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  • richardmitnick 2:19 pm on January 24, 2020 Permalink | Reply
    Tags: "New Cages to Trap Molecules Push Boundaries of Protein Design", , “We are most excited about the fundamental and interdisciplinary aspect of this project which shows the power of simple chemical intuition in addressing a complex biological puzzle” he said., Biology, Can we make larger cages; can we encapsulate bigger cargo; can we actually deliver it into the cells?, , , UC San Diego Division of Biological Sciences- Section of Molecular Biology- with UC San Diego’s Crystallography and Cryo-EM (cryo-electron microscopy) facilities.,   

    From UC San Diego: “New Cages to Trap Molecules Push Boundaries of Protein Design” 

    From UC San Diego

    January 22, 2020
    Melissa Miller


    A rotating view of the protein cage. Iron (red/orange spheres) and zinc (blue) are the metals that bond with proteins (gray) to make up the structure. The yellow sphere shows the central cavity. Video by Rohit Subramanian, Tezcan Lab at UC San Diego.

    1
    Protein design is a popular and rapidly growing field, with scientists engineering novel protein cages—capsule-like nanostructures for purposes such as gene therapy and targeted drug delivery. Many of these structures fashioned in the lab, while perhaps aesthetically pleasing to chemists, have holes too big to trap a target molecule or don’t open on command, limiting their functional scope.

    But new research findings, by UC San Diego Professor of Chemistry and Biochemistry Akif Tezcan, offer a protein architecture with small holes—“pores” in chemistry jargon. The findings, published in Nature, push the boundaries of synthetic protein design past what is considered state-of-the-art.

    “If molecules can freely go back and forth through these holes, you’re not going to be able to store little things on the inside,” explained Tezcan. “Protein cages that people have designed before have the right shape and symmetry, but they’re mostly like Wiffle balls—they don’t necessarily isolate the interior from the exterior.”

    By tailoring the surface of small protein building blocks with multiple metal-binding sites, Tezcan’s team developed a new protein cage with small pores that trap molecules securely inside.

    “This project is a significant addition to the field because it demonstrates that minimal design can be used to generate modular, stimuli-responsible protein cages that approach the complexity of naturally evolved systems,” said co-author Rohit Subramanian, a graduate student in the Tezcan Lab.

    Additionally, the new structure can be opened via chemical, thermal or redox (transfer of electrons between a set of atoms, molecules or ions with the same chemical formula) reactions. According to Tezcan, the UC San Diego research team was ideally situated to create the new protein cage design with its inorganic chemistry insights—specifically metal coordination chemistry, which made the difference.

    The first author of the paper, titled Constructing Protein Polyhedra via Orthogonal Chemical Interactions, is Eyal Golub, a former postdoctoral scholar in the Tezcan Lab who conceived the project and performed many of the experiments.

    “In evaluating our designs, we discovered that one resulted in the formation of a six-protein cage instead of the 12-protein cage we were expecting,” said Golub. “This result was especially important for the project because it demonstrated an adaptability that permitted different types of cage symmetries using the same design scaffold.”

    Because protein cages have tightly interconnected, polyhedral shapes—like a soccer ball—their construction from simpler building blocks must meet stringent symmetry requirements. Other designers have largely avoided this challenge by using protein building blocks with inherent symmetries, connecting them via relatively strong interactions. These strategies, however, lead to highly porous architectures which cannot open and close like natural protein cages do. Viruses, for example, are examples of protein cages in nature. They contain genetic cargo in their interior and deliver them to host cells they infect. The UC San Diego researchers’ novel strategy allowed them to arrange the building blocks in precise orientations and proper symmetries for building protein cages while also controlling their dynamics via the metal ions.

    The paper also includes detailed visualizations of the protein cage made possible through collaborations with Professor Tim Baker and his group in the UC San Diego Division of Biological Sciences, Section of Molecular Biology, with UC San Diego’s Crystallography and Cryo-EM (cryo-electron microscopy) facilities.

    “We knew that we needed different techniques to understand the structures of our protein cages,” said Tezcan. “At UC San Diego, there’s always someone who has the expertise to help, somebody willing to collaborate and teach us how to do it.”

    As for the next step, Tezcan said there is more development to be done.

    “Can we make larger cages, can we encapsulate bigger cargo, can we actually deliver it into the cells? But we are most excited about the fundamental and interdisciplinary aspect of this project, which shows the power of simple chemical intuition in addressing a complex biological puzzle,” he said.

    This work was supported by the U.S. Department of Energy, Division of Materials Sciences, Office of Basic Energy Sciences (grant no. DE-SC0003844); the National Science Foundation, Division of Materials Research (grant no. DMR-1602537); an EMBO Long-Term Postdoctoral Fellowship (grant no. ALTF 1336-2015); a DFG Research Fellowship (grant no. DFG 393131496) and the National Institute of Health Chemical Biology Interfaces Training Grant UC San Diego (grant no. T32GM112584). The paper’s authors acknowledge the use of the UC San Diego Cryo-EM Facility, which is supported by NIH grants and a gift from the Agouron Institute. Crystallographic data were collected either at Stanford Synchrotron Radiation Lightsource (SSRL) or at the Lawrence Berkeley Natural Laboratory on behalf of the Department of Energy.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

     
  • richardmitnick 10:34 am on January 24, 2020 Permalink | Reply
    Tags: A nano-enabled platform developed at the center to create and deliver tiny aerosolized water nonodroplets containing non-toxic nature-inspired disinfectants wherever desired., , Biology, , Diarrheal diseases are big killers of kids too., Harvard Chan Center for Nanotechnology and Nanotoxicology looks to improve on soap and water., , Infectious diseases are still emerging., , Microorganisms are smarter than we thought and evolving new strains.,   

    From Harvard Gazette: “Disinfecting your hands with ‘magic’” 

    Harvard University


    From Harvard Gazette

    January 23, 2020
    Alvin Powell
    Photos by Kris Snibbe/Harvard Staff Photographer

    1
    Nanostructures can provide an alternative for hand hygiene that is airless and waterless. “… this is like magic. You don’t see; you don’t feel; you don’t smell; but your hands are sanitized,” says Associate Professor of Aerosol Physics Philip Demokritou.

