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  • richardmitnick 4:40 pm on January 19, 2023 Permalink | Reply
    Tags: "Special drone collects environmental DNA from trees", , , , , eDNA-Environmental DNA, , WSL [Eidgenössische Forschungsanstalt für Wald - Schnee und Landschaft][Institut fédéral de recherches sur la forêt - la neige et le paysage] (CH)   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Special drone collects environmental DNA from trees” 

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

    1.19.23
    Peter Rüegg

    1
    Photograph: Gottardo Pestalozzi / WSL.

    Researchers at ETH Zürich and WSL Swiss Federal Institute for Forest Snow and Landscape Research [Eidgenössische Forschungsanstalt für Wald – Schnee und Landschaft][Institut fédéral de recherches sur la forêt – la neige et le paysage] (CH) have developed a flying device that can land on tree branches to take samples. This opens up a new dimension for scientists previously reserved for biodiversity researchers.

    Ecologists are increasingly using traces of genetic material left behind by living organisms left behind in the environment, called environmental DNA (eDNA), to catalogue and monitor biodiversity. Based on these DNA traces, researchers can determine which species are present in a certain area.

    Obtaining samples from water or soil is easy, but other habitats – such as the forest canopy – are difficult for researchers to access. As a result, many species remain untracked in poorly explored areas.

    Researchers at ETH Zürich and the Swiss Federal Institute for Forest, Snow and Landscape Research Wald – Schnee und Landschaft, and the company SPYGEN have partnered to develop a special drone that can autonomously collect samples on tree branches.


    Special drone collects environmental DNA from trees. (Video: ETH Zürich)

    How the drone collects material

    The drone is equipped with adhesive strips. When the aircraft lands on a branch, material from the branch sticks to these strips. Researchers can then extract DNA in the lab, analyze it and assign it to genetic matches of the various organisms using database comparisons.

    But not all branches are the same: they vary in terms of their thickness and elasticity. Branches also bend and rebound when a drone lands on them. Programming the aircraft in such a way that it can still approach a branch autonomously and remain stable on it long enough to take samples was a major challenge for the roboticists.

    “Landing on branches requires complex control,” explains Stefano Mintchev, Professor of Environmental Robotics at ETH Zürich and WSL. Initially, the drone does not know how flexible a branch is, so the researchers fitted it with a force sensing cage. This allows the drone to measure this factor at the scene and incorporate it into its flight manoeuvre.

    3
    Scheme: DNA is extracted from the collected branch material, amplified, sequenced and the sequences found are compared with databases. This allows the species to be identified. (Graphic: Stefano Mintchev / ETH Zürich)

    Preparing rainforest operations at Zoo Zürich

    Researchers have tested their new device on seven tree species. In the samples, they found DNA from 21 distinct groups of organisms, or taxa, including birds, mammals and insects. “This is encouraging, because it shows that the collection technique works,“ says Mintchev, who co-​authored the study that has just appeared in the journal Science Robotics [below].

    The researchers now want to improve their drone further to get it ready for a competition in which the aim is to detect as many different species as possible across 100 hectares of rainforest in Singapore in 24 hours.

    To test the drone’s efficiency under conditions similar to those it will experience at the competition, Mintchev and his team are currently working at the Zoo Zurich’s Masoala Rainforest. „Here we have the advantage of knowing which species are present, which will help us to better assess how thorough we are in capturing all eDNA traces with this technique or if we’re missing something,“ Mintchev says.

    For this event, however, the collection device must become more efficient and mobilize faster. In the tests in Switzerland, the drone collected material from seven trees in three days; in Singapore, it must be able to fly to and collect samples from ten times as many trees in just one day.

    Collecting samples in a natural rainforest, however, presents the researchers with even tougher challenges. Frequent rain washes eDNA off surfaces, while wind and clouds impede drone operation. „We are therefore very curious to see whether our sampling method will also prove itself under extreme conditions in the tropics,” Mintchev says.

    Science Robotics
    See the science paper for instructive material with images and video.

    See the full article here .

    Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

    The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

    The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

    As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

    ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

    It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

    ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

    From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

    ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

    Reputation and ranking

    ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

    Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

    In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

    In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

    In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

    In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

     
  • richardmitnick 11:56 am on July 1, 2022 Permalink | Reply
    Tags: "The beauty and benefits of biodiversity", Adaptability lies at the very heart of speciation., , As well as working with living organisms the researchers also study the genetic material of specimens held in collections., , , , , , , eDNA-Environmental DNA, , , One of the most beautiful aspects of biodiversity is how species co-​evolve and exist together., , Species diversity is only one aspect of biodiversity-the others being habitat diversity and genetic diversity., Species diversity makes ecosystems resilient., The beauty of the world’s coral reefs never fails to amaze., , Time is of the essence because biodiversity is under threat and declining rapidly., Unfertilized minimally cultivated meadows and dry grasslands are incredibly diverse which makes them not just beautiful but essential., Using the eDNA method it took the researchers less than two years to confirm the presence of more fish species and families than experts had managed to identify during 13 years of reef dives.   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “The beauty and benefits of biodiversity” 

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

    01.07.2022
    Peter Rüegg

    1

    Biodiversity is beautiful, but it’s also vitally important. ETH researchers are getting to the heart of how species diversity and genetic diversity evolve – and why we must fight to preserve them.

    Spring is synonymous with bright yellow dandelions, lush green fields and cloudless blue skies, a captivating combination of colours that sends many people into raptures of delight. Yet biodiversity researchers such as Alex Widmer, Professor of Plant Ecological Genetics in the Department of Environmental Systems Science, take a rather different view: “I know too much about ecosystems to take any pleasure in something so monotonous,” he says. His notion of beauty tends more towards dry grasslands and natural meadows rich in different species. “A far cry,” he says, “from the picture-​postcard idyll.” He argues that such areas are beautiful in much less obvious ways. Unfertilized, minimally cultivated meadows and dry grasslands are incredibly diverse, he says, which makes them not just beautiful, but essential.

    “Species diversity makes ecosystems resilient,” says Widmer, “and at the core of that resilience is genetic diversity.” Without genetic diversity, he explains, species and organisms cannot adapt to existing and evolving environmental conditions. And it’s this adaptability that lies at the very heart of speciation.

    2
    Natural meadows exhibit high levels of diversity. (Photograph: Peter Rüegg)

    Loïc Pellissier, Professor of Ecosystems and Landscape Evolution in the Department of Environmental Systems Science, agrees that much of the beauty of biodiversity is hidden from view. One of the most beautiful aspects of biodiversity, he says, is how species co-​evolve and exist together. “All organisms have evolved to interact with each other, as anyone who works in species diversity will tell you. To me, ecosystems are like huge jigsaw puzzles, in which all the pieces fit together more or less perfectly.” His research focuses on how species diversity arises and evolves. Because this occurs over the course of millions of years, Pellissier relies on computer models to simulate geological processes and the evolutionary forces that lead to the formation of new species.

    Genetic diversity

    Pellissier also conducts numerous field projects to unlock the secrets of species diversity. He favours a new and increasingly popular method that enables ecologists to detect species and organisms from the DNA they leave behind in the environment – known for short as environmental DNA, or eDNA. Researchers simply collect water and soil samples and analyse them to see what genetic material they contain. They then match whatever DNA they find to the corresponding organisms, provided a reference is available for this. This method provides a relatively quick way to determine whether a species is present in an ecosystem or not – and it works for a wide variety of organisms. “eDNA gives us a new insight into an ecosystem’s diversity,” he says.

    Recently, Pellissier co-​authored a study on the diversity of reef fish worldwide. Researchers collected over 200 seawater samples from various tropical coral reefs and then “fished out” whatever fish DNA they could find. Using the eDNA method it took the researchers less than two years to confirm the presence of more fish species and families than experts had managed to identify during 13 years of reef dives.

    Yet species diversity is only one aspect of biodiversity, the others being habitat diversity and genetic diversity. “Of the three, genetic diversity is the one that has been most neglected,” says Widmer. “Studying and monitoring genetic diversity is much more difficult and time-​consuming than monitoring habitats or species numbers.” Hence the numerous inventories of Swiss plants, animals and habitats – from forests and wetlands to dry grasslands. “Yet there isn’t a single monitoring project in Switzerland that focuses on the genetic diversity of living things,” says Widmer, “This is despite the fact that genetic diversity is fundamental for species diversity and adaptability.”

    To fill this gap, Widmer has joined forces with the Swiss Federal Institute for Forest, Snow and Landscape Research WSL on a project that aims to add this crucial element to Switzerland’s existing biodiversity monitoring systems. With the support of the Swiss Federal Office for the Environment (FOEN), Widmer and his colleagues have already launched a pilot study of five different species, including two plant species, a butterfly and a toad. The fifth species in their study is the yellowhammer, a songbird commonly found in cultivated areas of Switzerland. The researchers have already sequenced the genomes of one hundred individual yellowhammers from right across the country.

