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  • richardmitnick 10:01 am on March 19, 2020 Permalink | Reply
    Tags: "Scientists Have Discovered the Origins of the Building Blocks of Life", , , Biology, ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life., ,   

    From Rutgers University: “Scientists Have Discovered the Origins of the Building Blocks of Life” 

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    From Rutgers University

    March 16, 2020

    Todd Bates

    Rutgers researchers retraced the evolution of enzymes over billions of years.

    This image shows a fold (shape) that may have been one of the earliest proteins in the evolution of metabolism. Image: Vikas Nanda/Rutgers University

    Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

    Their study, which predicts what the earliest proteins looked like 3.5 billion to 2.5 billion years ago, is published in the journal Proceedings of the National Academy of Sciences.

    The scientists retraced, like a many thousand piece puzzle, the evolution of enzymes (proteins) from the present to the deep past. The solution to the puzzle required two missing pieces, and life on Earth could not exist without them. By constructing a network connected by their roles in metabolism, this team discovered the missing pieces.

    “We know very little about how life started on our planet. This work allowed us to glimpse deep in time and propose the earliest metabolic proteins,” said co-author Vikas Nanda, a professor of Biochemistry and Molecular Biology at Rutgers Robert Wood Johnson Medical School and a resident faculty member at the Center for Advanced Biotechnology and Medicine. “Our predictions will be tested in the laboratory to better understand the origins of life on Earth and to inform how life may originate elsewhere. We are building models of proteins in the lab and testing whether they can trigger reactions critical for early metabolism.”

    A Rutgers-led team of scientists called ENIGMA (Evolution of Nanomachines in Geospheres and Microbial Ancestors) is conducting the research with a NASA grant and via membership in the NASA Astrobiology Program. The ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life.

    “We think life was built from very small building blocks and emerged like a Lego set to make cells and more complex organisms like us,” said senior author Paul G. Falkowski, ENIGMA principal investigator and a distinguished professor at Rutgers University–New Brunswick who leads the Environmental Biophysics and Molecular Ecology Laboratory. “We think we have found the building blocks of life – the Lego set that led, ultimately, to the evolution of cells, animals and plants.”

    The Rutgers team focused on two protein “folds” that are likely the first structures in early metabolism. They are a ferredoxin fold that binds iron-sulfur compounds, and a “Rossmann” fold, which binds nucleotides (the building blocks of DNA and RNA). These are two pieces of the puzzle that must fit in the evolution of life.

    Proteins are chains of amino acids and a chain’s 3D path in space is called a fold. Ferredoxins are metals found in modern proteins and shuttle electrons around cells to promote metabolism. Electrons flow through solids, liquids and gases and power living systems, and the same electrical force must be present in any other planetary system with a chance to support life.

    There is evidence the two folds may have shared a common ancestor and, if true, the ancestor may have been the first metabolic enzyme of life.

    The lead author is Hagai Raanan, a former post-doctoral associate in the Environmental Biophysics and Molecular Ecology Laboratory. Rutgers co-authors include Saroj Poudel, a post-doctoral associate, and Douglas H. Pike, a doctoral student in the ENIGMA project.

    See the full article here .


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  • richardmitnick 8:20 am on March 17, 2020 Permalink | Reply
    Tags: "Ocean acidification impacts oysters’ memory of environmental stress", , Biology, Study of the Olympia oyster and the Pacific oyster.,   

    From University of Washington: “Ocean acidification impacts oysters’ memory of environmental stress” 

    From University of Washington

    March 12, 2020
    Dan DiNicola
    School of Aquatic and Fishery Sciences

    Empty Pacific oyster shells are placed on a mat after being sampled. The effect of acidified waters on multiple generations of Pacific oysters can influence aquaculture in Washington and globally.Yaamini Venkataraman/University of Washington.

    As oceans absorb more carbon dioxide, they are becoming increasingly acidic and shifting the delicate balance that supports marine life. How species will cope with ocean acidification and the other consequences of global climate change is still very much unknown and could have sweeping consequences.

    Researchers from the University of Washington School of Aquatic and Fishery Sciences have discovered that ocean acidification impacts the ability of some oysters to pass down “memories” of environmental trauma to their offspring.

    The two papers were published in December in Ecological Applications and the Journal of Shellfish Research.

    “Warming and acidifying oceans negatively influence many marine species. However, some species that live in extreme environments, such as the intertidal, may be more resilient than others to these changes,” said Laura Spencer, one of the two lead authors and a graduate student in aquatic and fishery sciences. “Some species may even be able to pass on memories of harsh conditions to their offspring, making them more capable of surviving in similarly harsh environments.”

    A bed of Pacific and Olympia oysters in Puget Sound, Washington.Laura Spencer/University of Washington.

    Researchers studied two species of ecologically and commercially valuable oysters found throughout Puget Sound: the Olympia oyster and the Pacific oyster. Although oyster larvae are sensitive to acidifying oceans, adult oysters commonly occur in intertidal areas and estuaries where they must endure constantly fluctuating water conditions.

    It is this hardiness that has researchers hopeful that oysters can withstand an increasingly acidic ocean. If their resilience to stressors can be passed down to their offspring, it could promote an increased tolerance among the future population.