    Harvard Chan Center for Nanotechnology and Nanotoxicology looks to improve on soap and water.

    Nanosafety researchers at the Harvard T.H. Chan School of Public Health have developed a new intervention to fight infectious disease by more effectively disinfecting the air around us, our food, our hands, and whatever else harbors the microbes that make us sick. The researchers, from the School’s Center for Nanotechnology and Nanotoxicology, were led by Associate Professor of Aerosol Physics Philip Demokritou, the center’s director, and first author Runze Huang, a postdoctoral fellow there. They used a nano-enabled platform developed at the center to create and deliver tiny, aerosolized water nonodroplets containing non-toxic, nature-inspired disinfectants wherever desired. Demokritou talked to the Gazette about the invention and its application on hand hygiene, which was described recently in the journal ACS Sustainable Chemistry and Engineering.

    Q&A
    Philip Demokritou

    GAZETTE: Give us a quick overview of the problem you’re trying to solve.

    DEMOKRITOU: If you go back to the ’60s and the invention of many antibiotics, we thought that the chapter on infectious diseases would be closed. Of course, 60 years later, we now know that’s not true. Infectious diseases are still emerging. Microorganisms are smarter than we thought and evolving new strains. It’s a constant battle. And when I talk about infectious diseases, I’m mainly talking about airborne and foodborne diseases: For example, flu and tuberculosis are airborne diseases, respiratory diseases, which cause millions of deaths a year. Foodborne diseases also kill 500,000 people annually and cost our economy billions of dollars.

    GAZETTE: Diarrheal diseases are big killers of kids, too.

    DEMOKRITOU: It’s a big problem, especially in developing countries with fragmented health care systems.

    GAZETTE: What’s wrong with how we sanitize our hands?

    DEMOKRITOU: We hear all the time that you have to wash your hands. It’s a primary measure to reduce infectious diseases. More recently, we’re also using antiseptics. Alcohol is OK, but we are also using other chemicals like triclosan and chlorhexadine. There’s research linking these chemicals to the increase in antimicrobial resistance, among other drawbacks. In addition, some people are sensitive to frequent washes and rubbing with chemicals. That’s where new approaches come into play. So, within the last four or five years, we’ve been trying to develop nanotechnology-based interventions to fight infectious diseases.

    3
    Harvard Chan School’s Associate Professor Philip Demokritou (right) with research associate Nachiket Vaze (center) and postdoc fellow Runze Huang.

    GAZETTE: So the technology involved here — the engineered water nanostructures — is a couple of years old. What’s new is the application?

    DEMOKRITOU: We have the tools to make these engineered nanomaterials and, in this particular case, we can take water and turn it into an engineered water nanoparticle, which carries its deadly payload, primarily nontoxic, nature-inspired antimicrobials, and kills microorganisms on surfaces and in the air.

    It is fairly simple, you need 12 volts DC, and we combine that with electrospray and ionization to turn water into a nanoaerosol, in which these engineered nanostructures are suspended in the air. These water nanoparticles have unique properties because of their small size and also contain reactive oxygen species. These are hydroxyl radicals, peroxides, and are similar to what nature uses in cells to kill pathogens. These nanoparticles, by design, also carry an electric charge, which increases surface energy and reduces evaporation. That means these engineered nanostructures can remain suspended in air for hours. When the charge dissipates, they become water vapor and disappear.

    Very recently, we started using these structures as a carrier, and we can now incorporate nature-inspired antimicrobials into their chemical structure. These are not super toxic to humans. For instance, my grandmother in Greece used to disinfect her surfaces with lemon juice — citric acid. Or, in milk — and also found in tears — is another highly potent antimicrobial called lysozyme. Nisin is another nature-inspired antimicrobial that bacteria release when they’re competing with other bacteria. Nature provides us with a ton of nontoxic antimicrobials that, if we can find a way to deliver them in a targeted, precise manner, can do the job. No need to invent new and potentially toxic chemicals. Let’s go to nature’s pharmacy and shop.

    When we put these nature-inspired antimicrobials into the engineered water nanostructures, their antimicrobial potency increases dramatically. But we do that without using huge quantities of antimicrobials, about 1 percent or 2 percent by volume. Most of the engineered water nanostructure is still water.

    At this point, these engineered structures are carrying antimicrobials and are charged, and we can use the charge to direct them to surfaces by applying a weak electric field. You can also release them into the air — they’re highly mobile — and they can move around and inactivate flu virus, for example.

    GAZETTE: How would this work with food?

    DEMOKRITOU: This nano-enabled platform can be used as an intervention technology for food safety applications as well. When it comes to disinfecting our food, we’re still using archaic approaches developed in the ’50s. For instance, today we put our fresh produce into chlorine-based solutions, which leave residues that can compromise health. It leaves behind byproducts, which are toxic, and you have to find a way to deal with them as well.

    Instead, you can use the water nanoaerosols that contain nanogram levels of an active ingredient — nature-inspired and not toxic — and disinfect our food. Currently, this novel invention is being explored for use — from the farm to the fork — to enhance food safety and quality.

    3
    Source: “Inactivation of Hand Hygiene-Related Pathogens Using Engineered Water Nanostructures,” Runze Huang, Nachiket Vaze, Anand Soorneedi, Matthew D. Moore, Yalong Xue, Dhimiter Bello, Philip Demokritou

    GAZETTE: So when you use it on food, you would essentially spray the nanoparticles onto a head of lettuce, for example?

    DEMOKRITOU: It depends on the application. You can put this technology in your refrigerator, and it will kill microbes on food surfaces and in the air there and improve food safety. It will also increase shelf life, which is linked to spoilage microorganisms. You can also use this technology for air disinfection. The only thing you need is 12-volt DC, which you can power from your computer USB port. Imagine sitting on a train and you generate an invisible shield of these engineered water nanostructures that protects you and minimizes the risk of getting the flu.

    GAZETTE: If you’re on the train with a bunch of sick people?

