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  • richardmitnick 8:50 pm on February 20, 2018 Permalink | Reply
    Tags: , , Biology, PLANTS COLONIZED THE EARTH 100 MILLION YEARS EARLIER THAN PREVIOUSLY THOUGHT   

    From Astrobiology Magazine: “PLANTS COLONIZED THE EARTH 100 MILLION YEARS EARLIER THAN PREVIOUSLY THOUGHT” 

    Astrobiology Magazine

    Astrobiology Magazine

    Feb 20, 2018

    1

    For the first four billion years of Earth’s history, our planet’s continents would have been devoid of all life except microbes.

    All of this changed with the origin of land plants from their pond scum relatives, greening the continents and creating habitats that animals would later invade.

    The timing of this episode has previously relied on the oldest fossil plants which are about 420 million years old.

    New research, published in the journal Proceedings of the National Academy of Sciences USA, indicates that these events actually occurred a hundred million years earlier, changing perceptions of the evolution of the Earth’s biosphere.

    Plants are major contributors to the chemical weathering of continental rocks, a key process in the carbon cycle that regulates Earth’s atmosphere and climate over millions of years.

    The team used ‘molecular clock’ methodology, which combined evidence on the genetic differences between living species and fossil constraints on the age of their shared ancestors, to establish an evolutionary timescale that sees through the gaps in the fossil record.

    Dr Jennifer Morris, from the University of Bristol’s School of Earth Sciences and co-lead author on the study, explained: “The global spread of plants and their adaptations to life on land, led to an increase in continental weathering rates that ultimately resulted in a dramatic decrease the levels of the ‘greenhouse gas’ carbon dioxide in the atmosphere and global cooling.

    “Previous attempts to model these changes in the atmosphere have accepted the plant fossil record at face value – our research shows that these fossil ages underestimate the origins of land plants, and so these models need to be revised.”

    Co-lead author Mark Puttick described the team’s approach to produce the timescale. He said: “The fossil record is too sparse and incomplete to be a reliable guide to date the origin of land plants. Instead of relying on the fossil record alone, we used a ‘molecular clock’ approach to compare differences in the make-up of genes of living species – these relative genetic differences were then converted into ages by using the fossil ages as a loose framework.

    “Our results show the ancestor of land plants was alive in the middle Cambrian Period, which was similar to the age for the first known terrestrial animals.”

    One difficulty in the study is that the relationships between the earliest land plants are not known. Therefore the team, which also includes members from Cardiff University and the Natural History Museum, London, explored if different relationships changed the estimated origin time for land plants.

    Leaders of the overall study, Professor Philip Donoghue and Harald Schneider added: “We used different assumptions on the relationships between land plants and found this did not impact the age of the earliest land plants.

    “Any future attempts to model atmospheric changes in deep-time must incorporate the full range of uncertainties we have used here.”

    See the full article here .

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  • richardmitnick 10:19 am on February 19, 2018 Permalink | Reply
    Tags: , Biology, C1 complex, CryoEM-cryo electron microscopy, CryoET-Cryo electron tomography, U Utrecht   

    From U Utrecht: “Unexpected immune activation illustrated in the cold” 

    Utrecht University

    15 February 2018

    Monica van der Garde
    Public Information Officer
    m.vandergarde@uu.nl
    +31 (0)6 13 66 14 38

    Press Office Leiden University Medical Center
    pers@lumc.nl
    +31 6 11 37 11 46
    +31 71 526 8005

    q
    Combining CryoEM and CryoET lets researchers see the C1 complex in 3D (coloured model) bound to antibodies in a native state (background).

    Researchers at Utrecht University and Leiden University Medical Center, the Netherlands, have for the first time made a picture of an important on-switch of our immune system. Their novel technical approach already led to the discovery of not one, but two ways in which the immune system can be activated. This kind of new insights are important for designing better therapies against infections or cancer, according to team leaders Piet Gros and Thom Sharp. Their findings are published on February 16, 2018 in the journal Science.

    When invading microbes, viruses and tumours are detected in our bodies, our antibodies engage in an immediate defence strategy. They quickly raise warning signs on these aberrant surfaces that alert our body’s immune system of a security breach. This is the entry cue of several molecules, together called the C1 complex, that stick to the surface of the rogue cell and eliminate it from our body. Until recently, it was unknown how exactly invaders were recognized, and how this C1 complex was activated.

    Challenging

    Studying the C1 complex has been challenging since its components often clump together when taken out of their natural environment into a lab setting. Together with the international biotech company Genmab A/S, researchers from Utrecht University and Leiden University Medical Center have now developed a unique technical approach to studying it in a more natural environment – and discovered more than expected.

    Life-like detailed picture

    In order to capture the binding and interaction of the complex, Piet Gros, Utrecht University and Thom Sharp, Leiden University Medical Center, combined two imaging techniques, cryo electron microscopy (CryoEM) and cryo electron tomography (CryoET). “These technologies are exploding in the field,” describes Thom Sharp, “and each method gives us different but complementary information on the same complex.” When combined, these methods provide a more life-like detailed picture of the system.

