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  • richardmitnick 10:23 am on November 9, 2019 Permalink | Reply
    Tags: "Friendly bacteria collaborate to survive", , Bacteriology, , , Microbiology,   

    From University of Copenhagen: “Friendly bacteria collaborate to survive” 

    From University of Copenhagen

    10 October 2019

    Søren Johannes Sørensen
    Professor, Department Of Biology
    Mobile:+ 45 51 82 70 07
    Mail: sjs@bio.ku.dk

    Michael Skov Jensen
    Communications Officer, SCIENCE Management and Communication


    New microbial research at the University of Copenhagen suggests that ‘survival of the friendliest’ outweighs ‘survival of the fittest’ for groups of bacteria. Bacteria make space for one another and sacrifice properties if it benefits the bacterial community as a whole. The discovery is a major step towards understanding complex bacteria interactions and the development of new treatment models for a wide range of human diseases and new green technologies.

    New microbial research at the Department of Biology reveals that bacteria would rather unite against external threats, such as antibiotics, rather than fight against each other. The report has just been published in the scientific publication ISME Journal. For a number of years the researchers have studied how combinations of bacteria behave together when in a confined area. After investigating many thousands of combinations it has become clear that bacteria cooperate to survive and that these results contradict what Darwin said in his theories of evolution.

    “In the classic Darwinian mindset, competition is the name of the game. The best suited survive and outcompete those less well suited. However, when it comes to microorganisms like bacteria, our findings reveal the most cooperative ones survive,” explains Department of Biology microbiologist, Professor Søren Johannes Sørensen.

    Social bacteria work shoulder to shoulder

    By isolating bacteria from a small corn husk (where they were forced to “fight” for space) the scientists were able to investigate the degree to which bacteria compete or cooperate to survive. The bacterial strains were selected based upon their ability to grow together. Researchers measured bacterial biofilm, a slimy protective layer that shields bacteria against external threats such as antibiotics or predators. When bacteria are healthy, they produce more biofilm and become stronger and more resilient.

    Time after time, the researchers observed the same result: Instead of the strongest outcompeting the others in biofilm production, space was allowed to the weakest, allowing the weak to grow much better than they would have on their own. At the same time the researchers could see that the bacteria split up laborious tasks by shutting down unnecessary mechanisms and sharing them with their neighbors.

    “It may well be that Henry Ford thought that he had found something brilliant when he introduced the assembly line and worker specialization, but bacteria have been taking advantage of this strategy for a billion years,” says Søren Johannes Sørensen referring to the oldest known bacterial fossils with biofilm. He adds:

    “Our new study demonstrates that bacteria organize themselves in a structured way, distribute work and even to help each other. This means that we can find out which bacteria cooperate, and possibly, which ones depend on each another, by looking at who sits next to who.”


    Understanding invisible bacterial synergy

    The researchers also investigated what properties bacteria had when they were alone versus when they were with other bacteria. Humans often discuss the work place or group synergy, and how people inspire each other. Bacteria take this one step further when they survive in small communities.

    “Bacteria take our understanding of group synergy and inspiration to a completely different level. They induce attributes in their neighbors that would otherwise remain dormant. In this way groups of bacteria can express properties that aren’t possible when they are alone.
    When they are together totally new features can suddenly emerge,” Søren Johannes Sørensen explains.

    Understanding how bacteria interact in groups has the potential to create a whole new area in biotechnology that traditionally strives to exploit single, isolated strains, one at a time.

    “Bio-based society is currently touted as a solution to model many of the challenges that our societies face. However, the vast majority of today’s biotech is based on single organisms. This is in stark contrast to what happens in nature, where all processes are managed by cooperative consortia of organisms. We must learn from nature and introduce solutions to tap the huge potential of biotechnology in the future”, according to Søren Johannes Sørensen.

    Read the research article in the the ISME Journal.

    See the full article here .


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    Niels Bohr Institute Campus

    The University of Copenhagen (UCPH) (Danish: Københavns Universitet) is the oldest university and research institution in Denmark. Founded in 1479 as a studium generale, it is the second oldest institution for higher education in Scandinavia after Uppsala University (1477). The university has 23,473 undergraduate students, 17,398 postgraduate students, 2,968 doctoral students and over 9,000 employees. The university has four campuses located in and around Copenhagen, with the headquarters located in central Copenhagen. Most courses are taught in Danish; however, many courses are also offered in English and a few in German. The university has several thousands of foreign students, about half of whom come from Nordic countries.

    The university is a member of the International Alliance of Research Universities (IARU), along with University of Cambridge, Yale University, The Australian National University, and UC Berkeley, amongst others. The 2016 Academic Ranking of World Universities ranks the University of Copenhagen as the best university in Scandinavia and 30th in the world, the 2016-2017 Times Higher Education World University Rankings as 120th in the world, and the 2016-2017 QS World University Rankings as 68th in the world. The university has had 9 alumni become Nobel laureates and has produced one Turing Award recipient

  • richardmitnick 9:37 am on June 24, 2019 Permalink | Reply
    Tags: "Scientists Hit Pay Dirt with New Microbial Research Technique", (BONCAT+FACS-BONCAT Fluorescent Activated Cell Sorting, , BONCAT- short for Bioorthogonal Non-Canonical Amino Acid Tagging, DOE Office of Science' Joint Genome Institute (JGI), ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies, , Microbiology, Most soil microbes won’t grow in cultures in a laboratory, Soils are probably the most diverse microbial communities on the planet   

    From Lawrence Berkeley National Lab: “Scientists Hit Pay Dirt with New Microbial Research Technique” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    June 24, 2019
    Aliyah Kovner

    A better method for studying microbes in the soil will help scientists understand large-scale environmental cycles.

    Credit: Susan Brand and Marilyn Chung/Berkeley Lab

    Long ago, during the European Renaissance, Leonardo da Vinci wrote that we humans “know more about the movement of celestial bodies than about the soil underfoot.” Five hundred years and innumerable technological and scientific advances later, his sentiment still holds true.

    But that could soon change.

    In a report published in Nature Communications, a team of scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) detailed the first-ever successful use of a technique called BONCAT to isolate active microbes present in a sample of soil – an achievement that could enable a tidal wave of new research.

    “Soils are probably the most diverse microbial communities on the planet,” said Estelle Couradeau, first author of the study. “In every gram of soil, there are billions of cells from tens of thousands of species that, all together, perform important Earth nutrient cycles. They are the backbone of terrestrial ecosystems, and healthy soil microbiomes are key to sustainable agriculture. We now have the tools to see who these species are, but we don’t yet know how they do what they do. This proof-of-concept study shows that BONCAT is an effective tool that we could use to link active microbes to environmental processes.”

