.”

    Many students apparently think so, too. About 90 opted to do wiki projects, and are now busy tracking down and synthesizing previously published information on environmental-justice issues — food deserts, climate resilience, urban agriculture in Oakland and reform of the federal Toxic Substances Control Act among them.

    High-quality secondary research

    Wikipedia, the “free encyclopedia that anyone can edit,” does not accept original research. Instead, an army of volunteer editors, working in more than 200 languages, summarizes what’s been published elsewhere and provides hyperlinks to those sources. Wikipedia editors are expected to use neutral language and cite information from a range of perspectives.

    Students are drawn to this model, says lecturer and American Cultures coordinator Victoria Robinson, who worked with Gorman for her ethnic-studies course on the prison system and hired him for his new position. It appealed to students, she says, “that their work was not ‘opinion based’ and that it contributed new public information that could be viewed as reliable.”

    Creating a high-quality Wikipedia entry, however, is not as simple as it might seem. Recently, campus librarian Corliss Lee was a guest speaker in O’Rourke’s class. Her message to undergrads seated in a large lecture hall: There’s a lot of human knowledge that can’t be found via a Google search, and the campus library offers rich databases and peer-reviewed publications you can mine.

    Students doing Wikipedia projects are encouraged to look for sources in academic journals, Gorman says. One fundamental mission of UC is to enhance public access to knowledge. When you share knowledge that’s behind a paywall, you’re serving that core mission, he believes.

    A Wikipedian’s mission

    In the spirit of knowledge sharing, Gorman, in his new role, intends to write guidelines on designing and implementing Wikipedia-based class assignments, and post these how-to’s online for instructors everywhere to use.

    Systemic bias is another of his concerns — the fact that about 90 percent of Wikipedia editors are male, 80 percent are white (as extrapolated from survey results) and the lion’s share hail from developed nations.

    “Providing content not yet found on Wikipedia, in areas that suffer due to our systemic biases, is vital work” to be done at this time, he writes on the site and tells students in a slide-illustrated talk.

    O’Rourke says his students could help improve these lopsided stats. “Berkeley students are a unique and select group themselves,” he notes. But measured by racial and ethnic diversity, “our classroom is not similar to the Wikipedia high-contributor category. This is an experiment — to contribute to Wikipedia in a way that strengthens its content.”

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 2:27 pm on January 28, 2014 Permalink | Reply
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    From U.C Berkeley: “Researchers open door to new HIV therapy” 

    UC Berkeley

    January 28, 2014
    Robert Sanders

    People infected with the Human Immunodeficiency Virus (HIV) can stave off the symptoms of AIDS thanks to drug cocktails that mainly target three enzymes produced by the virus, but resistant strains pop up periodically that threaten to thwart these drug combos.

    aids
    The AIDS virus enters immune cells by binding to CD4 receptors embedded in the membrane (parallel lines) of the cell. But once a virus enters the cell, it makes a protein, Nef, that binds to the protein complex underlying CD4, tagging it for the waste bin. Potential anti-HIV drugs would disable one of the proteins (colored blobs) to which Nef binds, interfering with HIV’s strategy for spreading through the body. Image by James Hurley, UC Berkeley.

    Researchers at the University of California, Berkeley, and the National Institutes of Health have instead focused on a fourth protein, Nef, that hijacks host proteins and is essential to HIV’s lethality. The researchers have captured a high-resolution snapshot of Nef bound with a main host protein, and discovered a portion of the host protein that will make a promising target for the next-generation of anti-HIV drugs. By blocking the part of a key host protein to which Nef binds, it may be possible to slow or stop HIV.

    “We have imaged the molecular details for the first time,” said structural biologist James H. Hurley, UC Berkeley professor of molecular and cell biology. “Having these details in hand puts us in striking distance of designing drugs to block the binding site and, in doing so, block HIV infectivity.”