    In Spencer’s study, Olympia oysters were exposed to a combination of elevated temperatures and acidified conditions during winter months, mimicking what might happen under climate change. The higher water temperatures caused the oysters to spawn earlier; however, these effects were canceled out when combined with acidified conditions. Researchers then reared and transplanted the exposed oysters’ offspring to four estuaries in Puget Sound. They observed that the offspring whose parents were exposed to acidified conditions in the lab had higher survival rates in two of the four bays.

    Olympia oysters being measured for size and sampled for reproductive tissue after pH exposure.Laura Spencer/University of Washington.

    “We found that Olympia oyster adults were relatively resilient to acidification and warming when exposed during the winter,” said Spencer. “Most interestingly, we found evidence that adult exposure to acidified conditions can benefit offspring by improving survival.”

    This carryover effect demonstrates that the experiences of oyster parents have a direct impact on how their offspring perform, and juvenile oysters may be more resilient in certain environments when their parents have been pre-conditioned by similar stressors.

    In the other study, adult Pacific oysters were similarly exposed to acidified conditions in the lab. The oysters were then placed back in ambient water to recover before spawning. Researchers observed that the embryonic and larval offspring of female oysters exposed to these experimental conditions experienced poorer survival than a similar control group.

    An approximately 12-day-old oyster larvae feeding on algae, viewed under the microscopeLaura Spencer/University of Washington.

    “The conditions one generation of Pacific oysters experience can affect how their children perform,” said lead author Yaamini Venkataraman, a graduate student in aquatic and fishery sciences. “Even if oysters are not in stressful conditions when they reproduce, their previous stressful experiences can impact their offspring.”

    These two contrasting results are both encouraging and concerning to Washington’s shellfish industry, which generates nearly $150 million a year and provides over 2,700 jobs. While one study revealed that juvenile Olympia oysters benefited and experienced a survival advantage due to parental exposure to acidified conditions, the other study showed the embryonic and larval survival of Pacific oysters decreased with parental exposure. The authors believe these differing results could be species-specific or because the experiments focused on different life stages of oysters.

    Nevertheless, determining how and why some species, such as the Olympia oyster, tolerate ocean acidification and warming helps inform where to focus conservation resources and how to improve growing methods, said Spencer.

    UW doctoral student Yaamini Venkataraman examines oyster reproductive tissue.Photo courtesy of Yaamini Venkataraman.

    “We needed to broaden our understanding of environmental memory when thinking about how oysters or other organisms will persist in the face of climate change,” explained Venkataraman. “The aquaculture industry is part of the fiber of Washington, and understanding how oysters will respond to changes in their environment, like more acidic water conditions, across multiple generations is crucial to sustaining the industry.”

    This recent research shows that as the world’s oceans warm and become more acidic due to climate change, species tolerance or sensitivity can’t be defined by looking solely at one generation of oysters.

    Additional co-authors are Ryan Crim and Stuart Ryan with the Puget Sound Restoration Fund; Micah Horwith, who completed the work with Washington Department of Natural Resources but now works at Washington State Department of Ecology; and Steven Roberts, a UW professor of aquatic and fishery sciences.

    See the full article here .


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    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 4:04 pm on March 10, 2020 Permalink | Reply
    Tags: "Some domesticated plants ignore beneficial soil microbes", , Biology, Domestication yielded bigger crops often at the expense of plant microbiomes., ,   

    From UC Riverside: “Some domesticated plants ignore beneficial soil microbes” 

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    From UC Riverside

    March 10, 2020
    Holly Ober

    Domestication yielded bigger crops often at the expense of plant microbiomes.

    While domestication of plants has yielded bigger crops, the process has often had a negative effect on plant microbiomes, making domesticated plants more dependent on fertilizer and other soil amendments than their wild relatives.

    In an effort to make crops more productive and sustainable, researchers recommend reintroduction of genes from the wild relatives of commercial crops that restore domesticated plants’ ability to interact with beneficial soil microbes.

    Thousands of years ago, people harvested small wild plants for food. Eventually, they selectively cultivated the largest ones until the plump cereals, legumes, and fruit we know today evolved. But through millennia of human tending, many cultivated plants lost some ability to interact with soil microbes that provide necessary nutrients. This has made some domesticated plants more dependent on fertilizer, one of the world’s largest sources of nitrogen and phosphorous pollution and a product that consumes fossil fuels to produce.

    “I was surprised how completely hidden these changes can be,” said Joel Sachs, a professor of biology at UC Riverside and senior author of a paper published today in Trends in Ecology and Evolution. “We’re so focused on above ground traits that we’ve been able to massively reshape plants while ignoring a suite of other characteristics and have inadvertently bred plants with degraded capacity to gain benefits from microbes.”

    Bacteria and fungi form intimate associations with plant roots that can dramatically improve plant growth. These microbes help break down soil elements like phosphorous and nitrogen that the plants absorb through their roots. The microbes also get resources from the plants in a mutually beneficial, or symbiotic, relationship. When fertilizer or other soil amendments make nutrients freely available, plants have less need to interact with microbes.

    Sachs and first author Stephanie Porter of Washington State University, Vancouver, reviewed 120 studies of microbial symbiosis in plants and concluded that many types of domesticated plants show a degraded capacity to form symbiotic communities with soil microbes.

    “The message of our paper is that domestication has hidden costs,” Sachs said. “When plants are selected for a small handful of traits like making a bigger seed or faster growth, you can lose a lot of important traits relating to microbes along the way.”