    A close look at soil microbiomes

    For the past two years, Couradeau, her co-authors, and many other researchers from around the U.S. have been collaborating in a Berkeley Lab-led scientific focus area called ENIGMA (for Ecosystems and Networks Integrated with Genes and Molecular Assemblies) in order to dig deeper into the inner-workings of soil microbiomes. ENIGMA’s projects are a high priority for biologists and energy and Earth scientists not only because they help fill gaps in our knowledge of how the environment functions, but also because these fundamental insights could help applied scientists more effectively harness microbiomes to improve drought-resistance in crops, remove contaminants from the environment, and sustainably produce fuels and other bioproducts.

    Charles Paradis, now a post-doctoral researcher at Los Alamos National Laboratory, holds a soil core sample taken from the Oak Ridge Field Research Site in Tennessee. The BONCAT+FACS optimization testing reported in the current study used samples such as this one. (Credit: Lance E. King/Y-12 National Security Complex)

    However, because most soil microbes won’t grow in cultures in a laboratory, and because of their truly mind-boggling abundance in their natural habitats, investigating which microbial species do what is incredibly difficult. “There are many barriers to measuring microbial activities and interactions,” said Trent Northen, lead author and director of biotechnology for ENIGMA. “For example, soil microbiomes that remove waste from underground water reservoirs are found hundreds of feet below the surface. And in some ecosystems, up to 95% of the microbes are inactive at any given time.”

    Because direct observation is off the table, microbiologists typically collect environmental samples and rely on indirect approaches such as DNA sequencing to characterize the communities. However, most of the commonly used techniques fail to differentiate active microbes from those that are dormant or from the plethora of free-floating bits of DNA found in soil and sediment.

    Expanding the toolkit

    BONCAT, short for Bioorthogonal Non-Canonical Amino Acid Tagging, was invented by Caltech geneticists in 2006 as a way to isolate newly made proteins in cells. In 2014, Rex Malmstrom, Danielle Goudeau, and others at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility managed by Berkeley Lab, collaborated with Victoria Orphan’s lab at Caltech to adapt BONCAT into a tool that could identify active, symbiotic clusters of dozens to hundreds of marine microbes within ocean sediment. After further refining their approach, called BONCAT Fluorescent Activated Cell Sorting (BONCAT+FACS), they were able to detect individual active microbes.

    A graph representing how the addition of fluorescent tags allows scientists to sort microbial cells. (Estelle Couradeau/Berkeley Lab)

    As the name suggests, BONCAT+FACS allows scientists to sort single-cell organisms based on the presence or absence of fluorescent tagging molecules, which bind to a modified version of the amino acid methionine. When fluid containing the modified methionine is introduced to a sample of microbes, only those that are creating new proteins – the hallmark of activity – will incorporate the modified methionine into cells.

    In addition to being far more streamlined and reliable than previous methods of microbial identification, the entire process takes just a few hours – meaning it can tag active cells even if they are not replicating.

    Given that some soil microbes are notoriously slow-growing, many scientists were immediately interested in applying BONCAT+FACS to terrestrial soils. After three months of experimentation and optimization, the team of ENIGMA and JGI researchers devised a protocol that works smoothly and, most importantly, gives very reproducible results.

    “BONCAT+FACS is a powerful tool that provides a more refined method to determine which microbes are active in a community at any particular time,” said Malmstrom, who is also an author of the current study. “It also opens the door for us to experiment, to assess which cells are active under condition A and which cells become active or inactive when switched to condition B.”

    The next steps

    Moving forward, BONCAT+FACS will be a capability available to researchers who wish to collaborate through the JGI’s user programs. Northen and Malmstrom have already received several proposals from research groups eager to start working with the tool, including groups from Berkeley Lab who hope to use BONCAT to assess how environmental changes stimulate groups of microbes. “With BONCAT, we will be able to get immediate snapshots of how microbiomes react to both normal habitat fluctuations and extreme climate events – such as drought and flood – that are becoming more and more frequent,” said Northen.

    According to Couradeau, the team expects the approach will catalyze a variety of other important and intriguing lines of study, such as improving agricultural land practices, assessing antibiotic susceptibility in unculturable microbes, and investigating the completely unknown roles of Candidatus Dormibacteraeota – a phylum of soil bacteria, found across the world, that appear to remain dormant most of the time.

    Reflecting on how he and his colleagues achieved a goal that many have been pursuing, Malmstrom cited the diversity of scientists within ENIGMA and JGI. “This a true example of team science, because no single person had or will ever have the expertise to do it all.”

    The other researchers involved in this work were Joelle Sasse, Danielle Goudeau, Nandita Nath, Terry Hazen, Ben Bowen, and Romy Chakraborty. The study was funded by a discovery proposal grant awarded to Trent Northen as part of the ENIGMA Science Focus Area. Both ENIGMA and JGI are supported by the DOE Office of Science.

    See the full article here .


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    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.

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  • richardmitnick 2:15 pm on May 17, 2019 Permalink | Reply
    Tags: , Bacteria-killing viruses – bacteriophages, , Cholera outbreaks occur worldwide, In regions of the world lacking clean water and proper sanitation 2.5 billion people are at risk., , Microbiology, Phages are very specific and infect only their particular host species of bacteria., Phages infect and kill multi-drug resistant strains of bacteria just as well as drug-sensitive ones., Phages provide immediate protection., Potential weapons to fight bacteria that are resistant to multiple antibiotics   

    From The Conversation: “Viruses to stop cholera infections – the viral enemy of deadly bacteria could be humanity’s friend” 

    From The Conversation

    May 17, 2019

    Andrew Camilli
    Professor of Molecular Biology & Microbiology, Tufts University

    Minmin Yen
    Research Associate of Molecular Microbiology, Tufts University


    In the latest of a string of high-profile cases in the U.S., a cocktail of bacteria-killing viruses successfully treated a cystic fibrosis [Nature Biotechnology] patient suffering from a deadly infection caused by a pathogen that was resistant to multiple forms of antibiotics.

    Curing infections is great, of course. But what about using these bacteria-killing viruses – bacteriophages – to prevent infections in the first place? Could this work for some diseases? Although using viruses to prevent infections caused by bacterial infections might seem counterintuitive, in the case of bacteriophages: “The enemy of my enemy is my friend.”

    Discovered a little more than 100 years ago [BMC], bacteriophages, or phages, are generating renewed interest as potential weapons to fight bacteria that are resistant to multiple antibiotics – the so-called superbugs. Although the recent phage therapy has been focused on the treatment of sick patients, preventing infection stops a disease before it begins, keeping people healthy and preventing the spread of the germ to others.