    Reconstruction into a 3D representation

    For CryoEM, think of taking thousands of copies of the same convoluted complex and scattering them onto the sticky side of a piece of tape. The camera is in a fixed position and takes pictures of these particles, which may have landed right-side-up, on its side, on a point. CryoET, on the other hand, can image the complex in a more natural environment, as it is bound to the cell surface. It takes images from different angles of the complex, similar to a CT scan, where the particle rotates within the instrument. For both techniques, images are then reconstructed into a 3D representation of the complex.

    Very different mechanisms identified

    The researchers were surprised to find not one, but two ways in which the immune system can be activated: by physical distortion and by cross-activation. In some cases, the configuration of danger signals on a cell’s surface is sparse, and when antibodies bind, the entire complex must physically adjust or distort itself to properly fit. This adjustment of a single complex can set off an immune response. In other situations, where the danger signals are dense, multiple C1 complexes can help activate each other, like a neighbourhood watch system.

    First report

    This is the first report of two independent ways by which our immune system can be activated. In addition, the combination of CryoEM and CryoET enabled the visualization of details of these interactions that may enable researchers to create more specific therapeutics that can activate, slow down or stop the cascade of signals within our immune system.

    See the full article here .

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    Utrecht University (UU; Dutch: Universiteit Utrecht, formerly Rijksuniversiteit Utrecht) is a university in Utrecht, the Netherlands. It is one of the oldest universities in the Netherlands. Established March 26, 1636, it had an enrollment of 29,425 students in 2016, and employed 5,568 faculty and staff.[4] In 2011, 485 PhD degrees were awarded and 7,773 scientific articles were published. The 2013 budget of the university was €765 million.[5]

    The university is rated as the best university in the Netherlands by the Shanghai Ranking of World Universities 2013, and ranked as the 13th best university in Europe and the 52nd best university of the world.

    The university’s motto is “Sol Iustitiae Illustra Nos,” which means “Sun of Justice, shine upon us.” This motto was gleaned from a literal Latin Bible translation of Malachi 4:2. (Rutgers University, having a historical connection with Utrecht University, uses a modified version of this motto.) Utrecht University is led by the University Board, consisting of prof. dr. Bert van der Zwaan (Rector Magnificus) and Hans Amman.

     
  • richardmitnick 9:11 am on February 19, 2018 Permalink | Reply
    Tags: , Biology, Electric Eels, Electrocytes, ,   

    From The Atlantic: “A New Kind of Soft Battery, Inspired by the Electric Eel” 

    Atlantic Magazine

    The Atlantic Magazine

    Dec 13, 2017
    Ed Yong

    1
    Thomas Schroeder / Anirvan Guha

    In 1799, the Italian scientist Alessandro Volta fashioned an arm-long stack of zinc and copper discs, separated by salt-soaked cardboard. This “voltaic pile” was the world’s first synthetic battery, but Volta based its design on something far older—the body of the electric eel.

    This infamous fish makes its own electricity using an electric organ that makes up 80 percent of its two-meter length. The organ contains thousands of specialized muscle cells called Electric Eel. Each only produces a small voltage, but together, they can generate up to 600 volts—enough to stun a human, or even a horse. They also provided Volta with ideas for his battery, turning him into a 19th-century celebrity.

    Two centuries on, and batteries are everyday objects. But even now, the electric eel isn’t done inspiring scientists. A team of researchers led by Michael Mayer at the University of Fribourg have now created a new kind of power source [Nature] that ingeniously mimics the eel’s electric organ. It consists of blobs of multicolored gels, arranged in long rows much like the eel’s electrocytes. To turn this battery on, all you need to do is to press the gels together.

    Unlike conventional batteries, the team’s design is soft and flexible, and might be useful for powering the next generation of soft-bodied robots. And since it can be made from materials that are compatible with our bodies, it could potentially drive the next generation of pacemakers, prosthetics, and medical implants. Imagine contact lenses that generate electric power, or pacemakers that run on the fluids and salts within our own bodies—all inspired by a shocking fish.

    To create their unorthodox battery, the team members Tom Schroeder and Anirvan Guha began by reading up on how the eel’s electrocytes work. These cells are stacked in long rows with fluid-filled spaces between them. Picture a very tall tower of syrup-smothered pancakes, turned on its side, and you’ll get the idea.

    When the eel’s at rest, each electrocyte pumps positively charged ions out of both its front-facing and back-facing sides. This creates two opposing voltages that cancel each other out. But at the eel’s command, the back side of each electrocyte flips, and starts pumping positive ions in the opposite direction, creating a small voltage across the entire cell. And crucially, every electrocyte performs this flip at the same time, so their tiny voltages add up to something far more powerful. It’s as if the eel has thousands of small batteries in its tail; half are pointing in the wrong direction but it can flip them at a whim, so that all of them align. “It’s insanely specialized,” says Schroeder.

    2
    How an electric eel’s electrocytes work (Schroeder et al. / Nature).

    He and his colleagues first thought about re-creating the entire electric organ in a lab, but soon realized that it’s far too complicated. Next, they considered setting up a massive series of membranes to mimic the stacks of electrocytes—but these are delicate materials that are hard to engineer in the thousands. If one broke, the whole series would shut down. “You’d run into the string-of-Christmas-lights problem,” says Schroeder.