    DEMOKRITOU: Exactly, or on an airplane, anywhere you have microorganisms. Most planes recirculate the air, and all it takes is one sick guy — he doesn’t have to be sitting next to you — to get sick. Unfortunately, that’s a big problem. The newer airplanes have filtration to remove some of these pathogens. But this is a very versatile technology that you can pretty much take with you.

    GAZETTE: Let’s talk about hand hygiene.

    DEMOKRITOU: We know hand hygiene is very important, but in addition to the drawbacks of washing with water or using chemicals, the air dryers commonly used in the bathroom environment can aerosolize microbes and put them back in the air and even back on your hands. So there is room to utilize these engineered water nanostructures and develop an alternative that is airless and waterless — because it uses picogram levels of water, your hands will never get wet.

    GAZETTE: So you’re washing your hands, using water. But they don’t get wet?

    DEMOKRITOU: Exactly. And it disinfects hands in a matter of 15–20 seconds, as indicated in our recently published study.

    GAZETTE: As far as an application goes, do you see something similar to the hand driers we all use at highway rest stops? Only, when you stick your hands in, it doesn’t blow? Do you feel anything at all?

    DEMOKRITOU: You don’t feel anything. That’s the problem; this is like magic. You don’t see; you don’t feel; you don’t smell; but your hands are sanitized.

    GAZETTE: So how do people know anything’s happened? As humans we want some sort of stimulation.

    DEMOKRITOU: We could put a light and music to entertain people, but nobody can see a 25-nanometer particle. We are excited to see that there is interest from industry to pursue commercialization of this technology for hand hygiene. We may soon have an airless, waterless apparatus that can be used across the board, though not necessarily in the bathroom environment. This can be a battery-operated device, it can be placed around airports and other spots where people don’t have time or access to water to wash their hands.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Harvard University campus
    Harvard University is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 9:10 am on January 17, 2020 Permalink | Reply
    Tags: "America’s most widely consumed oil causes genetic changes in the brain", , Biology, , Soybean oil not only leads to obesity and diabetes but could also affect neurological conditions like autism; Alzheimer’s disease; anxiety; and depression., The findings only apply to soybean oil — not to other soy products,   

    From UC Riverside: “America’s most widely consumed oil causes genetic changes in the brain” 

    UC Riverside bloc

    From UC Riverside

    January 17, 2020
    Jules L Bernstein
    Senior Public Information Officer
    (951) 827-4580
    jules.bernstein@ucr.edu

    1
    news.ucr.edu

    New UC Riverside research shows soybean oil not only leads to obesity and diabetes, but could also affect neurological conditions like autism, Alzheimer’s disease, anxiety, and depression.

    Used for fast food frying, added to packaged foods, and fed to livestock, soybean oil is by far the most widely produced and consumed edible oil in the U.S., according to the U.S. Department of Agriculture. In all likelihood, it is not healthy for humans.

    It certainly is not good for mice. The new study, published this month in the journal Endocrinology, compared mice fed three different diets high in fat: soybean oil, soybean oil modified to be low in linoleic acid, and coconut oil.

    2
    Chart depicts consumption of edible oils in the U.S. for 2017/18. (USDA)

    The same UCR research team found in 2015 [PLOS ONE] that soybean oil induces obesity, diabetes, insulin resistance, and fatty liver in mice. Then in a 2017 study [Nature Scientific Reports], the same group learned that if soybean oil is engineered to be low in linoleic acid, it induces less obesity and insulin resistance.

    However, in the study released this month, researchers did not find any difference between the modified and unmodified soybean oil’s effects on the brain. Specifically, the scientists found pronounced effects of the oil on the hypothalamus, where a number of critical processes take place.

    “The hypothalamus regulates body weight via your metabolism, maintains body temperature, is critical for reproduction and physical growth as well as your response to stress,” said Margarita Curras-Collazo, a UCR associate professor of neuroscience and lead author on the study.

    3
    Comparison of oxytocin hormone in the hypothalamus of mice fed three different diets. The image on the far right shows very little oxytocin in mice fed a soybean oil diet. (UCR)

    The team determined a number of genes in mice fed soybean oil were not functioning correctly. One such gene produces the “love” hormone, oxytocin. In soybean oil-fed mice, levels of oxytocin in the hypothalamus went down.

    The research team discovered roughly 100 other genes also affected by the soybean oil diet. They believe this discovery could have ramifications not just for energy metabolism, but also for proper brain function and diseases such as autism or Parkinson’s disease. However, it is important to note there is no proof the oil causes these diseases.

    Additionally, the team notes the findings only apply to soybean oil — not to other soy products or to other vegetable oils.

    “Do not throw out your tofu, soymilk, edamame, or soy sauce,” said Frances Sladek, a UCR toxicologist and professor of cell biology. “Many soy products only contain small amounts of the oil, and large amounts of healthful compounds such as essential fatty acids and proteins.”

    A caveat for readers concerned about their most recent meal is that this study was conducted on mice, and mouse studies do not always translate to the same results in humans.

    Also, this study utilized male mice. Because oxytocin is so important for maternal health and promotes mother-child bonding, similar studies need to be performed using female mice.

    One additional note on this study — the research team has not yet isolated which chemicals in the oil are responsible for the changes they found in the hypothalamus. But they have ruled out two candidates. It is not linoleic acid, since the modified oil also produced genetic disruptions; nor is it stigmasterol, a cholesterol-like chemical found naturally in soybean oil.

    Identifying the compounds responsible for the negative effects is an important area for the team’s future research.

    “This could help design healthier dietary oils in the future,” said Poonamjot Deol, an assistant project scientist in Sladek’s laboratory and first author on the study.

    “The dogma is that saturated fat is bad and unsaturated fat is good. Soybean oil is a polyunsaturated fat, but the idea that it’s good for you is just not proven,” Sladek said.

    Indeed, coconut oil, which contains saturated fats, produced very few changes in the hypothalamic genes.