    We are microbiologists [Nature Communications] who study cholera because this ancient disease continues to thrive and can have a devastating impact on communities and entire countries. The Camilli lab has been focused on the disease for over two decades. We are interested in developing vaccines and phage products to prevent cholera from sickening people and triggering outbreaks.

    This cholera patient is drinking oral rehydration solution in order to counteract his cholera-induced dehydration. Centers for Disease Control and Prevention’s Public Health Image Library

    Cholera outbreaks occur worldwide

    In the case of cholera, which is caused by the bacterium Vibrio cholerae, prevention is preferred because it spreads like wildfire once it strikes a community. When this bacterial pathogen is ingested, it inhabits the small intestine, where it releases a potent toxin that triggers vomiting and watery diarrhea, which cause severe dehydration. The vomiting and diarrhea encourage the spread of the pathogen within households and contaminate local water sources. Left untreated, cholera kills 40% of its victims, sometimes within hours of the onset of symptoms. Fortunately, death can be largely prevented by prompt rehydration of cholera victims.

    In regions of the world lacking clean water and proper sanitation, 2.5 billion people are at risk, and the CDC estimates that there are up to 4 million cholera cases per year. New epidemics such as the recent massive epidemic in Yemen which has so far sickened over 1.2 million people and the outbreak in Mozambique are often the consequence of humanitarian crises. War and natural disasters often cause shortages of clean water and impact the poorest and most vulnerable communities.

    Cholera is highly transmissible in the community and within households. During outbreaks, an estimated 80% of cases are believed to result from rapid transmission within households, presumably occurring through contamination of household food, water or surfaces with diarrhea or vomit from the initial cholera victim.

    Family members typically experience cholera symptoms themselves two to three days after the initial household member became sick. Thus, the people in the most danger are usually siblings and loved ones taking care of the sick person. There is currently no approved medical intervention to immediately protect household members from contracting cholera when it strikes a household. Vaccines for cholera require at least 10 days to take effect, and thus miss the mark in this emergency situation.

    Prevention of cholera using phages

    To address this need, we developed a cocktail of phages to be taken orally each day by household members prior to, or soon after, exposure to Vibrio cholerae to protect them from contracting the disease. We believe the phages should remain in the intestinal tract long enough to serve as a shield against the incoming cholera bacteria. Although this has only been proven in animal models of cholera, we hope that the phage cocktail will work similarly in humans. There are three advantages to using phages in this manner.

    First, phages provide immediate protection. By acting fast, phages can eliminate the cholera bacteria from the gut in a targeted manner. That is important because cholera kills quickly.

    Second, phages infect and kill multi-drug resistant strains of bacteria just as well as drug-sensitive ones. This is crucial since the cholera bacteria have become multi-drug resistant [ALJM] in many parts of the world due to widespread antibiotic use [The Lancet].

    Third, in contrast to antibiotics, which kill bacteria indiscriminately, phages are very specific and infect only their particular host species of bacteria. Thus, when using phages against a pathogen, they will not disrupt the good bacteria residing in and on our patients’ bodies which are part of the microbiome. In research in our lab phages, called ICP1, ICP2 and ICP3, which we are using, kill only Vibrio cholerae and should not disrupt the good bacteria in the intestinal tract. This is important because our good bacteria are essential for defending the body against other pathogens and vital for our general nutrition and health.

    People fill buckets with water from a well that is alleged to be contaminated water with the bacterium Vibrio cholera, on the outskirts of Yemen. Yemen’s raging two-year conflict has served as an incubator for lethal cholera. AP Photo/Hani Mohammed

    From test tube to product

    In collaboration with international researchers, we have been studying the cholera bacteria and its phages for over two decades at Tufts University, trying to uncover the details of how cholera spreads and how phages might affect its spread. The use of phages for prevention of cholera transmission was a natural outcome of this research, but by no means was it straightforward.

    Development of our phage product required finding phages that kill Vibrio cholerae in the intestinal tract, having intimate knowledge of how the phages infect the bacteria and discovering how the bacteria become resistant to the phages and how this affects their virulence.

    Our goal now is to test the phage cocktail in people during a cholera epidemic. Specifically, we need to determine if it is effective at preventing cholera transmission to family members in households where cholera strikes.

    In this day and age, we need to change the paradigm of relying entirely on antibiotics to treat infections and develop other types of antimicrobial solutions. It’s time to bring phages in from the cold, and utilize them both for treating multi-drug resistant bacterial infections and in the prevention of infections.

    See the full article here .


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    The Conversation launched as a pilot project in October 2014. It is an independent source of news and views from the academic and research community, delivered direct to the public.
    Our team of professional editors work with university and research institute experts to unlock their knowledge for use by the wider public.
    Access to independent, high quality, authenticated, explanatory journalism underpins a functioning democracy. Our aim is to promote better understanding of current affairs and complex issues. And hopefully allow for a better quality of public discourse and conversation.

  • richardmitnick 11:57 am on May 9, 2019 Permalink | Reply
    Tags: A new genetically engineered shell based on natural structures and the principles of protein evolution., , Bacteria across our planet contain nanometer-sized factories that do many different things., , Microbiology, , , Natural protein shells   

    From Michigan State University: “Simpler and smaller: A new synthetic nanofactory inspired by nature” 

    Michigan State Bloc

    From Michigan State University

    May 2, 2019
    Igor Houwat
    MSU-DOE Plant Research Laboratory office
    (517) 353-2223


    Bacteria across our planet contain nanometer-sized factories that do many different things. Some make nutrients, others isolate toxic materials that could harm the bacteria. We have barely scratched the surface of their functional diversity.

    But all share a common exterior, a shell made of protein tiles, that Michigan State University researchers are learning how to manipulate in the lab. This will allow them to build factories of their own design, using the natural building blocks. Indeed, scientists see the structures as a source of new technologies. They are trying to repurpose them to do things they don’t in nature.

    In a new study, the lab of Cheryl Kerfeld reports a new genetically engineered shell, based on natural structures and the principles of protein evolution. The new shell is simpler, made of only a single designed protein. It will be easier to work with and, perhaps, even evolve in the lab. The study is published in ACS Synthetic Biology.

    Natural shells are made of up to three types of proteins. The most abundant is called BMC-H. Six BMC-H proteins come together to form a hexagon shape to tile the wall.

    At some time in evolutionary history, some pairs of BMC-H proteins became joined together, in tandem. Three of these mergers, called BMC-T, join to also form a hexagon shape.

    “The two halves of a BMC-T protein can evolve separately while staying next to each other, because they are fused together,” said Bryan Ferlez, a postdoc in the Kerfeld lab. “This evolution allows for diversity in the structures and functions of BMC-T shell proteins, something that we want to recreate by design in the lab.”

    Taking their cue from this natural evolution of shell proteins, the team created an artificial BMC-T protein, called BMC-H2, by fusing two BMC-H protein sequences together. The new design was successful.