    In the end, he and Guha opted for a much simpler setup, involving lumps of gel that are arranged on two separate sheets. Look at the image below, and focus on the bottom sheet. The red gels contain saltwater, while blue ones contain freshwater. Ions would flow from the former to the latter, but they can’t because the gels are separated. That changes when the green and yellow gels on the other sheet bridge the gaps between the blue and red ones, providing channels through which ions can travel.

    Here’s the clever bit: The green gel lumps only allow positive ions to flow through them, while the yellow ones only let negative ions pass. This means (as the inset in the image shows) that positive ions flow into the blue gels from only one side, while negative ions flow in from the other. This creates a voltage across the blue gel, exactly as if it was an electrocyte. And just as in the electrocytes, each gel only produces a tiny voltage, but thousands of them, arranged in a row, can produce up to 110 volts

    3
    Schroeder et al. / Nature.

    The eel’s electrocytes fire when they receive a signal from the animal’s neurons. But in Schroeder’s gels, the trigger is far simpler—all he needs to do is to press the gels together.

    It would be cumbersome to have incredibly large sheets of these gels. But Max Shtein, an engineer at the University of Michigan, suggested a clever solution—origami. Using a special folding pattern that’s also used to pack solar panels into satellites, he devised a way of folding a flat sheet of gels so the right colors come into contact in the right order. That allowed the team to generate the same amount of power in a much smaller space—in something like a contact lens, which might one day be realistically worn.

    For now, such batteries would have to be actively recharged. Once activated, they produce power for up to a few hours, until the levels of ions equalize across the various gels, and the battery goes flat. You then need to apply a current to reset the gels back to alternating rows of high-salt and low-salt. But Schroeder notes that our bodies constantly replenish reservoirs of fluid with varying levels of ions. He imagines that it might one day be possible to harness these reservoirs to create batteries.

    Essentially, that would turn humans into something closer to an electric eel. It’s unlikely that we’d ever be able to stun people, but we could conceivably use the ion gradients in our own bodies to power small implants. Of course, Schroeder says, that’s still more a flight of fancy than a goal he has an actual road map for. “Plenty of things don’t work for all sorts of reasons, so I don’t want to get too far ahead of myself,” he says.

    It’s not unreasonable to speculate, though, says Ken Catania from Vanderbilt University, who has spent years studying the biology of the eels. “Volta’s battery was not exactly something you could fit in a cellphone, but over time we have all come to depend on it,” he says. “Maybe history will repeat itself.”

    “I’m amazed at how much electric eels have contributed to science,” he adds. “It’s a good lesson in the value of basic science.” Schroeder, meanwhile, has only ever seen electric eels in zoos, and he’d like to encounter one in person. “I’ve never been shocked by one, but I feel like I should at some point,” he says.

    See the full article here .

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  • richardmitnick 5:47 pm on February 15, 2018 Permalink | Reply
    Tags: , Biology, , Cells Communicate in a Dynamic Code   

    From Caltech: “Cells Communicate in a Dynamic Code” 

    Caltech Logo

    Caltech

    02/15/2018

    Lori Dajose
    (626) 395-1217
    ldajose@caltech.edu

    1
    Artist’s concept of a cell expressing the Delta1 ligand (left) and a cell expressing the Delta4 ligand (right). While these two ligands activate cellular receptors in the same way, they do so in different patterns over time. In this way, a receiving cell can decode instructions.
    Credit: Caltech

    2
    Illustration of a message-receiving cell (bottom) expressing the Notch receptor, depicted as a satellite dish, to receive messages from cells expressing two different ligand “messages”, named Delta1 (left, blue) or Delta4 (right, red). The identity of the signaling molecule is encoded in pulsatile (left) or sustained (right) dynamics. These dynamics are in turn “decoded” by a module involving the genes HES1 and HEY1 (white box with dials) to control the cell’s decision to differentiate. Credit: Courtesy of the Elowitz laboratory

    A critically important intercellular communication system is found to encode and transmit more messages than previously thought.

    Multicellular organisms like ourselves depend on a constant flow of information between cells, coordinating their activities in order to proliferate and differentiate. Deciphering the language of intercellular communication has long been a central challenge in biology. Now, Caltech scientists have discovered that cells have evolved a way to transmit more messages through a single pathway, or communication channel, than previously thought, by encoding the messages rhythmically over time.

    The work, conducted in the laboratory of Michael Elowitz, professor of biology and bioengineering, Howard Hughes Medical Institute Investigator, and executive officer for Biological Engineering, is described in a paper in the February 8 issue of Cell.

    In particular, the scientists studied a key communication system called “Notch,” which is used in nearly every tissue in animals. Malfunctions in the Notch pathway contribute to a variety of cancers and developmental diseases, making it a desirable target to study for drug development.