    “If there’s one message I want people to take away, it’s this: reduce consumption of soybean oil,” Deol said about the most recent study.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    UC Riverside Campus

    The University of California, Riverside is one of 10 universities within the prestigious University of California system, and the only UC located in Inland Southern California.

    Widely recognized as one of the most ethnically diverse research universities in the nation, UCR’s current enrollment is more than 21,000 students, with a goal of 25,000 students by 2020. The campus is in the midst of a tremendous growth spurt with new and remodeled facilities coming on-line on a regular basis.

    We are located approximately 50 miles east of downtown Los Angeles. UCR is also within easy driving distance of dozens of major cultural and recreational sites, as well as desert, mountain and coastal destinations.

     
  • richardmitnick 9:30 am on January 9, 2020 Permalink | Reply
    Tags: "Coral reef resilience", , Biology, , , Katie Barott, , ,   

    From Penn Today: Women in STEM-“Coral reef resilience” Katie Barott 


    From Penn Today

    January 8, 2020
    Katherine Unger Baillie
    Eric Sucar, Photographer

    With coral reefs under threat from climate change, marine biologist Katie Barott of the School of Arts and Sciences is examining the strategies that may enable corals to bounce back from warming temperatures and acidifying oceans.

    1
    Marine biologist Katie Barott investigates the strategies certain corals may use to tolerate the warmer temperatures and acidic waters that climate change is bringing to the world’s oceans.

    Mass coral-bleaching events, which occur when high ocean temperatures cause coral to expel the algae that dwell inside them, are a relatively recent phenomenon. The first widespread bleaching event occurred in 1983, the year before Penn marine biologist Katie Barott was born.

    The next one happened about 15 years later. And the intervals between them continue to shrink. In 2014, one bleaching event in Hawaii was so extreme that it carried over to affect corals into a second summer.

    “They’re increasing in frequency, getting closer and closer,” says Barott, an assistant professor in the School of Arts and Sciences’ Department of Biology. “And the ocean temperature is getting warmer and warmer, so the severity is increasing, too.”

    Yet as dramatic as the phenomenon sounds—and appears—coral bleaching does not always equate with coral death. Algae can return to corals once ocean temperatures cool, and scientists have observed formerly white corals regain their color in subsequent seasons.

    In a multifaceted research project funded by a grant from the National Science Foundation (NSF), Barott and members of her lab are studying the mechanisms by which corals withstand the effects of climate change, which include not only the warmer temperatures that trigger bleaching but also acidification of ocean waters, a slower-moving creep with subtle yet significant consequences.

    2
    Bleached finger corals reside directly next to other corals that have withstood a bleaching event in Kaneohe Bay in Hawaii. Barrot’s research attempts to untangle some of the factors that cause some corals to be particularly hardy or resilient. (Image: Katie Barott)

    Barott’s work, based in Kaneohe Bay on Oahu, Hawaii, focuses on two of the bay’s dominant coral species: rice coral (Montipora capitata) and finger coral (Porites compressa). Barott began working there during a postdoctoral fellowship at the Hawaii Institute of Marine Biology, conducting studies on which the new work is based.

    Climate threats

    Corals are invertebrate animals that live in large colonies, together forming intricate skeletons of varied shapes. To obtain food, they rely heavily on a symbiotic relationship with algae, which establish themselves within the corals’ tissue and produce food and energy for the coral through photosynthesis. A change in temperature or pH can upset this partnership, triggering the algae’s expulsion.

    “That leaves the coral essentially starving,” Barott says.

    Since her postdoctoral days, Barott has been working with colleagues in Hawaii to monitor coral patches. After the 2014-15 bleaching event, researchers were surprised and heartened to find certain patches of corals didn’t succumb to the bleaching, even those located directly adjacent to stark white corals. And many of those that did bleach bounced back within a month or so of the onset of cooling autumn temperatures.

    At the time Barott was writing her NSF grant application, she planned to compare the differences between bleached and unbleached corals. Yet just as the grant kicked off in July, another bleaching event was unfolding in Hawaii.

    “That gave us this unexpected opportunity to go back to those same colonies to see if the ones that bleached last time were the same ones that bleached again this past fall,” she says. “And more or less we saw the same patterns: The ones that bleached last time bleached again this time and vice versa. That gives us compelling evidence that there’s something specific about these resilient individuals that is make them resist bleaching, even in very warm temperatures.”

    Mechanisms of resilience

    While high temperatures triggers bleaching, acidity plays a key role in coral vitality as well. Lower seawater pH impedes corals’ ability to build their calcium carbonite skeletons, resulting in weaker, more fragile structures.
    Barott collects finger corals to take back for further analysis. Her research projects include investigations of the algae that lives symbiotically with the coral, and the bacteria that compose the corals’ microbiome. (Image: Courtesy of Katie Barott)

    In earlier work, Barott had discovered that corals possess a pH “sensor” that can respond to changes in their environment. And, indeed, sea water acidity can vary widely in the course of a day, a season, or a year, swinging as much as 0.75 pH units in a day. Perhaps, Barott hypothesizes, coral have molecular “tools” that they use to withstand these daily fluctuations that they could also employ to contend with the gradual ocean acidification that is occurring as the concentration of CO2 in sea water rises.

    3
    Barott collects finger corals to take back for further analysis. Her research projects include investigations of the algae that lives symbiotically with the coral, and the bacteria that compose the corals’ microbiome. (Image: Courtesy of Katie Barott)

    “Maybe there are some reefs that are going to be more resistant to ocean acidification because they’re used to seeing these really large daily swings and are sort of primed to deal with that challenge,” she says.

    She’s also curious about how bleaching impacts corals’ ability to tolerate pH changes more generally. Using molecular tools, she and her students are investigating the epigenetic changes that affect how genes are “read” and translated into functional proteins in the organisms. Such changes could occur much more rapidly than coral, a long-lived species, could evolve to deal with a changing environment.

    In a variety of projects, the scientists are examining differences between species of coral, between species of the algal symbionts, and between populations located in different places in the Kaneohe lagoon.

    Early results suggest differences between the rice and finger coral in their strategies for managing bleaching.