    This evolutionary loss has turned into a loss for the environment as well.

    Excess nitrogen and phosphorous from fertilizer can leach from fields into waterways, leading to algae overgrowth, low oxygen levels, and dead zones. Nitrogen oxide from fertilizer enters the atmosphere, contributing to air pollution. Fossil fuels are also consumed to manufacture fertilizers.

    Some companies have begun selling nitrogen-fixing bacteria as soil amendments to make agriculture more sustainable, but Sachs said these amendments don’t work well because some domesticated plants can no longer pick up those beneficial microbes from the soil.

    “If we’re going to fix these problems, we need to figure out which traits have been lost and which useful traits have been maintained in the wild relative,” Sachs said. “Then breed the wild and domesticated together to recover those traits.”

    See the full article here .


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    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 10:13 am on March 9, 2020 Permalink | Reply
    Tags: , Biology, , ,   

    From University of Toronto: “With new federal funding, U of T researchers aid global effort to understand and control COVID-19” 

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    From University of Toronto

    March 06, 2020
    Geoffrey Vendeville

    U of T researchers are among several of the 47 research teams pursuing projects related to COVID-19 that are receiving support through a rapid federal funding competition. (Photo by Nick Iwanyshyn.)

    The University of Toronto and affiliated institutions will receive almost $6 million for research projects related to COVID-19, with $2.7 million to campus-based researchers, while $3.13 million will go to U of T researchers at affiliated hospitals – part of a $27 million federal investment in research related to the global outbreak.

    Patty Hajdu, Canada’s Minister of Health, announced the results of a rapid research funding competition in Montreal on Friday for projects related to the novel coronavirus, which has so far infected tens of thousands of people around the world.

    The focus of the research at U of T includes the development of rapid and low-cost diagnostics, antiviral compounds and statistical models to forecast disease transmission.

    Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives, said U of T researchers have the expertise and experience to make a major contribution to scientists’ understanding of the coronavirus and how to deal with it.

    “U of T and its partners are home to many leading experts in public health, medicine, biology and other fields that can collectively advance our knowledge of this new illness and help mitigate its impact,” said Goel, who was the founding head of Public Health Ontario. “Many of these research projects engage those who are also on the front-lines of our health system, helping to ensure that the research will be relevant and applied immediately and also inform the management of future infectious disease outbreaks.”

    As of March 6, the number of confirmed cases of COVID-19 worldwide has surpassed 100,000, with cases reported on every continent except Antarctica.

    One of the newly funded projects, based at the Sinai Health System, involves U of T researchers Allison McGeer and Samira Mubareka and aims to paint a better picture of how the virus spreads.

    McGeer is a professor at U of T’s Dalla Lana School of Public Health and in the departments of medicine and laboratory medicine and pathobiology in the Faculty of Medicine. She is also the director of the Infectious Disease Epidemiology Research Unit at Mount Sinai Hospital. Mubareka is an assistant professor in the department of laboratory medicine and pathobiology as well as a virologist at Sunnybrook Health Sciences Centre.

    Their team plans to collect data to shed light on how long a patient with the virus is infectious, and how the virus spreads to surfaces and through the air.

    “The importance is with risk management and mitigation,” Mubareka told U of T News.

    She added that removing some of the uncertainty around how the virus spreads can help hospitals make better use of their resources.

    “At some point resources will be finite, and if you have a really good sense of how long people shed [the virus] for, you know how long they will need to be isolated,” Mubareka said.

    The research team also plans to systematically collect samples containing the virus, serum and immune system cells to create a bio-bank that can be shared with researchers working on vaccines or treatments.

    Keith Pardee, an assistant professor at U of T’s Leslie Dan Faculty of Pharmacy, is part of a research team that involves experts in four countries who are collaborating on low-cost and easy-to-use diagnostic tests to improve the triaging of patients.

    During the Zika virus outbreak, the team developed diagnostics within weeks that met the U.S. Centers for Disease Control’s gold standard for use in clinical labs. With COVID-19, the researchers propose to design a suite of diagnostic tools including a “lab-in-a-box kit” that can be used to respond to a large outbreak, a package to help produce diagnostics on-site to support a sustained response and an on-the-spot test for rapid screening of patients – even in places like a cruise ship or airport.

    The team’s goal is to produce tools that will not only be useful in Canada but in countries with health-care systems less capable of handling mass emergencies.

    Another project led by Xiaolin Wei of U of T’s Dalla Lana School of Public Health seeks to produce guidelines to help health-care workers respond to COVID-19 and similar outbreaks in the future. Working with researchers in the Philippines and Sri Lanka, Wei will use front-line experiences in China to develop guidelines and training so health-care workers in these and other low-to-middle-income countries can manage COVID-19 patients and infection control.

    David Fisman, at Dalla Lana and the Institute of Health Policy, Management and Evaluation and the department of medicine in the Faculty of Medicine, is approaching the disease from another angle.

    Fisman and his colleagues – doctors, epidemiologists, public health professionals and statisticians – specialize in data analysis and modelling to help answer three basic questions about an epidemic: When will it peak? When will it end? And how big will it be?

