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Tag: University of Konstanz

  • Enhancing genomics and bioinformatics knowledge sharing

    Enhancing genomics and bioinformatics knowledge sharing

    Newswise — The African BioGenome Project, a large-scale international research project involving Konstanz bioinformatician Abdoallah Sharaf, successfully launched its “Open Institute”. The institute’s mission: accelerating knowledge exchange in biodiversity genomics and bioinformatics.

    The “blueprints” of all living organisms are encoded in the sequences of their DNAs’ base pairs. Knowledge about these genome sequences and the identification of functional subunits, such as genes, are of great importance for biodiversity conservation efforts and for the life sciences in general. For this reason, the African BioGenome Project (AfricaBP), founded in 2021, has set itself an ambitious goal: sequencing the genomes of 100,000 animal and plant species that occur only in Africa – and to do so within 10 years. What is more, the sequencing is to be conducted exclusively in Africa.

    A second goal of the AfricaBP, therefore, is to empower African scientists and institutions to obtain the required skill sets, capacity, and infrastructure to generate, analyze, and utilize genome sequences in labs across the continent. With the successful launch of AfricaBP’s Open Institute, the project has made an essential step towards reaching this goal, as Abdoallah Sharaf and his colleagues now describe in an article in Nature Biotechnology. Sharaf is a bioinformatician in the Department of Biology at the University of Konstanz (Germany), associate professor at Ain Shams University (Egypt), and Co-Chair of the AfricaBP pilot committee.

    Central goals of the Open Institute
    “The Open Institute aims to lower some of the barriers that often prevent the advancement of biodiversity genomics and bioinformatics knowledge exchange in Africa,” says Sharaf. To do so, the AfricaBP Open Institute focuses on five key priority areas:

    • Curriculum development
    • Technology development and infrastructure
    • Promoting grassroot knowledge exchange and equitable partnerships
    • Maximizing data ownership and sovereignty
    • Scientific enterprise and industry

    In 2022, the Open Institute started hosting widely-attended workshops in cooperation with African institutions and organizations as well as global partners. So far, over 700 participants from 29 countries have been trained in cutting-edge technologies in the fields of biodiversity and genomics. As many of the participants came from African countries with active genomics research, in the future, the Open Institute will broaden its outreach to increase the participation of scientists from regions that currently have minimal genomic activity. In line with this, five more workshops on various aspects of genomics and bioinformatics are planned by the end of 2023 – two of them online, three in a hybrid format.

    Tom Kariuki, Chief Executive Officer of the Science for Africa Foundation (SFA), applauds the project: “As the SFA Foundation, we are laser-focused on improving the quantity, quality, and productivity of science in Africa, which requires a skilled scientific workforce through the development of globally competitive science leaders in Africa. The Open Institute serves our objective of training future generations of scientists who will generate data to inform policy and Africa’s development agenda.”

    This text is an adapted version of the original press release of the African BioGenome Project.

    University of Konstanz

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  • REACH animal testing: Numbers in the debate

    REACH animal testing: Numbers in the debate

    Newswise — Sixteen years ago, the REACH chemical regulation came into force across Europe. REACH obliges the chemical industry to identify the health risks of all chemicals used in their products. The downside of REACH is that this hazard assessment requires a large number of animal tests. Just how many was not clear until now.

    The “Center for Alternatives to Animal Testing” (CAAT) based in Baltimore and at the University of Konstanz now wants to bring numbers into the REACH debate. In a current study, based on data from the European Chemicals Agency (ECHA), the researchers show that so far around 4.2 million animals have been used for hazard assessment under REACH (of which 1.3 million animals are in ongoing studies). An additional 3.5 to 6.9 million animal tests are expected due to the revision of REACH in 2022.

    Animal-free, alternative test methods were relatively rarely used. What is known as read-across methods (prediction of toxicity from comparison with structurally similar, already tested chemicals) were rejected in 75 percent of cases.

    Animal-free alternative methods
    The researchers from Konstanz and Baltimore advocate the use of animal-free alternative methods (New Approach Methodologies, NAMs). “Some of these new methods are not only suitable for large-scale chemical screenings, but also provide more meaningful results than animal testing, as the chemicals are tested on human cells – naturally in a petri dish”, explains Thomas Hartung, Director of the Center for Alternatives to Animal Testing (CAAT) and professor at the University of Konstanz.

    “Animal-free alternative methods are available for an increasing range of test purposes. The goal must be to adapt the legislation to the current state of scientific knowledge”, demands Marcel Leist, professor of in-vitro-toxicology at the University of Konstanz and co-director of the Center for Alternatives to Animal Testing Europe. The CAAT researchers emphasize the importance of bringing scientists, authorities and industry to the same table to advance the introduction of alternative methods.