    “To our surprise, BMC-H2 proteins form shells on their own,” said. Sean McGuire a former undergraduate research student and technician in the Kerfeld lab. “They look like wiffle balls, with gaps in the shell,”

    This is because natural shells are icoshedral, meaning that they are made of hexamers and pentamers—think of a soccer ball.

    Next, the team capped the gaps in the wiffle ball shell with BMC-P, the third type of shell protein that forms pentamers.

    “The result is a shell, about 25 nanometers wide, made up of only two protein types: the new BMC-H2 and BMC-P,” Bryan says. “It is around half the size of the structure built with all three protein types.”

    The next goal is to fit it with custom enzymes and fine tune it to enhance the chemical reactions within. The new ‘designer’ shell could have uses in biofuel production, medicine and industrial applications.

    See the full article here .


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    Michigan State Campus

    Michigan State University (MSU) is a public research university located in East Lansing, Michigan, United States. MSU was founded in 1855 and became the nation’s first land-grant institution under the Morrill Act of 1862, serving as a model for future land-grant universities.

    MSU pioneered the studies of packaging, hospitality business, plant biology, supply chain management, and telecommunication. U.S. News & World Report ranks several MSU graduate programs in the nation’s top 10, including industrial and organizational psychology, osteopathic medicine, and veterinary medicine, and identifies its graduate programs in elementary education, secondary education, and nuclear physics as the best in the country. MSU has been labeled one of the “Public Ivies,” a publicly funded university considered as providing a quality of education comparable to those of the Ivy League.

    Following the introduction of the Morrill Act, the college became coeducational and expanded its curriculum beyond agriculture. Today, MSU is the seventh-largest university in the United States (in terms of enrollment), with over 49,000 students and 2,950 faculty members. There are approximately 532,000 living MSU alumni worldwide.

  • richardmitnick 9:07 am on May 17, 2018 Permalink | Reply
    Tags: , Marsarchaeota microbes, Microbiology, , Yellowstone volcano   

    From Science Alert: “A New Yellowstone Park Discovery Points Back to The Origins of Life” 


    From Science Alert

    (Ajith Kumar/iStock)

    17 MAY 2018

    These microbes basically live in acid.

    Scientists have found a new lineage of microbes in the famously hot and acidic spring waters of Yellowstone National Park in the US, a discovery that promises to teach us more about the origins of life on our planet.

    These single-cell organisms, from the archaea domain of life, seem to thrive in the thermal springs of Yellowstone where iron oxide is the main mineral.

    Because the surface of Mars is made up of the same sort of materials, the researchers have named the lineage Marsarchaeota.

    The conditions inside the springs of Yellowstone are thought to match the conditions on the early Earth, and that’s why these Marsarchaeota microbes can be so helpful – they can show us how organisms sparked into life, and what role iron oxide may have played.

    “The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of Earth,” write the researchers [Nature Microbiology].

    “The broad distribution of Marsarchaeota in geothermal, microaerobic iron oxide mats suggests that similar habitat types probably played an important role in the evolution of archaea.”

    Using a variety of techniques – including microscopic analysis and genome sequencing – the team studied microbial mats in Yellowstone Park springs that are about as acidic as grapefruit juice.

    Two groups of Marsarchaeota were identified, one living in temperatures above 50 degrees Celsius (122 degrees Fahrenheit) and the other living in temperatures between 60 and 80 degrees Celsius (140 to 176 degrees Fahrenheit).

    Samples were taken from across Yellowstone Park, with these archaea lineages sometimes making up as much as half the organisms inside a single microbial mat.

    The mats themselves have been turned red by the iron oxide, which also slows the passage of water across the top of the mats. Oxygen is captured from the atmosphere and supplied to the Marsarchaoeta as water trickles over them – though the microbes are very deep, they only require low levels of oxygen.

    “Physics comes together with chemistry and microbiology,” says senior researcher William Inskeep, from Montana State University. “It’s like a sweet spot of conditions that this group of organisms likes.”

    By adding these archaea to “the universal tree of life”, we can get a better idea of the ancient organisms that first sprung up on the planet, and maybe then answer the broader question of how they evolved into multi-celled eukaryotes – animals and plants.

    One idea is that these Marsarchaeota might be involved in converting iron into a simpler form. They don’t produce iron oxide themselves, as other microbes do.

    “Iron cycling has been implicated as being extremely important in early Earth conditions,” says Inskeep.

    More close observation will be required to figure out how this particular type of microbe can flourish in these conditions, and what its role might have been before any other type of life appeared on Earth.

    And the potential benefits to science don’t end there. Further down the line these microorganisms could give us more clues about how life is potentially surviving on Mars, as well as some of the fundamentals about biology at higher temperatures.

    “Knowing about this new group of archaea provides additional pieces of the puzzle for understanding high-temperature biology,” says Inskeep.

    “That could be important in industry and molecular biology.”

    See the full article here .

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    • stewarthoughblog 11:43 pm on May 17, 2018 Permalink | Reply

      And what precisely about the origin of life is this supposed to point to? The Mars/iron association is hardly more than wishful association. There is some interesting science relative to archaea and such, but hardly any solution to any of the intractable naturalistic conjectures being offered as serious solutions to naturalistic origin of life. The prospect of offering any serious contribution to the origin of life is overly optimistic faith in an ideology that has no viable solutions.


  • richardmitnick 10:40 am on March 9, 2018 Permalink | Reply
    Tags: , , , , Microbiology,   

    From WCG “Microbiome Immunity Project Already Extending the Known Universe of Protein Structures” 

    New WCG Logo


    World Community Grid (WCG)

    WCG Microbiome Immunity Project

    7 Mar 2018
    By: Tomasz Kosciolek, PhD
    UC San Diego Center for Microbiome Innovation

    The Microbiome Immunity Project is off to a great start on predicting the structures of hundreds of thousands of bacterial proteins within the human gut. Read about their progress and their plans in their first project update.


    The Microbiome Immunity Project was created to better understand the role of the microbiome in intestinal immune response and diseases such as Type 1 Diabetes (T1D) and Inflammatory Bowel Disease (IBD). In this project, we predict structures of bacterial proteins and use this information to annotate their functions and to understand host-microbiome interactions which are responsible for the pathology of IBD and T1D. This is a massive undertaking, as the human gut microbiome has more than 2 million unique proteins, with hundreds of thousands of proteins potentially interacting with human cells. A project of this scale is only possible thanks to the power of World Community Grid.

    Our Progress So Far

    With your help, we have already predicted the structures of over 50,000 prioritized proteins! In the grand scheme of the 2 million unique bacterial proteins in our gut, this may not seem like a lot, but keep in mind that the experimental work to date covers only approximately 125,000 proteins. In only 6 months we have made tremendous progress by extending our universe of known protein structures by almost 28 percent!