    The team, which has experience dealing with SARS, H1N1 and Ebola, will use mathematical and statistical modelling to forecast the near-term course of the disease, make sense of “messy or noisy” public data and use the information to build simulations that can help guide Canadian health agencies’ decisions.

    Read a Q & A with Professor Fisman

    Other U of T experts who received federal grants for research related to the novel coronavirus are: Isaac Bogoch, of the Faculty of Medicine and the University Health Network; Prabhat Jha, of the Dalla Lana School of Public Health and St. Michael’s Hospital in the Unity Health Toronto network; Sachdev Sidhu, of the Donnelly Centre for Cellular and Biomolecular Research, the department of molecular genetics in the Faculty of Medicine and the Institute of Biomaterials and Biomedical Engineering; and Haibo Zhang, a professor in the department of physiology in the Faculty of Medicine who also works at St. Michael’s Hospital.

    In total, 47 research teams across the country received funding through several agencies and non-profits: the Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada, the Social Sciences and Humanities Research Council of Canada, the Canada Research Coordinating Committee, the International Development Research Centre and Genome Canada.

    In a statement, Theresa Tam, the chief public health officer of Canada, spoke of the importance of research in responding to emerging disease outbreaks.

    “The research to be undertaken by the successful teams will help to answer some of our most pressing questions about COVID-19 and help to develop the tools we need to effectively respond to this global public health emergency,” she said.

    See the full article here .


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    Founded in 1827, the University of Toronto has evolved into Canada’s leading institution of learning, discovery and knowledge creation. We are proud to be one of the world’s top research-intensive universities, driven to invent and innovate.

    Our students have the opportunity to learn from and work with preeminent thought leaders through our multidisciplinary network of teaching and research faculty, alumni and partners.

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  • richardmitnick 9:54 am on March 9, 2020 Permalink | Reply
    Tags: "Can the US make bioweapons obsolete?", , Biology, , Sandia National Lab   

    From Sandia Lab: “Can the US make bioweapons obsolete?” 

    From Sandia Lab

    March 9, 2020
    Paul Rhien

    Sandia experts help set vision to reach ambitious goal.

    “Making Bioweapons Obsolete: A Summary of Workshop Discussions,” released by Sandia National Laboratories and the Council on Strategic Risks addresses recommendations for significantly reducing and ultimately eliminating biothreats.

    As the threats posed by bioterrorism and naturally occurring infectious disease grow and evolve in the modern era, there is a rising potential for broad negative impacts on human health, economic stability and global security. To protect the nation from these dangers, Sandia National Laboratories has partnered with the Council on Strategic Risks in taking on the ambitious goal of making bioweapons obsolete.

    In a report released this week, “Making Bioweapons Obsolete: A Summary of Workshop Discussions,” Sandia and the council outline the discussion and recommendations that came out of the Making Bioweapons Obsolete workshop hosted at Sandia. The one-day meeting brought together government, national laboratories, academia, industry, policy and entrepreneur communities to address the challenges of mitigating and eliminating the risks bioweapons present. The workshop was the first in a planned series.

    The report captures the strategic vision the working group laid out for achieving this ambitious goal more effectively and rapidly. According to Anup Singh, director of Biological and Engineering Sciences at Sandia, addressing the rising threats bioweapons present across the U.S. and around the world will require using strategy, technology advances, policy and other tools.

    “This is an extremely interesting time in biotechnology with the revolutionary advances in genome editing, synthetic biology and convergent technologies such as artificial intelligence and robotics,” Singh said. “Academia and the private sector are driving a variety of biotechnology innovations and it is imperative that we engage them in solving the problem together with the traditional national security partners.”

    Drawing on the cross-discipline expertise of the working group, organizers aim to better understand the threat and how technology can both increase and mitigate the risk. The report focuses on identifying solutions that offer the biggest return and influencing national leadership to provide attention and resources to the issue and engage with academia and industry.

    “We need a moonshot-level, inspirational goal regarding biological threats,” said Andy Weber, senior fellow at the council. “When we convene top experts to explore the concept of making bioweapons obsolete, we are usually met with great enthusiasm and a feeling that the United States can really achieve this vision. Indeed, it is largely an expansion on the work the U.S. government has accomplished to date in addressing smallpox threats to America with an extensive vaccine stockpiling system and its development of vaccines for viruses such as Ebola.”

    The report highlights a wide range of considerations that must be addressed. The report:

    Provides insights on key technological trends.
    Raises questions of the data and information access required for rapidly characterizing and responding to biological attacks and outbreaks.
    Explores market and supply chain dynamics in depth.
    Points to significant U.S. government capacities that can be used and expanded, including its vast testing and evaluation infrastructure.
    Highlights the need for coordinated outreach and education to policymakers, in particular by academic and private sector experts.
    Drives home the critical importance of U.S. leadership.

    The workshop is the beginning of an important conversation in tackling the ambitious issue of eliminating or significantly reducing biothreats, explained Andy McIlroy, associate laboratory director of Integrated Security Solutions at Sandia.

    “With increased commitment, time, resources and leadership, we can make further strides in meeting this bold target,” McIlroy said. “I hope that we can continue this discussion to create a united, national vision that meets the urgency of the moment.”

    Future workshops will continue the wide-ranging discussion focused on engaging in a national dialogue and promoting better public-private collaboration in this grand mission. Sessions will focus on man-made threats from weapons of mass destruction, as well as the risks posed by advances in technology.