    Cells carry out their conversations using specialized communication molecules called ligands, which interact with corresponding molecular antennae called receptors. When a cell uses the Notch pathway to communicate instructions to its neighbors—telling them to divide, for example, or to differentiate into a different kind of cell—the cell sending the message will produce certain Notch ligands on its surface. These ligands then bind to Notch receptors embedded in the surface of nearby cells, triggering the receptors to release gene-modifying molecules called transcription factors into the interior of their cell. The transcription factors travel to the cell’s nucleus, where the cell’s DNA is stored, and activate specific genes. The Notch system thus allows cells to receive signals from their neighbors and alter their gene expression accordingly.

    Ligands prompt the activation of transcription factors by modifying the structure of the receptors into which they dock. All ligands modify their receptors in a similar way and activate the same transcription factors in a receiving cell, and for that reason, scientists generally assumed that the receiving cell should not be able to reliably determine which ligand had activated it, and hence which message it had received.

    “At first glance, the only explanation for how cells distinguish between two ligands, if at all, seems to be that they must somehow accurately detect differences in how strongly the two ligands activate the receptor. However, all evidence so far suggests that, unlike mobile phones or radios, cells have much more trouble precisely analyzing incoming signals,” says lead author and former Elowitz lab graduate student Nagarajan (Sandy) Nandagopal (PhD ’18). “They are usually excellent at distinguishing between the presence or absence of signal, but not very much more. In this sense, cellular messaging is closer to sending smoke signals than texting. So, the question is, as a cell, how do you differentiate between two ligands, both of which look like similar puffs of smoke in the distance?”

    Nandagopal and his collaborators wondered whether the answer lay in the temporal pattern of Notch activation by different ligands—in other words, how the “smoke” is emitted over time. To test this, the team developed a new video-based system through which they could record signaling in real time in each individual cell. By tagging the receptors and ligands with fluorescent protein markers, the team could watch how the molecules interacted as signaling was occurring.

    The team studied two chemically similar Notch ligands, dubbed Delta1 and Delta4. They discovered that despite the ligands’ similarity the two activated the same receptor with strikingly different temporal patterns. Delta1 ligands activated clusters of receptors simultaneously, sending a sudden burst of transcription factors down to the nucleus all at once, like a smoke signal consisting of a few giant puffs. On the other hand, Delta4 ligands activated individual receptors in a sustained manner, sending a constant trickle of single transcription factors to the nucleus, like a steady stream of smoke.

    These two patterns are the key to encoding different instructions to the cell, the researchers say. In fact, this mechanism enabled the two ligands to communicate dramatically different messages. By analyzing chick embryos, the authors discovered that Delta1 activated abdominal muscle production, whereas Delta4 strongly inhibited this process in the same cells.

    “Cells speak only a handful of different molecular languages but they have to work together to carry out an incredible diversity of tasks,” says Elowitz. “We’ve generally assumed these languages are extremely simple, and cells can basically only grunt at each other. By watching cells in the process of communicating, we can see that these languages are more sophisticated and have a larger vocabulary than we ever thought. And this is probably just the tip of an iceberg for intercellular communication.”

    The paper is titled Dynamic Ligand Discrimination in the Notch Signaling Pathway. In addition to Nandagopal and Elowitz, other Caltech co-authors are Leah Santat, who is also a Howard Hughes Medical Institute Investigator, and Marianne Bronner, the Albert Billings Ruddock Professor of Biology. Additional co-authors are Lauren LeBon of Calico Life Sciences and David Sprinzak of Tel Aviv University. Funding was provided by the Defense Advanced Research Projects Agency, the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute.

    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.”

    Caltech campus

     
  • richardmitnick 1:47 pm on February 15, 2018 Permalink | Reply
    Tags: , Biology, , , Life and death of proteins   

    From EMBL: “Life and death of proteins” 

    EMBL European Molecular Biology Laboratory bloc

    European Molecular Biology Laboratory

    15 February 2018
    Berta Carreño

    EMBL scientists create a turnover catalogue of almost 10.000 proteins from primary cells

    1
    Architecture dependent turnover of the nuclear pore subunits. Top row shows the nuclear pore subunits seen from top, bottom row shows subunits of the nuclear pore cut in half. IMAGE: Jan Kosinski/EMBL.

    Proteins perform countless functions in the cell, including transporting molecules, speeding up metabolic reactions and forming structural parts of the cell such as the nuclear pore complex. Protein turnover is a measure of the difference between protein synthesis and protein degradation and it is an important indicator of a cell’s activity in health and disease.

    EMBL group leaders Mikhail Savitski and Martin Beck, in close collaboration with Cellzome scientists Marcus Bantscheff and Toby Mathieson, have improved the accuracy of the detection of small changes in protein turnover by developing a better algorithmic treatment of raw mass spectrometry data. As a result, the researchers have published a turnover catalogue of 9699 unique proteins in Nature Communications. The paper focuses on protein complexes and demonstrates that subunits of protein complexes have consistent turnover rates.

    What did you do?

    We wanted to study protein homeostasis, or the balanced process behind protein synthesis and degradation in primary cells extracted from blood or living tissue. Primary cells provide a better understanding of the in vivo situation than cultured cells but, unfortunately, they have a short lifespan when compared to the protein complexes we wanted to study. To overcome this problem, we developed a better algorithmic treatment of raw mass spectrometry data. The improved algorithm accurately determines very small changes in proteins, allowing us to measure the turnover of 9699 unique proteins, including very long-lived proteins, such as the Histone H1.2 protein which has a half-life of 2242 hours. For the first time, we have a view of protein turnover at a cellular scale in several primary cell types, which will be a valuable resource for the scientific community.