    You may have already realized that at this pace, predicting all bacterial protein structures would take years to complete. Fortunately, we don’t have to predict every single structure, because proteins can be grouped into families. These families consist of proteins with similar structures and functions, enabling a comprehensive understanding of the family’s function with only one representative member per family. Once we identify protein families of interest, we will investigate them in more detail.

    In the meantime, we have adjusted our strategy on how to prioritize the predictions. Instead of looking only at bacterial genomes (genes of an individual bacterial species), we are investigating bacterial pangenomes (genes of all bacterial strains belonging to the same species). We then prioritize those pangenomes according to their prevalence between individuals in cohort studies investigating the role of microbiome in IBD and T1D. This approach enables us to have the most impact early in the project. We not only have thorough information on microbes involved in T1D and IBD specifically, but we have also expanded our knowledge of the microbiome in general.

    We are now extracting information from your predictions, and during the course of the project we plan to make the data available to the public for other exciting research. We are also working on methods to improve predictions of protein functions, enabling us to find the important protein families involved in T1D and IBD among thousands of predictions we have made so far.

    All this progress has been made possible thanks to your generous contributions! There is still a lot to discover about the microbiome, but with each computation that you support we are getting a step closer to having a more detailed picture of this important ecosystem inside each of our bodies and understanding IBD and T1D. So, thank you and let’s continue working together on unraveling the mysteries of microbiome!

    See the full article here.

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  • richardmitnick 12:52 pm on December 26, 2017 Permalink | Reply
    Tags: , , , J. William Schopf, John Valley, , Microbiology, Oldest fossils ever found show life on Earth began before 3.5 billion years ago, SIMS-secondary ion mass spectrometer, Some represent now-extinct bacteria and microbes from a domain of life called Archaea, The study describes 11 microbial specimens from five separate taxa, ,   

    From U Wisconsin Madison and UCLA: “Oldest fossils ever found show life on Earth began before 3.5 billion years ago” 

    U Wisconsin

    University of Wisconsin

    UCLA bloc


    December 18, 2017
    Kelly April Tyrrell

    Geoscience Professor John Valley, left, and research scientist Kouki Kitajima collaborate in the Wisconsin Secondary Ion Mass Spectrometer Lab (WiscSIMS) in Weeks Hall. Photo: Jeff Miller

    Researchers at UCLA and the University of Wisconsin–Madison have confirmed that microscopic fossils discovered in a nearly 3.5 billion-year-old piece of rock in Western Australia are the oldest fossils ever found and indeed the earliest direct evidence of life on Earth.

    An epoxy mount containing a sliver of a nearly 3.5 billion-year-old rock from the Apex chert deposit in Western Australia is pictured at the Wisconsin Secondary Ion Mass Spectrometer Lab (WiscSIMS) in Weeks Hall. Photo: Jeff Miller

    The study, published Dec. 18, 2017 in the Proceedings of the National Academy of Sciences, was led by J. William Schopf, professor of paleobiology at UCLA, and John W. Valley, professor of geoscience at the University of Wisconsin–Madison. The research relied on new technology and scientific expertise developed by researchers in the UW–Madison WiscSIMS Laboratory.

    J. William Schopf, U Wisconsin Madison

    John Valley, UCLA

    An example of one of the microfossils discovered in a sample of rock recovered from the Apex Chert. A new study used sophisticated chemical analysis to confirm the microscopic structures found in the rock are biological. Courtesy of J. William Schopf

    The study describes 11 microbial specimens from five separate taxa, linking their morphologies to chemical signatures that are characteristic of life. Some represent now-extinct bacteria and microbes from a domain of life called Archaea, while others are similar to microbial species still found today. The findings also suggest how each may have survived on an oxygen-free planet.

    The microfossils — so called because they are not evident to the naked eye — were first described in the journal Science in 1993 by Schopf and his team, which identified them based largely on the fossils’ unique, cylindrical and filamentous shapes. Schopf, director of UCLA’s Center for the Study of Evolution and the Origin of Life, published further supporting evidence of their biological identities in 2002.

    He collected the rock in which the fossils were found in 1982 from the Apex chert deposit of Western Australia, one of the few places on the planet where geological evidence of early Earth has been preserved, largely because it has not been subjected to geological processes that would have altered it, like burial and extreme heating due to plate-tectonic activity.

    But Schopf’s earlier interpretations have been disputed. Critics argued they are just odd minerals that only look like biological specimens. However, Valley says, the new findings put these doubts to rest; the microfossils are indeed biological.

    “I think it’s settled,” he says.

    Using a secondary ion mass spectrometer (SIMS) at UW–Madison called IMS 1280 — one of just a handful of such instruments in the world — Valley and his team, including department geoscientists Kouki Kitajima and Michael Spicuzza, were able to separate the carbon composing each fossil into its constituent isotopes and measure their ratios.

    Isotopes are different versions of the same chemical element that vary in their masses. Different organic substances — whether in rock, microbe or animal ­— contain characteristic ratios of their stable carbon isotopes.

    Using SIMS, Valley’s team was able to tease apart the carbon-12 from the carbon-13 within each fossil and measure the ratio of the two compared to a known carbon isotope standard and a fossil-less section of the rock in which they were found.

    “The differences in carbon isotope ratios correlate with their shapes,” Valley says. “If they’re not biological there is no reason for such a correlation. Their C-13-to-C-12 ratios are characteristic of biology and metabolic function.”

    Based on this information, the researchers were also able to assign identities and likely physiological behaviors to the fossils locked inside the rock, Valley says. The results show that “these are a primitive, but diverse group of organisms,” says Schopf.

    The team identified a complex group of microbes: phototrophic bacteria that would have relied on the sun to produce energy, Archaea that produced methane, and gammaproteobacteria that consumed methane, a gas believed to be an important constituent of Earth’s early atmosphere before oxygen was present.

    UW–Madison geoscience researchers on a 2010 field trip to the Apex Chert, a rock formation in western Australia that is among the oldest and best-preserved rock deposits in the world. Courtesy of John Valley

    It took Valley’s team nearly 10 years to develop the processes to accurately analyze the microfossils — fossils this old and rare have never been subjected to SIMS analysis before. The study builds on earlier achievements at WiscSIMS to modify the SIMS instrument, to develop protocols for sample preparation and analysis, and to calibrate necessary standards to match as closely as possible the hydrocarbon content to the samples of interest.

    In preparation for SIMS analysis, the team needed to painstakingly grind the original sample down as slowly as possible to expose the delicate fossils themselves — all suspended at different levels within the rock and encased in a hard layer of quartz — without actually destroying them. Spicuzza describes making countless trips up and down the stairs in the department as geoscience technician Brian Hess ground and polished each microfossil in the sample, one micrometer at a time.