    The Council on Strategic Risks is a nonprofit, nonpartisan security policy institute devoted to anticipating, analyzing and addressing core systemic risks to security in the 21st century, with special examination of the ways in which these risks intersect and exacerbate one another. For more on council’s program on making bioweapons obsolete visit the Janne E. Nolan Center on Strategic Weapons.

    See the full article here .


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    Sandia National Laboratory

    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.

  • richardmitnick 1:02 pm on February 23, 2020 Permalink | Reply
    Tags: "A chemist investigates how proteins assume their shape", , Biology, , Matt Shoulders, , Protein misfolding   

    From MIT News: “A chemist investigates how proteins assume their shape” 

    MIT News

    From MIT News

    February 23, 2020
    Anne Trafton

    Matt Shoulders. Images: Gretchen Ertl.

    Matt Shoulders hopes to shed light on diseases linked to flawed protein folding.

    When proteins are first made in our cells, they often exist as floppy chains until specialized cellular machinery helps them fold into the right shapes. Only after achieving this correct structure can most proteins perform their biological functions.

    Many diseases, including genetic disorders like cystic fibrosis and brittle bone disease, and neurodegenerative diseases like Alzheimer’s, are linked to defects in this protein folding process. Matt Shoulders, a recently tenured associate professor in the Department of Chemistry, is trying to understand how protein folding happens in human cells and how it goes wrong, in hopes of finding ways to prevent diseases linked to protein misfolding.

    “In the human cell, there are tens of thousands of proteins. The vast majority of proteins must eventually attain some well-defined three-dimensional structure to carry out their functions,” Shoulders says. “Protein misfolding and protein aggregation happen a lot, even in healthy cells. My research group’s interest is in how cells get proteins folded into a functional conformation, in the right place and at the right time, so they can stay healthy.”

    In his lab at MIT, Shoulders uses a variety of techniques to study the “proteostasis network,” which comprises about a thousand components that cooperate to enable cells to maintain proteins in the right conformations.

    “Proteostasis is exceedingly important. If it breaks down, you get disease,” he says. “There’s this whole system in cells that helps client proteins get to the shapes they need to get to, and if folding fails the system responds to try and address the problem. If it can’t be solved, the network actively works to dispose of misfolded or aggregated client proteins.”

    Building new structures

    Growing up in the Appalachian Mountains, Shoulders was homeschooled by his mother, along with his five siblings. The family lived on a small farm near Blacksburg, Virginia, where his father was an accounting professor at Virginia Tech. Shoulders credits his grandfather, a chemistry professor at Ohio Northern University and Alice Lloyd College, with kindling his interest in chemistry.

    “My family had a policy that the kids helped clean up the kitchen after dinner. I hated doing it,” he recalls. “Fortunately for me, there was one exception: If we had company, and if you were in an adult conversation with the company, you could get out of cleaning the kitchen. So I spent many hours, starting at the age of 5 or 6, talking about chemistry with my grandfather after dinner.”

    Before starting college at nearby Virginia Tech, Shoulders spent a couple of years working as a carpenter.

    “That’s when I discovered that I really liked building things,” he says. “When I went to college I was thinking about fields to get into, and I realized chemistry was an opportunity to merge those two things that I had begun to find very exciting — building things but also thinking at the molecular level. A big part of what chemists do is make things that have never been made before, by connecting atoms in different ways.”

    As an undergraduate, Shoulders worked in the lab of chemistry professor Felicia Etzkorn, devising ways to synthesize complex new molecules, including stable peptides that mimic protein functions. In graduate school at the University of Wisconsin, he worked with Professor Ronald Raines, who is now on the faculty at MIT. At Wisconsin, Shoulders began to study protein biophysics, with a focus on the physical and chemical factors that control which structure a given protein adopts and how stable the structure is.

    For his graduate studies, Shoulders analyzed how proteins fold while in a solution in a test tube. Once he finished his PhD, he decided to delve into how proteins fold in their natural environment: living cells.

    “Experiments in test tubes are a great way to get some insight but, ultimately, we want to know how the biological system works,” Shoulders says. To that end, he went to the Scripps Research Institute to do a postdoc with professors Jeffery Kelly and Luke Wiseman, who study diseases caused by protein misfolding.

    Neurodegenerative diseases like Alzheimer’s and Parkinson’s diseases are perhaps the best known protein misfolding disorders, but there are thousands of others, most of which affect smaller numbers of people. Kelly, Wiseman, and many others, including the late MIT biology professor Susan Lindquist, have shown that protein misfolding is linked to cellular signaling pathways involved in stress responses.

    “When protein folding goes awry, these signaling pathways recognize it and try to fix the problem. If they succeed, then all is well, but if they fail, that almost always leads to disease,” Shoulders says.

    Disrupted protein folding

    Since joining the MIT faculty in 2012, Shoulders and his students have developed a number of chemical and genetic techniques for first perturbing different aspects of the proteostasis network and then observing how protein folding is affected.

    In one major effort, Shoulders’ lab is exploring how cells fold collagen. Collagen, an important component of connective tissue, is the most abundant protein in the human body and, at more than 4,000 amino acids, is also quite large. There are as many as 50 different diseases linked to collagen misfolding, and most have no effective treatments, Shoulders says.