    We focused our analysis on protein complexes, particularly on the nuclear pore complex, which is very big and is composed of several sub-complexes. We discovered that there are protein turnover levels that are specific to a given sub-complex. Proteins which are peripheral to the complex, that joined later in evolution, turn out to have much faster turnover than the ones that form the core structure and have been there for a longer time. Contrary to previous understanding, our data clearly suggests that there is a turnover mechanism for the nuclear pore in non-dividing cells. This is exciting because it opens new research in this direction.

    Why is understanding protein turnover important?

    Protein turnover is important for understanding cellular homeostasis. Our work delineates the tools to study the mechanisms controlling it and will help researchers study a wide range of things, such as ageing, brain function, cancer and neurodegeneration.

    Science paper:
    Systematic analysis of protein turnover in primary cells, Nature Communications.

    See the full article here .

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    EMBL European Molecular Biology Laboratory campus

    EMBL is Europe’s flagship laboratory for the life sciences, with more than 80 independent groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its 1800 employees, from many nations, operate across five sites: the main laboratory in Heidelberg, and outstations in Grenoble; Hamburg; Hinxton, near Cambridge (the European Bioinformatics Institute), and Monterotondo, near Rome. Founded in 1974, EMBL is an inter-governmental organisation funded by public research monies from its member states. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Around 200 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

     
  • richardmitnick 12:51 pm on February 13, 2018 Permalink | Reply
    Tags: , Biology, DropSynth, , ,   

    From UCLA Newsroom: “UCLA scientists develop low-cost way to build gene sequences” 


    UCLA Newsroom

    February 12, 2018
    Sarah C.P. Williams

    1
    UCLA scientists used DropSynth to make thousands of bacterial genes with different versions of phosphopantetheine adenylyltransferase, or PPAT (pictured). Sriram Kosuri/UCLA.

    A new technique pioneered by UCLA researchers could enable scientists in any typical biochemistry laboratory to make their own gene sequences for only about $2 per gene. Researchers now generally buy gene sequences from commercial vendors for $50 to $100 per gene.

    The approach, DropSynth, which is described in the January issue of the journal Science, makes it possible to produce thousands of genes at once. Scientists use gene sequences to screen for gene’s roles in diseases and important biological processes.

    “Our method gives any lab that wants the power to build its own DNA sequences,” said Sriram Kosuri, a UCLA assistant professor of chemistry and biochemistry and senior author of the study. “This is the first time that, without a million dollars, an average lab can make 10,000 genes from scratch.”

    Increasingly, scientists studying a wide range of subjects in medicine — from antibiotic resistance to cancer — are conducting “high-throughput” experiments, meaning that they simultaneously screen hundreds or thousands of groups of cells. Analyzing large numbers of cells, each with slight differences in their DNA, for their ability to carry out a behavior or survive a drug treatment can reveal the importance of particular genes, or sections of genes, in those abilities.

    Such experiments require not only large numbers of genes but also that those genes are sequenced. Over the past 10 years, advances in sequencing have enabled researchers to simultaneously determine the sequences of many strands of DNA. So the cost of sequencing has plummeted, even as the process of generating genes has remained comparatively slow and expensive.

    “There’s an ongoing need to develop new gene synthesis techniques,” said Calin Plesa, a UCLA postdoctoral research fellow and co-first author of the paper. “The more DNA you can synthesize, the more hypotheses you can test.”

    The current methods for synthesizing genes, he said, either limit the length of a gene to about 200 base pairs — the sets of nucleotides that made up DNA — or are prohibitively expensive for most labs.

    The new method involves isolating small sections of thousands of genes in tiny droplets of water suspended in an oil. Each section of DNA is assigned a molecular “bar code,” which identifies the longer gene to which it belongs.

    Then, the sections, which initially are present in only very small amounts, are copied many times to increase their number. Finally, small beads are used to sort the mixture of DNA fragments into the right combinations to make longer genes, and the sections are combined. The result is a mixture of thousands of the desired genes, which can be used in experiments.

    To show that technique worked, the scientists used DropSynth to make thousands of bacterial genes — each as long as 669 base pairs in length. Each gene encoded a different bacterium’s version of the metabolic protein phosphopantetheine adenylyltransferase, or PPAT, which bacteria need to survive. Because PPAT is critical to bacteria that cause everything from sinus infections to pneumonia and food poisoning, it’s being studied as a potential antibiotic target.

    The researchers created a mixture of the thousands of versions of PPAT with DropSynth, and then added each gene to a version of E. coli that lacked PPAT and tested which ones allowed E. coli to survive. The surviving cells could then be used to screen potential antibiotics very quickly and at a low cost.

    DropSynth could potentially also be useful in engineering new proteins. Currently, scientists can use computer programs to design proteins that meet certain parameters, such as the ability to bind to certain molecules, but DropSynth could offer researchers hundreds or even thousands of options from which to choose the proteins that best fit their needs.