    Each microfossil is about 10 micrometers wide; eight of them could fit along the width of a human hair.

    Valley and Schopf are part of the Wisconsin Astrobiology Research Consortium, funded by the NASA Astrobiology Institute, which exists to study and understand the origins, the future and the nature of life on Earth and throughout the universe.

    Studies such as this one, Schopf says, indicate life could be common throughout the universe. But importantly, here on Earth, because several different types of microbes were shown to be already present by 3.5 billion years ago, it tells us that “life had to have begun substantially earlier — nobody knows how much earlier — and confirms it is not difficult for primitive life to form and to evolve into more advanced microorganisms,” says Schopf.

    Earlier studies by Valley and his team, dating to 2001, have shown that liquid water oceans existed on Earth as early as 4.3 billion years ago, more than 800 million years before the fossils of the present study would have been alive, and just 250 million years after the Earth formed.

    “We have no direct evidence that life existed 4.3 billion years ago but there is no reason why it couldn’t have,” says Valley. “This is something we all would like to find out.”

    UW–Madison has a legacy of pushing back the accepted dates of early life on Earth. In 1953, the late Stanley Tyler, a geologist at the university who passed away in 1963 at the age of 57, was the first person to discover microfossils in Precambrian rocks. This pushed the origins of life back more than a billion years, from 540 million to 1.8 billion years ago.

    “People are really interested in when life on Earth first emerged,” Valley says. “This study was 10 times more time-consuming and more difficult than I first imagined, but it came to fruition because of many dedicated people who have been excited about this since day one … I think a lot more microfossil analyses will be made on samples of Earth and possibly from other planetary bodies.”

    See the full U Wisconsin article here .
    See the full uCLA article by Stuart Wolpert here.
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    UC LA Campus

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

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

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

    In achievement and prestige, the University of Wisconsin–Madison has long been recognized as one of America’s great universities. A public, land-grant institution, UW–Madison offers a complete spectrum of liberal arts studies, professional programs and student activities. Spanning 936 acres along the southern shore of Lake Mendota, the campus is located in the city of Madison.

    • stewarthoughblog 1:44 am on December 27, 2017 Permalink | Reply

      Schopf’s wishful speculation that what was discovered indicates life must be common is intellectually insulting with his failure that somehow live emerged rapidly, which strains the slow, methodical Darwinian theory of how life developed, given the relative complexity of the microorganisms. This is a wonderful discovery, but does nothing to solve the origin of life and raises serious questions about the power of naturalism to explain the origin of life as well as the rapid development of higher order complex organisms.

      The only extraterrestrial organisms that will be found will be those of Earth origin.


  • richardmitnick 8:33 am on October 19, 2017 Permalink | Reply
    Tags: All important research in what is a chipping away of the many unknowns in the stories of the origins of Earth and the origin of life, , , Flow of electrons (electricity) from the core of the Earth, Geobiochemistry, , , Microbiology   

    From Many Worlds: “2.5 Billions Years of Earth History in 100 Square Feet’ 

    NASA NExSS bloc


    Many Words icon

    Many Worlds

    Marc Kaufman

    Scalding hot water from an underground thermal spring creates an iron-rich environment similar to what existed on Earth 2.5 billion years ago. (Nerissa Escanlar)

    Along the edge of an inlet on a tiny Japanese island can be found– side by side – striking examples of conditions on Earth some 2.4 billion years ago, then 1.4 billion years ago and then the Philippine Sea of today.

    First is a small channel with iron red, steaming and largely oxygen-free water – filled from below with bubbling liquid above 160 degrees F. This was Earth as it would have existed, in a general way, as oxygen was becoming more prevalent on our planet some 2.4 billion years ago. Microbes exist, but life is spare at best.

    Right next to this ancient scene is region of green-red water filled with cyanobacteria – the single-cell creatures that helped bring masses of oxygen into our atmosphere and oceans. Locals come to this natural “onsen” for traditional hot baths, but they have to make their way carefully because the rocky floor is slippery with green mats of the bacteria.

    And then there is the Philippine Sea, cool but with spurts of warm water shooting up from below into the cove.

    All of this within a area of maybe 100 square feet.

    It is a unique hydrothermal scene, and one recently studied by two researchers from the Earth-Life Science Institute in Tokyo – microbiologist Shawn McGlynn and ancient virus specialist Tomohiro Mochizuki.

    They were taking measurements of temperature, salinity and more, as well as samples of the hot gas and of microbial life in the iron-red water. Cyanobacterial mats are collected in the greener water, along with other visible microbe worlds.

    Microbiologist Shawn McGlynn of the Earth Life Science Institute in Tokyo scoops some iron-rich water from a channel on Shikine-jima Island, 100 miles from Tokyo. (Nerissa Escanlar)

    The scientific goals are to answer specific questions – are the bubbles the results of biology or of geochemical processes? What are the isotopic signatures of the gases? What microbes and viruses live in the super-hot sections? And can cyanobacteria and iron co-exist?

    All are connected, though, within the broad scientific effort underway to ever more specifically understand conditions on Earth through the eons, and how those conditions can help answer fundamental questions of how life might have begun.

    “We really don’t know what microbiology looked like 2.5 billion or 1.5 billion years ago,” said McGlynn, “But this is a place we can go where we can try to find out. It’s a remarkable site for going back in time.”

    In particular, there are not many natural environments with high levels of dissolved iron like this site. Yet scientists know from the rock record that there were periods of Earth history when the oceans were similarly filled with iron.

    Mochizuki elaborated: “We’re trying to figure out what was possible chemically and biologically under certain conditions long ago.

    “If you have something happening now at this unusual place – with the oxygen and iron mixing in the hot water to turn the water red – then there’s a chance that what we find today was there as well billions of years ago. ”

    Tomohiro Mochizuki at collecting samples directly from the spot where 160 degree F water pushes up through the rock at Jinata hot spring. (Nerissa Escanlar)

    The Jinata hot springs, as the area is known, is on Shikine-jima Island, one of the furthest out in the Izu chain of islands that starts in Tokyo Bay. More than 100 miles from Tokyo itself, Shikine-jima is nonetheless part of Tokyo Prefecture.

    The Izu islands are all volcanic, created by the underwater movements of the Philippine and Pacific tectonic plates. That boundary remains in flux, and thus the hot springs and volcanoes. The terrain can be pretty rugged: in English, Jinata translates to something like Earth Hatchet, since the hot spring is at the end of a path through what does look like a rock rising that had been cut through with a hatchet.