    Another major area of interest is the evolution of proteins, especially viral proteins. Shoulders and his group have shown that flu viruses’ rapid evolution depends in part on their ability to hijack some components of the proteostasis network of the host cells they infect. Without this help, flu viruses can’t adapt nearly as rapidly.

    In the long term, Shoulders hopes that his research will help to identify possible new ways to treat diseases that arise from aberrant protein folding. In theory, restoring the function of a single protein involved in folding could help with a variety of diseases linked to misfolding.

    “You might not need one drug for each disease — you might be able to develop one drug that treats many different diseases,” he says. “It’s a little speculative right now. We still need to learn much more about the basics of proteostasis network function, but there is a lot of promise.”

    See the full article here .

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  • richardmitnick 10:53 am on February 17, 2020 Permalink | Reply
    Tags: "Edaphic Factors Are Important to Explain and Predict Impact of Climate Change on Species Distribution", , Biology, , , ,   

    From Chinese Academy of Sciences: “Edaphic Factors Are Important to Explain and Predict Impact of Climate Change on Species Distribution” 

    From Chinese Academy of Sciences

    Feb 14, 2020
    ZHANG Nannan

    Examples of habitats that support edaphic specialists (Image by Wikimedia Commons)

    The climate change crisis has resulted in an emphasis on the role of broad-scale climate in controlling species distributions. A key metric for predicting the impacts of climate change on species and ecosystems is the local velocity of climate change: how fast a species must move across the landscape to track its preferred climate in space. However, other ecologically important environmental variables will move much more slowly (e.g., some soil properties) or not at all (e.g., underlying geology).

    In a review published in Trends in Ecology & Evolution, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) pointed out that the relative neglect of local edaphic factors risks weakening people’s ability to explain past responses to climate change and predict future ones.

    The researchers focused on some immovable environmental variables and specifically on the soil types with extreme chemical and/or physical properties that develop on regionally rare geological substrates, such as limestone karsts, ultramafic rocks, and granite inselbergs (i.e. isolated hills or mountains rising abruptly from a plain, like islands in the sea).

    By consulting a large amount of literature, the researchers found that in warmer regions of the world, the edaphic specialists (i.e. species of plants and animals in specific substrates) appear to have accumulated in situ over millions of years, persisting despite climate change by local movements, plastic responses, and genetic adaptation. However, past climates were usually cooler than today and rates of warming slower, while edaphic islands are now exposed to multiple additional threats, including mining.

    They further found that species distribution models used to predict climate change responses can include edaphic factors, but these are rarely mapped at a high enough spatial resolution.

    “Using low-resolution edaphic data for predictions is likely to give misleading results”, said Prof. Richard Corlett, principal investigator of the study.

    “We need to improve our understanding of the mechanistic basis for edaphic endemism, in order to predict the vulnerability of these endemics to climate change and other anthropogenic impacts. Reciprocal transplants and resource-addition experiments should be useful for this” said Prof. Richard Corlett.

    “We also need to improve the species distribution models used to predict climate change impacts”, added Dr. Corlett.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. Comprising a comprehensive research and development network, a merit-based learned society and a system of higher education, CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches.

    Since its founding, CAS has fulfilled multiple roles — as a national team and a locomotive driving national technological innovation, a pioneer in supporting nationwide S&T development, a think tank delivering S&T advice and a community for training young S&T talent.

    Now, as it responds to a nationwide call to put innovation at the heart of China’s development, CAS has further defined its development strategy by emphasizing greater reliance on democratic management, openness and talent in the promotion of innovative research. With the adoption of its Innovation 2020 programme in 2011, the academy has committed to delivering breakthrough science and technology, higher caliber talent and superior scientific advice. As part of the programme, CAS has also requested that each of its institutes define its “strategic niche” — based on an overall analysis of the scientific progress and trends in their own fields both in China and abroad — in order to deploy resources more efficiently and innovate more collectively.

    As it builds on its proud record, CAS aims for a bright future as one of the world’s top S&T research and development organizations.

  • richardmitnick 11:27 am on February 15, 2020 Permalink | Reply
    Tags: (DIC)-Dissolved Inorganic Carbon, (TA)-Total Alkalinity, , Biology, , , , , , The wet lab then becomes a bedlam of buckets containing rocks; corals; sponges; and shell fragments; occasional deep sea litter; and an assortment of marine creatures that I have never seen before., You need to know how to tie knots.   

    From Schmidt Ocean Institute: “Darling it’s better, Down in a Wet(ter) Lab at Sea” 

    From Schmidt Ocean Institute

    Jill Brouwer

    Cruise Log: The Great Australian Deep-Sea Coral and Canyon Adventure

    Trying to understand a constantly moving ocean system is a huge challenge. Accurately measuring the chemistry of the ocean is important for understanding many processes, including nutrient and carbon cycling; ocean circulation and movement of water masses; as well as ocean acidification and climate change. On this expedition, the water chemistry team has the important job of analyzing the seawater in three canyon systems. We are measuring Dissolved Inorganic Carbon (DIC) and Total Alkalinity (TA) on board, while also saving samples for later analysis of stable isotopes, trace elements, and nutrients.

    Jill and Carlin using the CTD rosette to collect water samples from the depths of the Bremer Canyon.