    “One really resists the bleaching, but if it does succumb then it fares a lot worse than the one that bleaches more readily,” says Barott. “That one seems to be more susceptible to losing its symbionts, but if it does it recovers fast and has lower overall mortality.”

    Planning for the future

    Barott’s group is collaborating with others in Hawaii to see if hardier corals could be propagated to rebuild damaged reef communities.

    “We’re at the proof-of-principle stage,” she says, “where we’re trying to figure out if some of these differences are heritable.”

    4
    Tank experiments in Barott’s lab in Philadelphia complement field work done in Oahu, Hawaii.

    While some of that work is being completed in Hawaii, carefully tended tanks in the basement of the Leidy Laboratories of Biology allow Barott and her students to complete experiments in Philadelphia on corals. Using both corals shipped from the field and sea anemones, a useful stand-in for corals due to their ease of care and rapid reproduction, the lab has been tracking the impacts of temperature and pH stress on energy systems, genetics, and even the microbiome of corals, the bacteria with which the corals and algae cohabitate.

    “The surface of coral is analogous to the lining of your lungs or intestines,” Barott says. “It’s covered in cilia, it’s got a mucus layer over the top of it, and there are tons and tons of bacteria that live in that mucus layer. We think those bacteria are playing a role in the health of the coral, but we don’t know if it’s playing a role in their temperature sensitivity, so that’s something we’ll be looking at.”

    With this “whole organism” approach, Barott’s aims to inject some optimism and scientific rigor into what is a largely dire outlook for corals worldwide. Encouragingly, she notes, this year’s bleaching event in Hawaii was much less severe than predicted, and corals that had bleached in 2014 were less strongly affected by this year’s event.

    “These reefs are facing a lot of impacts, not just from climate but also from local development, sedimentation, nutrient pollution,” she says. “Our hope is to predict how corals will respond to these challenges and maybe one day use our findings to assist them in rebuilding resilient reefs.”

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Penn campus

    Academic life at Penn is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

    Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

     
  • richardmitnick 8:32 am on January 3, 2020 Permalink | Reply
    Tags: "Life could have emerged from lakes with high phosphorus", , Biology, , ,   

    From University of Washington: “Life could have emerged from lakes with high phosphorus” 

    U Washington

    From University of Washington

    December 30, 2019
    Hannah Hickey

    1
    Eastern California’s Mono Lake has no outflow, allowing salts to build up over time. The high salts in this carbonate-rich lake can grow into pillars. Matthew Dillon/Flickr

    Life as we know it requires phosphorus. It’s one of the six main chemical elements of life, it forms the backbone of DNA and RNA molecules, acts as the main currency for energy in all cells and anchors the lipids that separate cells from their surrounding environment.

    But how did a lifeless environment on the early Earth supply this key ingredient?

    “For 50 years, what’s called ‘the phosphate problem,’ has plagued studies on the origin of life,” said first author Jonathan Toner, a University of Washington research assistant professor of Earth and space sciences.

    The problem is that chemical reactions that make the building blocks of living things need a lot of phosphorus, but phosphorus is scarce. A new UW study, published Dec. 30 in the Proceedings of the National Academy of Sciences, finds an answer to this problem in certain types of lakes.

    The study focuses on carbonate-rich lakes, which form in dry environments within depressions that funnel water draining from the surrounding landscape. Because of high evaporation rates, the lake waters concentrate into salty and alkaline, or high-pH, solutions. Such lakes, also known as alkaline or soda lakes, are found on all seven continents.

    The researchers first looked at phosphorus measurements in existing carbonate-rich lakes, including Mono Lake in California, Lake Magadi in Kenya and Lonar Lake in India.

    While the exact concentration depends on where the samples were taken and during what season, the researchers found that carbonate-rich lakes have up to 50,000 times phosphorus levels found in seawater, rivers and other types of lakes. Such high concentrations point to the existence of some common, natural mechanism that accumulates phosphorus in these lakes.

    Today these carbonate-rich lakes are biologically rich and support life ranging from microbes to Lake Magadi’s famous flocks of flamingoes. These living things affect the lake chemistry. So researchers did lab experiments with bottles of carbonate-rich water at different chemical compositions to understand how the lakes accumulate phosphorus, and how high phosphorus concentrations could get in a lifeless environment.

    The reason these waters have high phosphorus is their carbonate content. In most lakes, calcium, which is much more abundant on Earth, binds to phosphorus to make solid calcium phosphate minerals, which life can’t access. But in carbonate-rich waters, the carbonate outcompetes phosphate to bind with calcium, leaving some of the phosphate unattached. Lab tests that combined ingredients at different concentrations show that calcium binds to carbonate and leaves the phosphate freely available in the water.

    “It’s a straightforward idea, which is its appeal,” Toner said. “It solves the phosphate problem in an elegant and plausible way.”

    Phosphate levels could climb even higher, to a million times levels in seawater, when lake waters evaporate during dry seasons, along shorelines, or in pools separated from the main body of the lake.

    “The extremely high phosphate levels in these lakes and ponds would have driven reactions that put phosphorus into the molecular building blocks of RNA, proteins, and fats, all of which were needed to get life going,” said co-author David Catling, a UW professor of Earth & space sciences.

    2
    Colored dots show the level of phosphorus measured in different carbonate-rich lakes around the world. Existing carbonate-rich lakes can contain up to 50,000 times the levels of phosphate found in seawater, with the highest levels measured in British Columbia’s Goodenough and Last Chance lake system (yellow dots).Toner et al/PNAS

    The carbon dioxide-rich air on the early Earth, some four billion years ago, would have been ideal for creating such lakes and allowing them to reach maximum levels of phosphorus. Carbonate-rich lakes tend to form in atmospheres with high carbon dioxide. Plus, carbon dioxide dissolves in water to create acid conditions that efficiently release phosphorus from rocks.

    “The early Earth was a volcanically active place, so you would have had lots of fresh volcanic rock reacting with carbon dioxide and supplying carbonate and phosphorus to lakes,” Toner said. “The early Earth could have hosted many carbonate-rich lakes, which would have had high enough phosphorus concentrations to get life started.”