    About CAAT-Europe
    The Center for Alternatives to Animal Testing Europe (CAAT-Europe) based in Konstanz was founded by Thomas Hartung and Marcel Leist. It is committed to reducing animal testing worldwide through the development and introduction of alternative methods. It combines research and information work, and creates exchange between scientists, authorities and industry. The CAAT scientists are also directly involved in the development of animal-free alternative methods. The 3R network Baden-Württemberg, Germany, as well as the Swiss Doerenkamp-Zbinden Foundation support their efforts. With the professorship of Marcel Leist, the University of Konstanz established the first professorship for alternative methods to animal testing in 2006. Among other achievements, the research team developed the world’s first in vitro toxicity test for the peripheral nervous system.

     

    University of Konstanz

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  • What Darwin would discover today

    What Darwin would discover today

    Newswise — “If Charles Darwin had had the opportunity to dive off the Cape Verde Islands, he would have been completely thrilled”, Eduardo Sampaio is convinced, because Darwin would have seen a fascinating, species-rich landscape. But he lacked the diving equipment. Thus, in his notes The Voyage of the Beagle, Darwin described Cape Verde as a barren landscape.

    Eduardo Sampaio, affiliate member of the Cluster of Excellence “Centre for the Advanced Study of Collective Behaviour” (CASCB) at the University of Konstanz, had quite the opposite experience. He was invited on board the ship Captain Darwin by filmmaker Victor Rault to continue his octopus research.

    Victor Rault, 30, set sail from Plymouth on the Captain Darwin in 2021, following in the footsteps of Darwin’s HMS Beagle. He wants to explore how the ecosystem has changed since Darwin’s voyage on the HMS Beagle in 1832. Researchers and citizens have been invited to travel along and conduct experiments in the spirit of Darwin. “When Victor told me about his project, I was baffled”, recalls biologist Eduardo Sampaio from Portugal. He says: “It was immediately clear to me that it’s an excellent idea to retrace the path of Charles Darwin. I was more than keen to jump on board!”

    What do octopuses see in a mirror image?
    Eduardo Sampaio spent ten days on the Captain Darwin. The focus was on the dives: The biologist, who works with the Max Planck Institute of Animal Behavior, actually wanted to observe the joint hunting behaviour of octopuses and fish. However, as it was mating season, the animals rarely showed themselves. If they came out, they wanted to interact with other octopuses and did not hunt at all.

    So, he spontaneously changed his research project and conducted a mirror test instead: “We wanted to determine whether the octopuses could realize that they were seeing another individual in the mirror.” In the evening on board, the crew watched the video footage: “When the octopus approached the mirror, it changed colour – but only the side facing the mirror changed. That was very fascinating to watch”, says Eduardo Sampaio. In a further experiment, the researcher now wants to test whether the octopuses can even recognize themselves.

    Bringing Darwin’s research style up to date
    In the evenings, Eduardo Sampaio read Darwin’s The Origin of Species, because “it inspired me”. Often, he wondered: “How can we update Darwin’s kind of scientific work with the new methods we have today, like machine learning and computer vision, to better understand how animals move in their natural habitats or use different strategies to exploit social information?” He does not have an answer yet, but may find it the next time he sails on the Captain Darwin.

    Great support for scientists who do not have the necessary resources
    Eduardo Sampaio will be back on board the Captain Darwin: “This trip, launched as a Citizen Science project, is a great support for researchers who don’t have the means to do this kind of field research, especially for researchers from disadvantaged areas and in countries where research structures are not so well equipped.” Much of the work that researchers usually have to handle themselves was taken over, such as obtaining permits, purchasing equipment and raising funds. “I also realized that citizens can play a much more active role in science than just collecting data”, says Eduardo Sampaio, who hopes that this sailing trip will be a prelude to more exciting Citizen Science expeditions. Eduardo Sampaio and Victor Rault also wrote a report about the collaboration published in PLOS Biology on 15 November 2022.

    Key facts

    • Dr Eduardo Sampaio from the Cluster of Excellence “Centre for the Advanced Study of Collective Behaviour” and researcher at the Max Planck Institute of Animal Behavior participated in a Citizen Science-led expedition
    • Publication on the benefits of such research projects in PLOS Biology: Sampaio E, Rault V (2022) Citizen-led expeditions can generate scientific knowledge and prospects for researchers. PLoS Biol 20(11):e3001872. https://doi.org/10.1371/journal.pbio.3001872

    University of Konstanz

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