    4
    The beauty of the world’s coral reefs never fails to amaze. Yet behind such splendour, there lies much more – namely, a diverse habitat for a host of marine life. (Photograph: Stocksy)

    As well as working with living organisms, the researchers also study the genetic material of specimens held in collections. “This tells us whether populations from over 100 years ago were as diverse as today’s, or whether some of that genetic diversity has been lost,” says Widmer. Research into biodiversity in Switzerland has already revealed a sharp decline in species diversity, he notes: “We’d like to find out whether the same applies to genetic diversity.” Once the pilot study is complete, Widmer’s goal is to set up a large-​scale monitoring project encompassing up to 50 species. These would be examined at regular intervals to detect changes in their genetic diversity. However, it is still unclear whether this complex and ambitious project will receive the necessary funding.

    Fragile and endangered beauty

    Time is of the essence because biodiversity is under threat and declining rapidly. It is only by firmly fitting together the many different pieces of the biodiversity puzzle that we can slow the extinction of individual species. Reduce this network by half, and species will die out a thousand times faster – and when external pressures such as climate change are factored in, species extinction will occur a thousand times faster again.

    “Biodiversity is essential to our lives,” says Widmer. “It impacts everything from our mental well-​being to whether we have food on the table.” Diverse ecosystems are much more stable and better geared for the future than monotonous, species-​poor habitats. Pellissier nods in agreement: “Biodiversity is like classical art in the sense that it can’t be replaced. If the earth loses its biological riches, it will lose its magic.”

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

    The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

    The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

    As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

    ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

    It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

    ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

    From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

    ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

    Reputation and ranking

    ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

    Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

    In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

    In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

    In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

    In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

     
  • richardmitnick 8:00 am on June 23, 2022 Permalink | Reply
    Tags: "BGCs": biosynthetic gene clusters, "Tapping the ocean as a source of natural products", , , , eDNA-Environmental DNA, , , Ocean Microbiome, , , Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Tapping the ocean as a source of natural products” 

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

    6.22.22
    Peter Rüegg

    Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.

    1
    Marine bacteria are a significant reservoir of undiscovered chemical compounds that could be of interest to humans.
    Credit: Helena Klein.

    The oceans are teeming with countless forms of life, from the world’s largest creature – the blue whale – to miniscule microorganisms. In addition to their vast numbers, these microorganisms are also crucial for ensuring that the entire eco-​ and climate system work properly. For instance, there are photosynthetically active varieties such as cyanobacteria that produce around 50 percent of the oxygen in the atmosphere. Moreover, by removing carbon dioxide from the atmosphere, microorganisms help counter global warming.

    Despite this significant role, research into the diversity of microorganisms found in the ocean has thus far been only rudimentary. So, a group of researchers led by Shinichi Sunagawa, Professor of Microbiome Research, is working closely with Jörn Piel’s group to investigate this diversity. Both groups are at the Institute of Microbiology at ETH Zürich.

    To detect new natural products made by bacteria, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at different depths from every ocean region in the world. The data came from such sources as ocean expeditions and observation platforms positioned out at sea.

    Thanks to modern technologies like environmental DNA (eDNA) analysis, it has become easier to search for new species and discover which known organisms can be found where. But what is hardly known at all is what special effects the marine microorganisms offer – in other words, what chemical compounds they make that are important for interactions between organisms. In the best-​case scenario, such compounds would benefit humans as well. Underpinning the research is the assumption that the ocean microbiome harbours great potential for natural products that could prove beneficial, for instance for their antibiotic properties.

    The extracted eDNA present in the samples was sequenced by the original researchers of the various expeditions. By reconstructing entire genomes on the computer, the scientists succeeded in decrypting the encoded information – the blueprints for proteins. Finally, they consolidated this new data together with the existing 8,500 genome data sets for marine microorganisms in a single database.

    This gave them 35,000 genomes to draw on when searching for new microbial species and, in particular, for promising biosynthetic gene clusters (BGCs). A BGC is a group of genes that provide the synthetic pathway for a natural product.

    New species and new molecules discovered

    In this genome data, the researchers detected not only many potentially useful BGCs – some 40,000 in all – but also previously undiscovered species of bacteria belonging to the phylum Eremiobacterota. This group of bacteria had been known to exist only in terrestrial environments and didn’t exhibit any special biosynthetic diversity.