    Another recent study by the two authors showed that these types of lakes can also provide abundant cyanide to support the formation of amino acids and nucleotides, the building blocks of proteins, DNA and RNA. Before then researchers had struggled to find a natural environment with enough cyanide to support an origin of life. Cyanide is poisonous to humans, but not to primitive microbes, and is critical for the kind of chemistry that readily makes the building blocks of life.

    The research was funded by the Simons Foundation’s Collaboration on the Origins of Life.

    See the full article here .


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    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 12:10 pm on December 18, 2019 Permalink | Reply
    Tags: "Oxford researchers move one step further towards understanding how life evolved", , Biology, , ,   

    From University of Oxford: “Oxford researchers move one step further towards understanding how life evolved” 

    U Oxford bloc

    From University of Oxford

    16 December 2019
    Ruth Abrahams
    ruth.abrahams@admin.ox.ac.uk
    +44 (0)1865 280730.

    A fundamental problem for biology is explaining how life evolved. How did we get from simple chemical reactions in the prebiotic soup, to animals and plants?

    A key step in explaining life is that about 4 billion years ago, all we had was just the simplest molecules that could replicate themselves. These are called ‘replicators’ – the earliest form of life, so simple that that they are almost chemistry rather than biology. Somehow they joined together to cooperate to form more complex things. This was the basis of the genome that builds us today.

    But why did they join together? Why did they cooperate? Any cooperation could be easily exploited by ‘cheating’ replicators that didn’t cooperate. Did it require special environmental conditions?

    Today, researchers from the Department of Zoology at the University of Oxford show, in Nature Ecology & Evolution, that replicators could have solved this problem themselves. If some replicators were a bit cooperative, and some were a bit ‘sticky’ then this would lead to clumps of cooperating replicators that would evolve to become more and more cooperative, eventually producing simple genomes, and then eventually, all of life that we see around us today.

    Lead researcher, Samuel Levin, at the Department of Zoology, Oxford, said: ‘As humans, we care about how things start. Our results help to solve some of that puzzle and are also relevant for trying to figure out how common we might expect complex life in the universe to be: how easy are these early steps?

    ‘I was surprised by the jump in cooperation you get when you allow coevolution — it was higher than I expected. There seems to be some sort of cyclical feedback.’

    Co-author, Professor Stuart West, at the Department of Zoology, Oxford, said: ‘Our results show us that the same issues that we think about today, with humans (cooperating and cheating) can help explain how life evolved. Life evolved as societies of cooperating replicators / molecules.’

    Authors tested their hypothesis using mathematical models. They wrote equations which distilled down evolution in early life, and then added stickiness and cooperation to see what happened. They showed, mathematically, that more complex life could evolve only when stickiness and cooperation were allowed to coevolve at the same time.

    See the full article here.


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    Please help promote STEM in your local schools.

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    U Oxford campus

    Oxford is a collegiate university, consisting of the central University and colleges. The central University is composed of academic departments and research centres, administrative departments, libraries and museums. The 38 colleges are self-governing and financially independent institutions, which are related to the central University in a federal system. There are also six permanent private halls, which were founded by different Christian denominations and which still retain their Christian character.

    The different roles of the colleges and the University have evolved over time.

     
  • richardmitnick 8:16 am on December 17, 2019 Permalink | Reply
    Tags: "Researchers reveal how enzyme motions catalyze reactions", Biology, , , Enzymes, , ,   

    From SLAC National Accelerator Lab: “Researchers reveal how enzyme motions catalyze reactions” 

    From SLAC National Accelerator Lab

    December 16, 2019
    Ali Sundermier

    What they learned could lead to a better understanding of how antibiotics are broken down in the body, potentially leading to the development of more effective drugs.

    1
    This illustration shows how an enzyme moves and changes as it catalyzes complex reactions and breaks down organic compounds. (10.1073/pnas.1901864116)

    In a time-resolved X-ray experiment, researchers uncovered, at atomic resolution and in real time, the previously unknown way that a microbial enzyme breaks down organic compounds.

    The team, led by Mark Wilson at the University of Nebraska Lincoln (UNL) and Henry van den Bedem at the Department of Energy’s SLAC National Accelerator Laboratory (now at Atomwise Inc.), published their findings last week in the Proceedings of the National Academy of Sciences. What they learned about this enzyme, whose structure is similar to one that is implicated in neurodegenerative diseases such as Parkinson’s, could lead to a better understanding of how antibiotics are broken down by microbes and to the development of more effective drugs.

    Previously, the researchers used SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) to obtain the structure of the enzyme at very low temperatures using X-ray crystallography.

    SLAC/SSRL

    In this study, Medhanjali Dasgupta, a UNL graduate student who was the study’s first author, used the Linac Coherent Light Source (LCLS), SLAC’s X-ray laser, to watch the enzyme and its substrate within the crystal move and change as it went through a full catalytic cycle at room temperature.

    SLAC/LCLS

    The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions.

    SSRL and LCLS are DOE Office of Science user facilities. This work was funded by the DOE Office of Science and the National Institutes of Health, among other sources.

    See the full article here .


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    SLAC/LCLS


    SLAC/LCLS II projected view


    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.


     
  • richardmitnick 2:18 pm on December 10, 2019 Permalink | Reply
    Tags: "Scientists Find a Shipworm That Eats and Lives Inside Rocks", , Biology, , , Lithoredo abatanica   

    From Discover Magazine : “Scientists Find a Shipworm That Eats, and Lives Inside, Rocks” 

    DiscoverMag

    From Discover Magazine

    1
    Unlike any other shipworm known to science, Lithoredo abatanica chews through, leaving behind twisted tunnels. (Credit: Marvin A. Altamia and J. Reuben Shipway)

    Between a rock and a hard place? That’s just where Lithoredo likes it.

    Researchers found the new-to-science shipworm, a kind of clam, in the Abatan River on the Philippines’ Bohol Island. It was a stunning sight.