    The team is still working on reducing DropSynth’s error rate. In the meantime, though, the scientists have made the instructions publicly available on their website. All of the chemical substances needed to replicate the approach are commercially available.

    The study’s other authors are graduate students Nathan Lubock and Angus Sidore of UCLA, and Di Zhang of the University of Pennsylvania.

    Funding for the study was provided by the Netherlands Organisation for Scientific Research, the Human Frontier Science Program, the National Science Foundation, the National Institutes of Health, the Searle Scholars Program, the U.S. Department of Energy, and Linda and Fred Wudl.

    See the full article here .

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    UC LA Campus

    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

     
  • richardmitnick 11:43 am on February 12, 2018 Permalink | Reply
    Tags: , , Biology, Lena Struwe launches Botany Depot – a global botanical education resource,   

    From Rutgers University: “Lena Struwe launches Botany Depot – a global botanical education resource” 

    Rutgers University
    Rutgers University

    February 12, 2018

    1
    Hands-on investigations of a living begonia plant from the Floriculture greenhouse and freshly collected branches from Rutgers Gardens collection enhances the lab experience for botany students at Rutgers. Photo: Susanne Ruemmele.

    Professor Lena Struwe in the Department of Ecology, Evolution, and Natural Resources and the Department of Plant Biology launched a new website, Botany Depot at the end of January. It is a global website for creative ideas and materials for teaching botany in the 21st century for all ages, situations, and levels.

    2
    Sugarcane, bamboo, and corn are some of the grasses that students compare in the botany lab focused on grass biodiversity. Photo: Susanna Ruemmele.

    Here you can find links and downloads to resources and publications, lesson plans, manuals and handouts, figures, and a lot more – all shared freely by botanical educators.

    The Botany Depot was invented and is administered by Lena Struwe, a Rutgers professor and the director of its Chrysler Herbarium. With time, Botany Depot will include materials and resources developed and shared by botanical educators in many countries and regions.

    Many of the resources are materials developed by Struwe for college level classes at Rutgers University, but these can also be used by teachers working with students of other ages, and also by interested amateur naturalists or professional botanists.

    Initial offerings included a manual to the 50 most common plant families in the temperate regions of the world, and links to Chris Martine’s videos in his series Plants are Cool Too. The website is currently being built up, and more resources are being added continuously.

    Since its inception two weeks ago, it has already attracted attention through Twitter and Facebook, had nearly 1500 page visits, and over 50 people have downloaded materials.

    3
    Students in a botany lab are comparing dried ethnobotanical samples with fresh plant materials. Photo: Susanne Ruemmele.

    “I wanted to build an inspirational resource that is easy to navigate, download from, and will excite educators all over the world, and show that that botany can be taught in innovative, hands-on, and exciting ways,” Struwe explained. “After all, plants are all around us and without them we humans would be dead, so these organisms are more important than many students realize. Botany is also fun, beautiful, and fascinating – in the world of plants there is always something everybody can relate to, but many people have not had the chance to discover this yet.”

    Botany Depot also has a facebook page.

    See the full article here .

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    rutgers-campus

    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    Rutgers smaller
    Please give us back our original beautiful seal which the University stole away from us.
    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

     
  • richardmitnick 8:25 am on February 10, 2018 Permalink | Reply
    Tags: , Biology, , Methane,   

    From JPL-Caltech: “NASA-led Study Solves a Methane Puzzle” 

    NASA JPL Banner

    JPL-Caltech

    January 2, 2018
    Alan Buis
    Jet Propulsion Laboratory, Pasadena, California
    818-354-0474
    Alan.Buis@jpl.nasa.gov

    Written by Carol Rasmussen
    NASA’s Earth Science News Team

    1
    A reduction in global burned area in the 2000s had an unexpectedly large impact on methane emissions. Credit: NASA/GSFC/SVS.

    A new NASA-led study has solved a puzzle involving the recent rise in atmospheric methane, a potent greenhouse gas, with a new calculation of emissions from global fires. The new study resolves what looked like irreconcilable differences in explanations for the increase.

    Methane emissions have been rising sharply since 2006. Different research teams have produced viable estimates for two known sources of the increase: emissions from the oil and gas industry, and microbial production in wet tropical environments like marshes and rice paddies. But when these estimates were added to estimates of other sources, the sum was considerably more than the observed increase. In fact, each new estimate was large enough to explain the whole increase by itself.

    Scientist John Worden of NASA’s Jet Propulsion Laboratory in Pasadena, California, and colleagues focused on fires because they’re also changing globally. The area burned each year decreased about 12 percent between the early 2000s and the more recent period of 2007 to 2014, according to a new study using observations by NASA’s Moderate Resolution Imaging Spectrometer satellite instrument. The logical assumption would be that methane emissions from fires have decreased by about the same percentage. Using satellite measurements of methane and carbon monoxide, Worden’s team found the real decrease in methane emissions was almost twice as much as that assumption would suggest.

    When the research team subtracted this large decrease from the sum of all emissions, the methane budget balanced correctly, with room for both fossil fuel and wetland increases. The research is published in the journal Nature Communications.