    Sunagawa and his team named a new family of these bacteria as Eudoremicrobiaceae, and also were able to demonstrate that these bacteria are common and widespread: one species belonging to this family, Eudoremicrobium malaspinii, accounts for up to 6 percent of all bacteria present in certain areas of the ocean.

    “The relatives in the ocean possess what for bacteria is a giant genome. Fully decrypting it was technically challenging because the organisms had not been cultivated before,” Sunagawa says. Moreover, the new bacteria turned out to belong to the group of microorganisms that boasts the highest BGC diversity of all the samples examined. “As things stand, they are the most biosynthetically diverse family in the oceanic water column,” he says.

    The researchers looked at two Eudoremicrobiaceae BGCs in detail. One was a gene cluster containing the genetic code for enzymes that, according to Sunagawa, have never been found in this constellation in a bacterial BGC before. The other examined example was a bioactive natural product that inhibits a proteolytic enzyme.

    Validating experiments led to a surprise

    In collaboration with the group led by Jörn Piel, the researchers used experiments to validate the structure and function of both natural products. Since E. malaspinii could not be cultivated, Piel’s team had to graft genes into a model bacterium so they would act as blueprints for the natural products. This bacterium then produced the corresponding substances. Lastly, the researchers isolated the molecules from the cells, determined the structure and validated the biological activity.

    This was necessary because in one case, the enzymatic activity predicted by computer programs did not tally with the results of the experiments. “Computer predictions for what chemical reactions an enzyme will trigger have their limitations,” Sunagawa says. “This is why such predictions have to be validated in the lab if there’s any doubt.”

    Doing so is an expensive and time-​consuming endeavour that’s simply not viable for a database of 40,000 potential natural products. “However, our database has plenty to offer, and it’s accessible to all researchers who wish to use it,” Sunagawa says.

    Beyond the continued collaboration with Piel’s group to discover new natural products, Sunagawa wants to investigate unresolved questions in the evolution and ecology of oceanic microorganisms. These include how microorganisms are dispersed in the ocean given that they can spread over great distances only passively. He also wants to discover what ecological or evolutionary benefits certain genes create for microbes. Sunagawa suspects the BGCs may play a major role.

    Science paper:
    Nature

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

    The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

    The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

    As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

    ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

    It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

    ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

    From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

    ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

    Reputation and ranking

    ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

    Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

    In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

    In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

    In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

    In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

     
  • richardmitnick 6:14 pm on December 15, 2017 Permalink | Reply
    Tags: Beth Shapiro, CALeDNA project, , eDNA-Environmental DNA, Erika Zavaleta, eSIE- Environmental DNA for Science Investigation and Education, , Two UCSC biologists receive Howard Hughes Medical Institute Professor awards, UC Conservation Genomics Consortium,   

    From UCSC: “Two UCSC biologists receive Howard Hughes Medical Institute Professor awards” 

    UC Santa Cruz

    UC Santa Cruz

    December 13, 2017
    Tim Stephens
    stephens@ucsc.edu

    1
    Beth Shapiro (photo by C. Lagattuta)

    2
    Erika Zavaleta (photo by Matt Kroll)

    With funding from the Howard Hughes Medical Institute (HHMI), biologists at UC Santa Cruz will be using biodiversity surveys and field research to get more students engaged in science.

    Beth Shapiro and Erika Zavaleta, both professors of ecology and evolutionary biology, are among a select group of innovators in science education chosen this year for funding through the HHMI Professors Program.

    Zavaleta’s proposal won her a five-year, $1 million grant to create an inclusive and coordinated pathway that will engage students in ecology and conservation biology and support them all the way through to graduation. The program will provide increased access to research-based field courses and internships, along with sustained mentoring and a supportive community.

    “We have so many awesome field courses at UCSC, and I want to make sure they’re accessible to a full range of students and link them together into a pathway that will launch a diverse new generation of conservation leaders,” Zavaleta said.

    Environmental DNA

    Shapiro teamed up with Robert Wayne, a molecular ecologist at UCLA, to win a collaborative award of $1.5 million for a program to get large numbers of students involved in biodiversity surveys using environmental DNA. Environmental DNA (eDNA) is a highly sensitive molecular approach for cataloging biodiversity in any ecosystem by analyzing the DNA fragments found in soil and other environmental samples.