    “It is unlike any other shipworm, both in its appearance and its unusual habits, and this was apparent from the very first moment I laid eyes on it,” says marine biologist Dan Distel, executive director of the Ocean Genome Legacy Center at Northeastern University and senior author of the June paper describing the animal in the journal Proceedings of the Royal Society B.

    Shipworms got their name because they bore through wood that’s in contact with water, eating the material. They leave behind tunnels lined with the calcium carbonate that they secrete, similar to the way their clam kin build shells. Shipworms have been a maritime plague for millennia, destroying boats and piers. But Lithoredo abatanica nibbled its way down a different evolutionary path. This shipworm eats rock.

    2
    Individuals such as this 4-inch-long specimen secrete calcium carbonate that hardens into a burrow lining. (Credit: Marvin A. Altamia and J. Reuben Shipway)

    Distel’s field colleagues, acting on a tip from an earlier French expedition about shipworms apparently boring into the Abatan River’s bedrock, had to strap on snorkeling gear to search for the animals.

    “[We] picked up these rocks, swam them over to the bank and proceeded to crack [them] open with a hammer and chisel,” says Reuben Shipway, the paper’s lead author and a marine biologist at the University of Portsmouth. “Splitting the rock open to reveal several shipworms inside was just so bizarre.”

    Specimens of Lithoredo range from less than an inch to more than a foot long. Perhaps not surprisingly, given its unique diet, the animal lacks the sharp, wood-chewing pseudo-teeth of all its relatives and instead has broad, spatula-like chompers.

    2
    Holes in a piece of limestone made by the new species of shipworm. (Credit: Marvin A. Altamia and J. Reuben Shipway)

    Finding the rock-eating shipworm raises a broader issue. Because the shell-like burrow linings of shipworms can survive in the fossil record long after the wood around them is gone, these tube-like structures have been used by researchers as a proxy for the presence of woody material in ancient environments.

    Lithoredo’s dining preference for limestone means that scientists can no longer make such an assumption. The animals who left the linings behind might have just been rocking out.

    “I think people tend to assume that nearly everything is known about the diversity of life on our planet, but nothing could be further from the truth,” says Distel. “The world is full of amazing creatures that have yet to be discovered, creatures that are stranger than fiction.”

    See the full article here.

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  • richardmitnick 1:36 pm on December 10, 2019 Permalink | Reply
    Tags: "Meet the microorganism that likes to eat meteorites", , , Biology, , , , For this study the researchers ran tests on material from a meteorite labeled Northwest Africa 1172 (NWA 1172)., , Redox is is a type of chemical reaction in which the oxidation states of atoms are changed and is common in biological processes., The microbe M. sedula,   

    From University of Vienna via EarthSky: “Meet the microorganism that likes to eat meteorites” 

    From University of Vienna

    via

    1

    EarthSky

    December 10, 2019
    Paul Scott Anderson

    At least one type of microbe on Earth not only likes to eat meteorites but actually prefers them as a food source, according to a new international scientific study.

    1
    Meteorite dust fragments colonized and bioprocessed by the microbe M. sedula. Image via Tetyana Milojevic/ Universität Wien.

    You’ve gotta eat to live. That’s a truism not just for humans but for other lifeforms, including microbes. Now an international team of scientists has announced a new study, showing that at least one type of earthly bacteria has a fondness for extraterrestrial food: meteorites, or rocks from space. These microbes even seem to prefer space rocks to their usual earthly fare of earthly rocks.

    The intriguing peer-reviewed results were published in Nature Scientific Reports on December 2, 2019.

    Astrobiologist Tetyana Milojevic of the University of Vienna in Austria led the research, which demonstrated that an ancient single-celled bacteria known as Metallosphaera sedula (M. sedula) can not only process material in meteorites for food, but will even colonize meteorites faster than earthly rocks.

    M. sedula belong to a family of bacteria known as lithotrophs; that is, they derive their energy from inorganic sources. The term “lithotroph” was created from the Greek terms ‘lithos’ (rock) and ‘troph’ (consumer), meaning “eaters of rock.”

    For this study, the researchers ran tests on material from a meteorite labeled Northwest Africa 1172 (NWA 1172). They found that the microbes colonized the material much more quickly than they would terrestrial material.

    3
    Graphic showing the ingestion of inorganic material by the microbe M. sedula in the meteorite NWA 1172. Image via Tetyana Milojevic/ Universität Wien.

    As Milojevic said in a statement:

    “Meteorite-fitness seems to be more beneficial for this ancient microorganism than a diet on terrestrial mineral sources. NWA 1172 is a multimetallic material, which may provide much more trace metals to facilitate metabolic activity and microbial growth. Moreover, the porosity of NWA 1172 might also reflect the superior growth rate of M. sedula.”

    This is certainly interesting, suggesting that M. sedula actually prefers the material coming from space over its local, home-grown, earthly food sources.

    4
    Scanning electron microscope image of meteorite NWA 1172, showing colonization of M. sedula microbes. Image via Tetyana Milojevic/ Universität Wien/ Daily Mail.

    So how did the scientists make these findings?

    “They examined the meteorite-microbial interface at nanometer scale – one billionth of a meter – and traced how the material was consumed, investigating the iron redox behavior. Redox is is a type of chemical reaction in which the oxidation states of atoms are changed, and is common in biological processes. By combining several analytical spectroscopy techniques with transmission electron microscopy, they found a set of biogeochemical fingerprints left upon M. sedula growth on the meteorite. As Milojevic explained:

    Our investigations validate the ability of M. sedula to perform the biotransformation of meteorite minerals, unravel microbial fingerprints left on meteorite material, and provide the next step towards an understanding of meteorite biogeochemistry.”

    See the full article here .

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    The University of Vienna (German: Universität Wien) is a public university located in Vienna, Austria. It was founded by Duke Rudolph IV in 1365 and is one of the oldest universities in the German-speaking world. With its long and rich history, the University of Vienna has developed into one of the largest universities in Europe, and also one of the most renowned, especially in the Humanities. It is associated with 15 Nobel prize winners and has been the academic home to a large number of scholars of historical as well as of academic importance.