    Most methane molecules in the atmosphere don’t have identifying features that reveal their origin. Tracking down their sources is a detective job involving multiple lines of evidence: measurements of other gases, chemical analyses, isotopic signatures, observations of land use, and more. “A fun thing about this study was combining all this different evidence to piece this puzzle together,” Worden said.

    Carbon isotopes in the methane molecules are one clue. Of the three methane sources examined in the new study, emissions from fires contain the largest percentage of heavy carbon isotopes, microbial emissions have the smallest, and fossil fuel emissions are in between. Another clue is ethane, which (like methane) is a component of natural gas. An increase in atmospheric ethane indicates increasing fossil fuel sources. Fires emit carbon monoxide as well as methane, and measurements of that gas are a final clue.

    Worden’s team used carbon monoxide and methane data from the Measurements of Pollutants in the Troposphere instrument on NASA’s Terra satellite and the Tropospheric Emission Spectrometer instrument on NASA’s Aura to quantify fire emissions of methane. The results show these emissions have been decreasing much more rapidly than expected.

    Combining isotopic evidence from ground surface measurements with the newly calculated fire emissions, the team showed that about 17 teragrams per year of the increase is due to fossil fuels, another 12 is from wetlands or rice farming, while fires are decreasing by about 4 teragrams per year. The three numbers combine to 25 teragrams a year — the same as the observed increase.

    Worden’s coauthors are at the National Center for Atmospheric Research, Boulder, Colorado; and the Netherlands Institute for Space Research and University of Utrecht, both in Utrecht, the Netherlands.

    See the full article here .

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    NASA JPL Campus

    Jet Propulsion Laboratory (JPL) is a federally funded research and development center and NASA field center located in the San Gabriel Valley area of Los Angeles County, California, United States. Although the facility has a Pasadena postal address, it is actually headquartered in the city of La Cañada Flintridge [1], on the northwest border of Pasadena. JPL is managed by the nearby California Institute of Technology (Caltech) for the National Aeronautics and Space Administration. The Laboratory’s primary function is the construction and operation of robotic planetary spacecraft, though it also conducts Earth-orbit and astronomy missions. It is also responsible for operating NASA’s Deep Space Network.

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  • richardmitnick 3:19 pm on February 6, 2018 Permalink | Reply
    Tags: , Biology, , FLUCS – microscopy becomes interactive, Max Planck Institute of Molecular Cell Biology   

    From Max Planck Institute of Molecular Cell Biology: “FLUCS – microscopy becomes interactive” 

    Max Planck Institute of Molecular Cell Biology

    February 06, 2018

    Simple motion inside biological cells, such as the streaming of cytoplasm – the liquid cell interior – is widely believed to be essential for cells and the development of complex organisms. But due to the lack of suitable tools, this intracellular motion could so far not be tested as hypothesized. Now, a team of researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden found a way to induce and control motion within living cells and early embryos. Rather than using microscopes simply for observations, the team around Moritz Kreysing managed to actively guide central developmental processes in worm embryos by a new cell-biological technique called FLUCS. This new microscopy paradigm paves the way towards a systematic understanding of how complex organisms develop and what keeps them protected from malfunction and disease. These findings were published in the current issue of the journal Nature Cell Biology.

    1
    Flow of cell fluid in a worm embryo: a new microscope allows researchers to change the flow direction. As a result, the head-to-tail body axis of the embryo is reversed. © MPI f. Molecular Cell Biology and Genetics.

    A central question in biology is how entire organisms develop from single fertilized eggs. And although genetic research has revealed deep insights into this enigmatic subject in recent years, one particular aspect of development remained elusive. For an organism to develop a structured body, biomolecules need to move to specific sites inside the embryo, similar to building material on a construction site. A particularly important example for this distribution of material inside cells is the polarization of an embryo, which defines where the head and tail of a worm will grow. But until now, it has remained controversial which transport mechanisms define this head-tail polarization so precisely, because it was not possible to move the inside of an embryo without harming it.

    A team of researchers around Moritz Kreysing in collaboration with other groups at MPI-CBG, as well as the Faculty of Mathematics and the Biotechnology Center, both of the TU Dresden, has now succeeded in inducing controlled flows in living embryos with a non-invasive laser technology called FLUCS (focused-light-induced-cytoplasmic-streaming). With this truly revolutionary tool at hand (see figure), the researchers were able to probe the function of cytoplasmic motion in the process of embryo polarization.

    Matthäus Mittasch, the leading author of the study says: “With FLUCS, microscopy of growing embryos becomes truly interactive”. And indeed: with the help of realistic computer simulations the researchers even managed to reverse the head-to-tail body axis of worm embryos with FLUCS, leading to inverted development.

    Lead investigator Moritz Kreysing, with a dual affiliation to the Center for Systems Biology Dresden, concludes: “The ability to actively move the interior of biological cells will help to understand how these cells change shape, how they move, divide, respond to external signals, and ultimately how entire organisms emerge guided by microscale motion.” On the medical side, FLUCS has the potential to improve our understanding of developmental defects, aid in-vitro fertilization, organism cloning, and the discovery of new drugs.

    See the full article here .