    Knotty and Nice

    There are some quirks of successfully doing chemistry at sea that I definitely did not consider before this voyage. Firstly, you need to know how to tie knots. Making sure all the instruments, reagent bottles, and yourselves are secured is just as important as doing the actual chemistry. The precious sample counts for nothing if it flies across the room because you forgot to put it on a non-slip mat. The movement of the boat transforms normal lab activities into fun mini challenges – opening oven or fridge doors as the ship moves with the weather, pipetting as you hit a large wave, storing sample vials in a giant freezer. It is weird (but comforting) to see our analytical instruments strapped to the bench, and doing most of my work out of a sink – the safest place to keep samples. I particularly enjoy the arts and crafts component that comes with bubble wrapping and storing samples to prevent them from being damaged by sudden movements.

    After the chemistry work is done for the day, ROV SuBastian [below] comes aboard with all kinds of creepy-crawlies from the deep sea. All the biology and geology samples that have been collected from the dive are carried into the wet lab to be sorted, processed, and archived. The lab then becomes a bedlam of buckets containing rocks, corals, sponges, shell fragments, occasional deep sea litter, and an assortment of marine creatures that I have never seen before. Surrounding these specimens is an eclectic mix of scientists who all bring their own unique interests and passions to the group.


    To name a few; Julie, Paolo, and their team are interested in finding calcifying corals for their paleoceanography studies. They study the chemistry of the ocean thousands of years ago, recorded by coral skeletons when they were formed. We also have Andrew from the Western Australian Museum, who is doing his PhD on specialized barnacles that live in sponges, but is interested in pretty much everything. It is not just the big things we are looking for either. Aleksey and Netra are on the lookout for tiny single-cell organisms called Foraminifera that we have found in the water column, sediments, and attached to things like corals and whale bones.

    Netra, Jill, and Angela investigating the latest samples to arrive in the wet lab of R/V Falkor.

    This Stephanocyanthus is a soft cup coral.

    This Caryophylliidae is from a family of stony corals.

    Working in a wet lab at sea has its share of challenges, but considering the important scientific discoveries that are facilitated by us being out here, the cool (and in some cases totally new) marine life we are encountering, as well as the incredible views of sun glint and waves through the lab window, I would not choose to be anywhere else. To all the undergraduate students reading this, I encourage you to seek out as much volunteer/work experience as you can. Getting involved in science firsthand is an invaluable experience: you get to work with incredible people, gain useful skills, and learn so much more about yourself and your areas of interest than you can from the classroom. Perhaps most importantly, you get to share all the exciting things you learn with others!


    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Our Vision
    The world’s oceans understood through technological advancement, intelligent observation, and open sharing of information.

    Schmidt Ocean Institute RV Falkor

    Schmidt Ocean Institute ROV Subastian

    Schmidt Ocean Institute is a 501(c)(3) private non-profit operating foundation established in March 2009 to advance oceanographic research, discovery, and knowledge, and catalyze sharing of information about the oceans.

    Since the Earth’s oceans are a critically endangered and least understood part of the environment, the Institute dedicates its efforts to their comprehensive understanding across intentionally broad scope of research objectives.

    Eric and Wendy Schmidt established Schmidt Ocean Institute in 2009 as a seagoing research facility operator, to support oceanographic research and technology development focusing on accelerating the pace in ocean sciences with operational, technological, and informational innovations. The Institute is devoted to the inspirational vision of our Founders that the advancement of technology and open sharing of information will remain crucial to expanding the understanding of the world’s oceans.

  • richardmitnick 11:32 pm on February 12, 2020 Permalink | Reply
    Tags: , Biology, Biophysical chemistry, Chromophores, Macromolecular crystallography, , Photoisomerization, , ,   

    From SLAC National Accelerator Lab: “Researchers show how electric fields affect a molecular twist within light-sensitive proteins” 

    From SLAC National Accelerator Lab

    February 12, 2020
    By Ali Sundermier

    A better understanding of this phenomenon, which is crucial to many processes that occur in biological systems and materials, could enable researchers to develop light-sensitive proteins for areas such as biological imaging and optogenetics.

    A team of scientists from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University has gained insight into how electric fields affect the way energy from light drives molecular motion and transformation in a protein commonly used in biological imaging. A better understanding of this phenomenon, which is crucial to many processes that occur in biological systems and materials, could enable researchers to finely tune a system’s properties to harness these effects, for instance using light to control neurons in the brain. Their findings were published in Science in January.

    Twist and shout

    Human vision, photosynthesis and other natural processes harvest light with proteins that contain molecules known as chromophores, many of which twist when light hits them. The hallmark of this twisting motion, called photoisomerization, is that part of the molecule rotates around a particular chemical bond.

    When light hits certain chromophores in proteins, it causes them to twist and change shape. This atomic reconfiguration, known as photoisomerization, changes the molecule’s chemical and physical properties. The hallmark of this process is a rotation that occurs around a chemical bond in the molecule. New research shows that the electric fields within a protein play a large role in determining which bond this rotation occurs around. (Chi-Yun Lin/Stanford University)

    “Something about the protein environment is steering this very specific and important process,” says Steven Boxer, a biophysical chemist and Stanford professor who oversaw the research. “One possibility is that the distribution of atoms in the molecular space blocks or allows rotation about each chemical bond, known as the steric effect. An alternative has to do with the idea that when molecules with double bonds are excited, there is a separation of charge, and so the surrounding electric fields might favor the rotation of one bond over another. This is called the electrostatic effect.”