    “Environmental DNA is both a powerful tool for doing cutting-edge science and a great way to get people interested in science,” Shapiro said. “It’s fairly easy for a first experience, and yet the range of questions you can address is incredibly broad. It’s a gateway to all kinds of different science.”

    Shapiro and Wayne spearheaded the UC Conservation Genomics Consortium, which Wayne directs, and their HHMI project builds on the consortium’s work. Called Environmental DNA for Science Investigation and Education (eSIE), the three-tiered program starts with getting thousands of students involved in initial sampling efforts, either independently, with guidance from online instruction modules and mobile apps, or through organized sampling campaigns called “bioblitzes” at UC Natural Reserves and other sites throughout California. The consortium has been running bioblitzes through its CALeDNA project, and recruitment efforts are already under way to broaden the participation of students, including under-represented groups.

    “We want them to go out and have a positive first experience participating in actual field work and collecting samples and data that will be used by scientists, including themselves if they want to keep doing it,” Shapiro said.

    The second tier of the program will be a biodiversity course designed for both science majors and non-majors, using eDNA as a springboard for increasing science literacy and introducing students to some of the many ways science is relevant to important issues in society. Finally, the program includes funding to support students who want to do independent research projects with faculty mentors.

    Field courses

    Zavaleta’s program aims to build existing field research courses into a more coherent pathway that will guide students interested in ecology and conservation from their freshman or transfer year to graduation. Large introductory lecture courses required early in science majors are often blamed for attrition, and under-represented groups and disadvantaged students drop science majors at much higher rates than other students. Zavaleta said inquiry-based field courses and research opportunities provide experiences that can keep students engaged and inspired.

    “By combining the emotional rewards of nature and friendship, shared experience and co-creation, field courses provide the kind of experience that led many, including me, to careers in ecology and conservation biology,” she said. “They also create the kind of immersive experience that is so important to learning and is a big part of forming an understanding of the natural world.”

    Zavaleta wants to lower the barriers that can keep some students from participating in field courses by offering scholarships to cover course fees and building more capacity and diversity among the faculty and graduate students who teach the courses. She also wants to increase opportunities for undergraduates to get research experience through paid internships. A new staff mentorship position will help students take advantage of opportunities such as scholarships and research internships and will provide guidance throughout the program. These efforts will be coordinated and funded through a new Center to Advance Mentored, Inquiry-based Opportunities (CAMINO).

    “The idea is to provide wraparound support and build a community for all kinds of students, so we avoid the situation where they get inspired by a great course and then fall of a cliff when they face the big lecture courses required before they can move on,” Zavaleta said. “It’s also important that we measure and communicate the outcomes of this effort so that we understand what works and can sustain it and scale it up.”

    The HHMI Professors Program began in 2002, and Manuel Ares, professor of molecular, cell, and developmental biology at UCSC, was among that first cohort of HHMI Professors. This year, out of 177 proposals, only 12 were chosen for funding. In addition to producing two of the funded proposals, UC Santa Cruz submitted four of the 26 finalist proposals that made it through the first two rounds of peer review.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    UCO Lick Shane Telescope
    UCO Lick Shane Telescope interior
    Shane Telescope at UCO Lick Observatory, UCSC

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    UC Santa Cruz campus
    The University of California, Santa Cruz, opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

    UCSC is the home base for the Lick Observatory.

    Lick Observatory's Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building
    Lick Observatory’s Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building

    Search for extraterrestrial intelligence expands at Lick Observatory
    New instrument scans the sky for pulses of infrared light
    March 23, 2015
    By Hilary Lebow
    1
    The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch) UCSC Lick Nickel telescope

    Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

    “Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego who led the development of the new instrument while at the University of Toronto’s Dunlap Institute for Astronomy & Astrophysics.

    Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by UC Berkeley researchers. The infrared project takes advantage of new technology not available for that first optical search.

    Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

    5
    UCSC alumna Shelley Wright, now an assistant professor of physics at UC San Diego, discusses the dichroic filter of the NIROSETI instrument. (Photo by Laurie Hatch)

    Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

    “The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

    The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

    Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

    “We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

    Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

    “This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

    NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

    “Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

    NIROSETI will be fully operational by early summer and will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

    The NIROSETI team also includes Geoffrey Marcy and Andrew Siemion from UC Berkeley; Patrick Dorval, a Dunlap undergraduate, and Elliot Meyer, a Dunlap graduate student; and Richard Treffers of Starman Systems. Funding for the project comes from the generous support of Bill and Susan Bloomfield.

    Please help promote STEM in your local schools.

    STEM Icon

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