    Hot springs and underwater thermal vents have loomed large in thinking about origins of life since it became known in recent decades that both generally support abundant life – microbial and larger – and supply nutrients and even energy in the form of electricity from vents and electron transfers from chemical reactions.

    And so not surprisingly, vents are visited and sampled not infrequently by ELSI scientists. McGlynn was on another hydrothermal vent field trip in Iceland over the summer with, among others, ELSI Origins Network fellow Donato Gionovelli and ELSI principal investigator and electrochemist Ruyhei Nakamura..

    McGlynn’s work is focused on how electrons flow between elements and compounds, a transfer that he sees as a basic architecture for all life. With so many compelling flows occurring in such a small space, Jinata is a superb laboratory.

    The volcanic Izu island chain, starting in Tokyo Bay and going out into the Philippine Sea.

    For Mochizuki, the site turned out to be exciting but definitely not a goldmine. That’s because his speciality is viruses that live at very high temperatures, and even the bubbling hot spring in the iron trench measured about 73 degrees C (163 degrees F.) The viruses he incubates live at temperatures between closer to 90 C (194 F), not far from the boiling point.

    His goal in studying these high-temperature (hyperthermophilic) viruses is to look back to the earliest days of life forming on Earth, using viruses as his navigators. Since life is thought by many scientists to have begun in a super hot RNA world, Mochizuki wants to look at viruses still living in those conditions today to see what they can tell us.

    So far, he explained, what they have told us is that the RNA in the earliest lifeforms on Earth – denizens of the Archaean kingdom – did not have viruses. And this is puzzling.

    So Mochizuki is always interested in going to sample hot springs and thermal vents to collect high temperature viruses, and to look for surprises.

    Though the bubbling waters were so hot that both researchers had difficulty standing in the water with boots on and holding their collection vials with gloves, it was not hot enough for what Mochizuki is after. But that certainly didn’t stop him from taking as many samples as he could, including some for other ELSI researchers doing different work but still needing interesting samples.

    Researchers often need to be inventive on field trips, and that was certainly the case at Jinata. When McGlynn first tried to sample the bubbles at the scalding spring, his hands and feet quickly felt on fire and he had to retreat.

    To speed the process, he and Mochizuki built a funnel out of a large plastic water bottle, a device that allowed the bubbles to be collected and directed into the sample vial without the gloved hands being so close to the heat. The booted feet, however, remained a problem and the heat just had to be endured.

    Nearby the steaming bubbling of the hot spring were collections of what appeared to be fine etchings on the bottom of the red channel. These faint designs, McGlynn explained, were the product of a microbe that makes it’s way along the bottom and deposits lines of processed iron oxide as it goes. So while the elegant designs are not organic, the creatures that creates them surely is.

    “Touch the area and the lines go poof,” McGlynn said. “That’s because they’re just the iron oxide; nothing more. Next to us is the water with much less iron and a lot more oxygen, and so there are blooms of (green) cyanobacteria. Touch them and they don’t go poof, they stick to your hand because they’re alive.”

    Patterns created by microbes as they deposit iron oxide at the bottom of small channel. (Marc Kaufman)

    McGlynn also collects some of the the poofs to get at the microbes making the unusual etchings. It may be a microbe never identified before.

    As a microbiologist, he is of course interested in identifying and classifying microbes. He initially thought the microbes in the iron channel would be anaerobic, but he found that even tiny amount of oxygen making their way into the springs from the atmosphere made most aerobic, or possibly anaerobes capable of surviving with oxygen (which usually is toxic to them.)

    He also found that laboratory studies that found cyanobacteria would not flourish in the presence of iron were not accurate in nature, or certainly were not accurate at Jinata onsen.

    But it is that flow of electrons that really drives McGlynn – he even dreams of them at night, he told me.

    One of the goals of his work, and that of his colleague and sometimes collaborator at ELSI, geobiochemist Yuichiro Ueno, is to answer some of the outstanding questions about that flow of electrons (electricity) from the core of the Earth. The energy transits through the mantle, to the surface and then often is in contact with the biosphere (all living things) before it enters the atmosphere and sometimes disappears into space.

    He likened the process to the workings of a gigantic battery, with the iron core as the cathode and the oxygen in the atmosphere as the anode. Understanding the chemical pathways traveled by the electrons today, he is convinced, will tell a great deal about conditions on the early Earth as well.

    It’s all important research in what is a chipping away of the many unknowns in the stories of the origins of Earth and the origin of life.

    A boundary between where the very hot iron-rich water meets and the less hot water with thriving cyanobacteria colonies at Jinata.

    The field work also illustrated the hit-and-miss nature of these kind of outings. While McGlynn has not come up with Jinata surprises or novel understandings, he was so taken with the setting that he wondered if a seemly empty building not too far from the site could be turned into an ELSI marine lab.

    And while Mochizuki did not find sufficiently hot water for his work, he might still be coming back to the island, or others nearby. That’s because he learned of a potentially much hotter spring at a spot where the sea hits one of the island’s steep cliffs – a site that requires boat access that was unsafe in the choppy waters during this particular visit.

    In addition, McGlynn and Mochizuki did make some surprising discoveries, though they didn’t involve microbes, electron transfer or viruses.

    During a morning visit to a different hot spring, they came across a team of what turned out to be officials of the Izu islands – all dressed in suits and ties. They were visiting Shikine-jima as part of a series of joint islands visit to assess economic development opportunities.

    The officials were intrigued to learn what the scientists were up to, and made some suggestions of other spots to sample. One was an island occupied by Japanese self-defense forces and generally closed to outsiders. But the island is known to have areas of extremely hot water just below the surface of the land, sometimes up to 100 C (212 F.)

    The officials gave their cards and told the scientists to contact them if they wanted to get onto that island for sampling. And as for the official from Shikine-jima, he was already thinking big.

    “It would be a very good thing,” he said, “if you found the origin of life on our island.

    See the full article here .

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    About Many Worlds

    There are many worlds out there waiting to fire your imagination.

    Marc Kaufman is an experienced journalist, having spent three decades at The Washington Post and The Philadelphia Inquirer, and is the author of two books on searching for life and planetary habitability. While the “Many Worlds” column is supported by the Lunar Planetary Institute/USRA and informed by NASA’s NExSS initiative, any opinions expressed are the author’s alone.

    This site is for everyone interested in the burgeoning field of exoplanet detection and research, from the general public to scientists in the field. It will present columns, news stories and in-depth features, as well as the work of guest writers.