    Hurley, cell biologist Juan Bonifacino of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) of the National Institutes of Health and their colleagues report their findings in a paper published today (Jan. 28) by the open-access, online journal eLife.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 6:42 pm on January 22, 2014 Permalink | Reply
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    From UC Berkeley: “Turkeys inspire smartphone-capable early warning system for toxins” 

    UC Berkeley

    Some may think of turkeys as good for just lunch meat and holiday meals, but bioengineers at UC Berkeley saw inspiration in the big birds for a new type of biosensor that changes color when exposed to chemical vapors. This feature makes the sensors valuable detectors of toxins or airborne pathogens.

    turkeys
    Researchers took inspiration from the way turkey skin color is altered to create a new sensor that can change color when exposed to volatile chemicals. (Photos by Valerie Burtchett)

    Turkey skin, it turns out, can shift from red to blue to white, thanks to bundles of collagen that are interspersed with a dense array of blood vessels. It is this color-shifting characteristic that gives turkeys the name “seven-faced birds” in Japanese and Korean.

    The researchers say that spacing between the collagen fibers changes when the blood vessels swell or contract, depending upon whether the bird is excited or angry. The amount of swelling changes the way light waves are scattered and, in turn, alters the colors we see on the bird’s head.

    Seung-Wuk Lee, UC Berkeley associate professor of bioengineering, led a research team in mimicking this color-changing ability to create biosensors that can detect volatile chemicals.

    “In our lab, we study how light is generated and changes in nature, and then we use what we learn to engineer novel devices,” said Lee, who is also a faculty scientist at the Lawrence Berkeley National Laboratory.

    The researchers created a mobile app, the iColour Analyser, to show that a smartphone photo of the sensor’s color bands could be used to help identify chemicals of interest, such as vapor of the explosive TNT. They described their experiments in a study published today (Tuesday, Jan. 21) in the journal Nature Communications.

    Sensors that give off color readings are easier to use and read than conventional biosensors. However, the major color-based sensors in development elsewhere can only detect a limited range of chemicals and, according to the researchers, they can be very difficult to manufacture.

    “Our system is convenient, and it is cheap to make,” said Lee. “We also showed that this technology can be adapted so that smartphones can help analyze the color fingerprint of the target chemical. In the future, we could potentially use this same technology to create a breath test to detect cancer and other diseases.”

    graph
    Bio-inspired sensors are made from bacteriophages that mimic the collagen fibers in turkey skin. When exposed to target chemicals, the collagen-like bundles expand or contract, generating different colors. The researchers also created a mobile app to be used with smartphones to help analyze the sensor’s color bands. (Schematic courtesy of the Seung-Wuk Lee Laboratory)

    In copying this turkey-skin design, Lee and his team employed a technique they pioneered to mimic nanostructures like collagen fibers. The researchers found a way to get M13 bacteriophages, benign viruses with a shape that closely resembles collagen fibers, to self-assemble into patterns that could be easily fine-tuned.

    The researchers found that, like collagen fibers, these phage-bundled nanostructures expanded and contracted, resulting in color changes. The exact mechanism behind the shrinking or expanding phage bundles is still unclear, but it’s possible that the small amount of water in the phage is reacting to the chemical vapors, the researchers said.

    The turkey-inspired biosensors were exposed to a range of volatile organic compounds, including hexane, isopropyl alcohol and methanol, as well as TNT, at concentrations of 300 parts per billion. The researchers found that the viruses swelled rapidly, resulting in specific color patterns that served as “fingerprints” to distinguish the different chemicals tested.

    The researchers showed that the biosensor’s specificity to a target chemical could be increased by genetically engineering the DNA in the M13 bacteriophage to bind with sites specific to TNT. The biosensor was then exposed to two additional chemicals, DNT and MNT, which have similar molecular structures to TNT. The engineered biosensor successfully distinguished TNT from the other chemicals with distinct color bands.

    The biosensors were also able to signal changes in relative humidity, ranging from 20 percent to 90 percent, becoming redder with moister air and bluer with drier air.

    The study lead author is Jin-Woo Oh, a former postdoctoral researcher in Lee’s lab and now an assistant professor in the Department of Nanomaterial Engineering at Pusan National University in South Korea.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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