     
  • richardmitnick 4:40 pm on December 8, 2019 Permalink | Reply
    Tags: , Biology, , , Rare diseases are not as rare as you might think., They may be undiagnosed, To diagnose and treat a disease we need to know how to define and characterize the disease.   

    From Lawrence Berkeley National Lab: “News Center Rare Disease Q&A: What Rare Diseases Are and Why That Matters” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    December 3, 2019
    Aliyah Kovner
    akovner@lbl.gov
    510-486-6376

    1

    Rare diseases are … rare, right? Not as rare as you might think. As much as 10% of the population is thought to have a “rare disease.” Unfortunately, due to a lack of understanding, many rare diseases remain very difficult to diagnose and treat.

    Inspired by the enormous unmet needs of people with rare diseases, a group of scientists from across the globe has teamed up to develop open-access tools and resources for sharing disease characteristics and treatment information. The research is centered around an artificial intelligence-enabled catalog of disease descriptions called Mondo, which, like a Wikipedia for rare diseases, can be added to and improved by the scientific and medical community.

    In a recent commentary in Nature Reviews Drug Discovery, the group explained how agreeing on precise definitions of each rare disease can lead to more accurate diagnoses and better treatments. They also shared results from a preliminary analysis that suggests that the number of different rare diseases may be higher than previously estimated.

    The project team, led by Melissa Haendel of Oregon Health & Science University, and Tudor Oprea of the University of New Mexico, includes Lawrence Berkeley National Laboratory (Berkeley Lab) researchers Chris Mungall, Nomi Harris, Deepak Unni, and Marcin Joachimiak. We spoke with Chris and Nomi about the project and why they are participating in it.

    How do we decide what qualifies as a rare disease?

    Nomi: There’s no single definition of “rare disease” because it depends on which region or group you’re talking about. In the U.S., a rare disease is legally defined as one that affects fewer than 200,000 people; in the EU, a rare disease is one that affects fewer than 1 in 2,000 people. Some diseases are rare in some groups but common in others – for example, Tay-Sachs disease is rare in the general population, but much more common in Ashkenazi Jews, and tuberculosis is rare in the U.S. but is one of the top 10 causes of death worldwide.

    All of us almost certainly know someone who has a rare disease, though they may be undiagnosed.

    How are the current systems or protocols for classifying rare diseases translating into problems in patient care?

    Nomi: To diagnose and treat a disease, we need to know how to define and characterize the disease. For common diseases, there are many cases to observe, so we have a pretty good idea of what that disease looks like – what the symptoms are, how to test for it, how to treat it. For rare diseases, there may be only scattered information – maybe one physician in South America has seen a case, and one researcher in China, but they aren’t sharing their information, so we don’t have a complete picture of what that disease looks like. And if we can’t precisely define a disease, then it’s hard to reliably diagnose it, and even harder to treat it optimally.

    Our preliminary analysis, included in the commentary, suggests that the number of rare diseases may be higher than we thought – maybe around 10,000 different diseases, rather than the 5,000-7,000 that has previously been estimated. That means that distinct rare diseases (for example, different varieties of thyroid cancer) have probably been lumped together, when there might be different subtypes that benefit from different treatments.

    What needs to be done to improve and expedite rare disease research, diagnosis, and treatment?

    Chris: As Nomi mentioned, it’s hard to come up with the best treatment for a disease if you’re not even sure what exactly that disease looks like, or if it is confused with a similar disease. To address this, our team is working to catalog the whole landscape of rare diseases. We’re bringing together separate efforts in rare disease research, and developing computational tools to help experts come up with a precise definition for each rare disease. We developed a new artificial intelligence algorithm that helps disambiguate and unify the disease definitions from different databases and reference sources. We call this unified set of disease definitions “Mondo,” from the Italian word for “world,” because it brings together information from all over the world.

    To accelerate this important work, we hope that funding and regulatory agencies, patient advocacy groups, and biomedical researchers will join together to support a coordinated effort to build a complete catalog of rare diseases.

    How can Berkeley Lab play a role in this effort?

    Chris: Berkeley Lab has been at the forefront of efforts to establish standards for representing and sharing biomedical data. My specialty is ontologies, which are like specialized vocabularies for precisely describing a class of things, such as symptoms, diseases, biochemical processes, or even entire ecological systems. One of the most widely used ontologies in biological science, the Gene Ontology, was launched by a team that included several Berkeley Lab researchers. My group has helped to build many other important biomedical ontologies, including Mondo, and we write computational tools to help others build, use, and expand ontologies.

    There are many advantages to engaging in this type of work at Berkeley Lab, including the presence of leading researchers in computer science, biology, and other relevant fields, and also a commitment to open science – meaning that anyone in the world is free to not only use the resources we develop, but also to contribute to them. When we’re attacking a big problem like accurately defining all rare diseases, we can use all the help we can get!

    Berkeley Lab is a great place to engage in this research, but I also want to recognize the key contributions of our talented Mondo collaborators at Oregon State University, the Jackson Laboratory, the European Bioinformatics Institute, and many others.

    What motivated you both, personally, to join this project?

    Chris: One of my main areas of research is characterizing and interpreting regions of the genome using ontologies. Many rare diseases are Mendelian, which means the cause of the disease can be traced back to changes within or affecting parts of the genome. Other rare diseases may be environmental, or a mixture of environmental and genetic, and I’m very interested in how the environment influences the health of complex organisms like humans. This led to the creation of Mondo as a way to annotate genomes and environments. My role was developing the algorithms that used different kinds of reasoning to bring together multiple sources of information and organize it coherently.

    Nomi: My master’s thesis involved applying artificial intelligence techniques to predict the risk of inheriting genetic disorders. After that, I worked for years on bioinformatics projects that didn’t directly relate to human health. I was excited to have a chance to get back into the medical realm and contribute to a project that we hope will ultimately help to improve the prospects of those with rare diseases.

    See the full article here .

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    LBNL campus

    LBNL Molecular Foundry

    Bringing Science Solutions to the World
    In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the UC Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

    A U.S. Department of Energy National Laboratory Operated by the University of California.

    University of California Seal

     
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