    About NExSS

    The Nexus for Exoplanet System Science (NExSS) is a NASA research coordination network dedicated to the study of planetary habitability. The goals of NExSS are to investigate the diversity of exoplanets and to learn how their history, geology, and climate interact to create the conditions for life. NExSS investigators also strive to put planets into an architectural context — as solar systems built over the eons through dynamical processes and sculpted by stars. Based on our understanding of our own solar system and habitable planet Earth, researchers in the network aim to identify where habitable niches are most likely to occur, which planets are most likely to be habitable. Leveraging current NASA investments in research and missions, NExSS will accelerate the discovery and characterization of other potentially life-bearing worlds in the galaxy, using a systems science approach.
    The National Aeronautics and Space Administration (NASA) is the agency of the United States government that is responsible for the nation’s civilian space program and for aeronautics and aerospace research.

    President Dwight D. Eisenhower established the National Aeronautics and Space Administration (NASA) in 1958 with a distinctly civilian (rather than military) orientation encouraging peaceful applications in space science. The National Aeronautics and Space Act was passed on July 29, 1958, disestablishing NASA’s predecessor, the National Advisory Committee for Aeronautics (NACA). The new agency became operational on October 1, 1958.

    Since that time, most U.S. space exploration efforts have been led by NASA, including the Apollo moon-landing missions, the Skylab space station, and later the Space Shuttle. Currently, NASA is supporting the International Space Station and is overseeing the development of the Orion Multi-Purpose Crew Vehicle and Commercial Crew vehicles. The agency is also responsible for the Launch Services Program (LSP) which provides oversight of launch operations and countdown management for unmanned NASA launches. Most recently, NASA announced a new Space Launch System that it said would take the agency’s astronauts farther into space than ever before and lay the cornerstone for future human space exploration efforts by the U.S.

    NASA science is focused on better understanding Earth through the Earth Observing System, advancing heliophysics through the efforts of the Science Mission Directorate’s Heliophysics Research Program, exploring bodies throughout the Solar System with advanced robotic missions such as New Horizons, and researching astrophysics topics, such as the Big Bang, through the Great Observatories [Hubble, Chandra, Spitzer, and associated programs. NASA shares data with various national and international organizations such as from the [JAXA]Greenhouse Gases Observing Satellite.

  • richardmitnick 11:31 am on December 22, 2015 Permalink | Reply
    Tags: , Microbiology,   

    From U Michigan: “Duhaime Lab undergrad awarded prestigious ASM fellowship” 

    U Michigan bloc

    University of Michigan

    Dec 21, 2015
    Gail Kuhnlein

    Alexi Schnur is attempting to isolate Lake Erie viruses that infect the bloom-forming bacterium Microcystis, the algae responsible for toxic algal blooms in Western Lake Erie.

    Alexi Schnur, an undergraduate who has worked in the lab of Dr. Melissa Duhaime since her first week freshman year, was awarded a prestigious American Society for Microbiology Undergraduate Research Fellowship. Schnur is attempting to isolate and describe viruses infecting the harmful algal bloom-forming bacterium, Microcystis, that ravages Lake Erie each summer.

    Schnur is a currently a junior in the Michigan Biology Academy Scholars Program (M-BIO) and the Undergraduate Research Opportunities Program (UROP) at the University of Michigan. Duhaime, a research scientist in the Department of Ecology and Evolutionary Biology, is Schnur’s mentor on her research project: “Microcystis Viruses – Hunting the Killers of Lake Erie’s Algal Blooms.” Schnur is an interdisciplinary astronomy major who plans to declare microbiology as another major once she finishes the introductory classes. She’s been interested in microbiology since becoming an undergraduate, which led her to virology studies in the Duhaime lab, where she is an undergraduate researcher.


    “Along with fellow U-M undergrad, Paulina Devlin, I am currently trying to isolate Microcystis viruses on seven different cultures of non-colonial strains of the bacterium Microcystis,” Schnur said. Non-colonial strains are bacterial strains that are not forming colonies, but are single-cellular strains. “Viruses were collected weekly from Lake Erie during the 2014 and 2015 bloom seasons, May through November. We then apply these to the Microcystis cultures and monitor for clearing of the culture, which would indicate infection and the presence of Microcystis-infecting viruses.

    “Our work is not motivated by trying to eliminate the bloom. We suspect that there is a complicated relationship between Microcystis and its viruses in Lake Erie, and it is improbable that one virus exists that would kill the bloom-forming Microcystis in all places and across the entire bloom season. Isolating a virus from Lake Erie that is found to infect Microcystis would be an important step to learning more about these relatively unknown viruses and the role they play in the evolution of the bloom during a summer season. We also have metagenomic data of the Microcystis viruses during the 2014 bloom that would allow us to possibly identify and track a Microcystis virus through the genomic data to learn about their evolution and ecology if we are unable to isolate a virus in the lab.”

    They have evidence of Lake Erie viruses that have killed several strains of Microcystis. Their next challenge is to isolate these infecting viruses and reproduce the results, which she said is proving to be a real challenge.

    Currently, Schnur plans to attend graduate school for microbiology to obtain her doctorate degree. A future career track she is considering is to research extremophiles (microbes that live in/on inhospitable environments).

    The ASM fellowship is aimed at highly competitive students who wish to pursue graduate careers (Ph.D. or M.D./Ph.D.) in microbiology. Fellows have the opportunity to conduct full-time summer research at their home institution with an ASM mentor and present their research results at the 2016 ASM Microbe Meeting in Boston, Mass. if their abstract is accepted.

    Each fellow receives up to a $4,000 stipend, a two-year ASM student membership, and funding for travel expenses to the ASM Research Capstone Institute and ASM Microbe Meeting.

    The American Society for Microbiology is the largest single life science society, composed of over 39,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.

    See the full article here .

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    U MIchigan Campus

    The University of Michigan (U-M, UM, UMich, or U of M), frequently referred to simply as Michigan, is a public research university located in Ann Arbor, Michigan, United States. Originally, founded in 1817 in Detroit as the Catholepistemiad, or University of Michigania, 20 years before the Michigan Territory officially became a state, the University of Michigan is the state’s oldest university. The university moved to Ann Arbor in 1837 onto 40 acres (16 ha) of what is now known as Central Campus. Since its establishment in Ann Arbor, the university campus has expanded to include more than 584 major buildings with a combined area of more than 34 million gross square feet (781 acres or 3.16 km²), and has two satellite campuses located in Flint and Dearborn. The University was one of the founding members of the Association of American Universities.

    Considered one of the foremost research universities in the United States,[7] the university has very high research activity and its comprehensive graduate program offers doctoral degrees in the humanities, social sciences, and STEM fields (Science, Technology, Engineering and Mathematics) as well as professional degrees in business, medicine, law, pharmacy, nursing, social work and dentistry. Michigan’s body of living alumni (as of 2012) comprises more than 500,000. Besides academic life, Michigan’s athletic teams compete in Division I of the NCAA and are collectively known as the Wolverines. They are members of the Big Ten Conference.

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