    A different tune

    To find out more about this process, the researchers looked at green fluorescent protein, a protein frequently used in biological imaging whose chromophore can respond to light in a number of ways that are sensitive to its local environment within the protein, producing fluorescent light of various colors and intensities.

    Stanford graduate students Matt Romei and Chi-Yun Lin, who led the study, tuned the electronic properties of the chromophore within the protein by introducing chemical groups that systematically added or subtracted electrons from the chromophore to engineer an electric field effect. Then they measured how this affected the chromophore’s twisting motion.

    With the help of coauthor Irimpan Mathews, a scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), the researchers used an X-ray technique called macromolecular crystallography at SSRL beamlines 7-1, 12-2 and 14-1 to map the structures of these tuned proteins to show that these changes had little effect on the atomic structure of the chromophore and surrounding protein.


    Then, using a combination of techniques, they were able to measure how changes to the chromophore’s electron distribution affected where rotation occurred when it was hit by light.

    “Until now, most of the research on photoisomerization in this particular protein has been either theoretical or focused on the steric effect,” Romei says. “This research is one of the first to investigate the phenomenon experimentally and show the importance of the electrostatic effect. Once we plotted the data, we saw these really nice trends that suggest that tuning the chromophore’s electronic properties has a huge impact on its bond isomerization properties.”

    Honing tools

    These results also suggest ways to design light-sensitive proteins by manipulating the environment around the chromophore. Lin adds that this same experimental approach could be used to study and control the electrostatic effect in many other systems.

    “We’re trying to figure out the principle that controls this process,” Lin says. “Using what we learn, we hope to apply these concepts to develop better tools in fields such as optogenetics, where you can selectively manipulate nerves to lead to certain functions in the brain.”

    Boxer adds that the idea that the organized electric fields within proteins are important for many biological functions is an emerging concept that could be of interest to a broad audience.

    “Much of the work in our lab focuses on developing methods to measure these fields and connect them with function such as enzymatic catalysis,” he says, “and we now see that photoisomerization fits into this framework.”

    This work was funded in part by the National Institutes of Health (NIH). SSRL is a DOE Office of Science user facility. The SSRL Structural Molecular Biology Program is supported by the NIH and the DOE Office of Biological and Environmental Research. Part of this work was performed at the Stanford Nano Shared Facilities and supported by the National Science Foundation.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition


    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.

    SSRL and LCLS are DOE Office of Science user facilities.

  • richardmitnick 12:14 pm on February 12, 2020 Permalink | Reply
    Tags: Atom or noise?, Biology, , , , , , Stanford’s Department of Bioengineering   

    From SLAC National Accelerator Lab: “Atom or noise? New method helps cryo-EM researchers tell the difference” 

    From SLAC National Accelerator Lab

    February 11, 2020
    Nathan Collins

    Cryogenic electron microscopy can in principle make out individual atoms in a molecule, but distinguishing the crisp from the blurry parts of an image can be a challenge. A new mathematical method may help.

    Cryogenic electron microscopy, or cryo-EM, has reached the point where researchers could in principle image individual atoms in a 3D reconstruction of a molecule – but just because they could see those details doesn’t always mean they do. Now, researchers at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have proposed a new way to quantify how accurate such reconstructions are and, in the process, how confident they can be in their molecular interpretations. The study was published February 10 in Nature Methods.

    Cryo-EM works by freezing biological molecules which can contain thousands of atoms so they can be imaged under an electron microscope. By aligning and combining many two-dimensional images, researchers can compute three-dimensional maps of an entire molecule, and this technique has been used to study everything from battery failure to the way viruses invade cells. However, an issue that has been hard to solve is how to accurately assess the true level of detail or resolution at every point in such maps and in turn determine what atomic features are truly visible or not.

    A cryo-EM map of the molecule apoferritin (left) and a detail of the map showing the atomic model researchers use to construct Q-scores. (Image courtesy Greg Pintilie)

    Wah Chiu, a professor at SLAC and Stanford, Grigore Pintilie, a computational scientist in Chiu’s group, and colleagues devised the new measures, known as Q-scores, to address that issue. To compute Q-scores, scientists start by building and adjusting an atomic model until it best matches the corresponding cryo-EM derived 3D map. Then, they compare the map to an idealized version in which each atom is well-resolved, revealing to what degree the map truly resolves the atoms in the atomic model.

    The researchers validated their approach on large molecules, including a protein called apoferritin that they studied in the Stanford-SLAC Cryo-EM Facilities. Kaiming Zhang, another research scientist in Chiu’s group, produced 3D maps close to the highest resolution reached to date – up to 1.75 angstrom, less than a fifth of a nanometer. Using such maps, they showed how Q-scores varied in predictable ways based on overall resolution and on which parts of a molecule they were studying. Pintilie and Chiu say they hope Q-scores will help biologists and others using cryo-EM better understand and interpret the 3D maps and resulting atomic models.

    The study was performed in collaboration with researchers from Stanford’s Department of Bioengineering. Molecular graphics and analysis were performed using the University of California, San Francisco’s Chimera software package. The project was funded by the National Institutes of Health.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition


    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.

    SSRL and LCLS are DOE Office of Science user facilities.

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