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    We are the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

    We do pioneering basic research. 500 curiosity-driven scientists from over 50 countries ask: How do cells form tissues? Our research programs span multiple scales of magnitude, from molecular assemblies to organelles, cells, tissues, organs, and organisms.

    The Max Planck Society is Germany’s most successful research organization. Since its establishment in 1948, no fewer than 18 Nobel laureates have emerged from the ranks of its scientists, putting it on a par with the best and most prestigious research institutions worldwide. The more than 15,000 publications each year in internationally renowned scientific journals are proof of the outstanding research work conducted at Max Planck Institutes – and many of those articles are among the most-cited publications in the relevant field.

    What is the basis of this success? The scientific attractiveness of the Max Planck Society is based on its understanding of research: Max Planck Institutes are built up solely around the world’s leading researchers. They themselves define their research subjects and are given the best working conditions, as well as free reign in selecting their staff. This is the core of the Harnack principle, which dates back to Adolph von Harnack, the first president of the Kaiser Wilhelm Society, which was established in 1911. This principle has been successfully applied for nearly one hundred years. The Max Planck Society continues the tradition of its predecessor institution with this structural principle of the person-centered research organization.

    The currently 83 Max Planck Institutes and facilities conduct basic research in the service of the general public in the natural sciences, life sciences, social sciences, and the humanities. Max Planck Institutes focus on research fields that are particularly innovative, or that are especially demanding in terms of funding or time requirements. And their research spectrum is continually evolving: new institutes are established to find answers to seminal, forward-looking scientific questions, while others are closed when, for example, their research field has been widely established at universities. This continuous renewal preserves the scope the Max Planck Society needs to react quickly to pioneering scientific developments.

     
  • richardmitnick 9:09 am on January 31, 2018 Permalink | Reply
    Tags: , Biology, Epileptic Seizures and Depression May Share a Common Genetic Cause Study Suggests, Focal epilepsy, ,   

    From Rutgers: “Epileptic Seizures and Depression May Share a Common Genetic Cause, Study Suggests” 

    Rutgers University
    Rutgers University

    January 31, 2018
    Todd B. Bates

    1
    In people with epilepsy, partial seizures are also known as focal seizures. While focal seizures start in one part of the brain, generalized seizures start in both sides of the brain. Image: National Institutes of Health.

    Rutgers and Columbia scientists assessed family histories of epilepsy and depression to find a possible genetic relationship.

    From the time of Hippocrates, physicians have suspected a link between epilepsy and depression. Now, for the first time, scientists at Rutgers University–New Brunswick and Columbia University have found evidence that seizures and mood disorders such as depression may share the same genetic cause in some people with epilepsy, which may lead to better screening and treatment to improve patients’ quality of life.

    The scientists studied dozens of unusual families with multiple relatives who had epilepsy, and compared the family members’ lifetime prevalence of mood disorders with that of the U.S. population.

    They found an increased incidence of mood disorders in persons who suffer from a type of the condition called focal epilepsy, in which seizures begin in just one part of the brain. But mood disorders were not increased in people with generalized epilepsy, in which seizures start on both sides of the brain.

    “Mood disorders such as depression are under-recognized and undertreated in people with epilepsy,” said Gary A. Heiman, the study’s senior author and associate professor in the Department of Genetics at Rutgers–New Brunswick. “Clinicians need to screen for mood disorders in people with epilepsy, particularly focal epilepsy, and clinicians should treat the depression in addition to the epilepsy. That will improve patients’ quality of life.”

    The results of the study – published online today in the journal Epilepsia – support the hypothesis that people with focal epilepsy, but not generalized epilepsy, are susceptible to mood disorders such as depression.

    “More research is needed to identify specific genes that raise risk for both epilepsy and mood disorders,” said Heiman, who works in the School of Arts and Sciences. “It’s important to understand the relationship between the two different disorders.”

    A relationship between epilepsy and mood disorders has been suspected for millennia, Heiman noted. Hippocrates, “the father of medicine,” wrote about it around 400 BC: “Melancholics ordinarily become epileptics, and epileptics, melancholics: what determines the preference is the direction the malady takes; if it bears upon the body, epilepsy, if upon the intelligence, melancholy.”

    Seizures in most people with epilepsy can be controlled by drugs and surgery. The fact remains, however, that epilepsy and mood disorders such as depression affect quality of life and increase disability and health care costs. Depression raises the risk for suicidal thoughts and attempts. Moreover, previous studies have shown that people who have both epilepsy and mood disorders tend to have worse seizure outcomes than those without mood disorders.

    In the U.S., about 2.3 million adults and more than 450,000 children and adolescents have epilepsy, and anyone can develop the disorder. In 2015, an estimated 16.1 million adults at least 18 years old in the U.S. had at least one major depressive episode in the past year, according to federal figures.

    “A number of genes have been found for epilepsy and understanding if these genes also might be causing depression is important,” Heiman said. “In particular, more studies should be done to understand the relationship between focal epilepsy and mood disorders.”

    See the full article here .

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    rutgers-campus

    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    Rutgers smaller
    Please give us back our original beautiful seal which the University stole away from us.
    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

     
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