DeepMind: AlphaFold reveals the structure of the protein universe

DeepMind: AlphaFold reveals the structure of the protein universe. “In partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI), we’re now releasing predicted structures for nearly all catalogued proteins known to science, which will expand the AlphaFold DB by over 200x – from nearly 1 million structures to over 200 million structures – with the potential to dramatically increase our understanding of biology.”

Syracuse University: The Art of Science: Students Participate in University’s First-Ever Bio-Art Class

Syracuse University: The Art of Science: Students Participate in University’s First-Ever Bio-Art Class. “Bio-art first came to the University in 2018, when Rossa and Hehnly established the Bio-Art Mixer in collaboration with the Canary Lab in VPA’s Department of Film and Media Arts. The open forum includes faculty, graduate students and members of the general public from different scientific and artistic backgrounds who share innovative research, foster ideas for new art and research projects, and view new science-inspired artworks from leading bio-artists from around the world.”

Nature: AnimalTraits – a curated animal trait database for body mass, metabolic rate and brain size

Nature: AnimalTraits – a curated animal trait database for body mass, metabolic rate and brain size. “Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera.”

Harvard Medical School: Data Deep Dive

Harvard Medical School: Data Deep Dive . “Minerva, available online to anyone, is named after the Roman goddess of wisdom. It allows users to access in-depth maps of tissue samples gathered during research, ranging from cancerous tumors to heart muscle in distress. On each map, users can zoom and pan, overlay features such as immune cells, and explore noteworthy areas. The maps also incorporate the expertise of scientists and medical doctors who can create narratives to guide users through the samples. “

University of Michigan: Body measurements for all 11,000 bird species released in open-access database

University of Michigan: Body measurements for all 11,000 bird species released in open-access database. “For each individual bird, we measured nine ‘morphological’ traits, related to physical aspects of their bodies: four beak measurements, three wing measurements, tail length, and tarsus length (lower leg). AVONET also includes body mass and hand-wing index, which is calculated from three wing measurements to give an estimate of flight efficiency, and so the ability of a species to disperse or move across the landscape. The final version contains measurements from 90,020 individual birds at an average of around nine individuals per species.”

Phys .org: Visually stunning tree of all known life unveiled online

Phys .org: Visually stunning tree of all known life unveiled online. “The OneZoom explorer… maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.”

New York Times: The Coronavirus Attacks Fat Tissue, Scientists Find

New York Times: The Coronavirus Attacks Fat Tissue, Scientists Find. “From the start of the pandemic, the coronavirus seemed to target people carrying extra pounds. Patients who were overweight or obese were more likely to develop severe Covid-19 and more likely to die. Though these patients often have health conditions like diabetes that compound their risk, scientists have become increasingly convinced that their vulnerability has something to do with obesity itself.”

Arizona State University: ASU Biocollections grant fuels digitization of millions of specimen records

Arizona State University: ASU Biocollections grant fuels digitization of millions of specimen records. “Arizona State University knows a thing or two about natural history. The ASU Natural History Collections are composed of nine different collections — ranking among the largest collections of Sonoran desert biota in the world. Thousands of specimens are tucked into trays, drawers and cupboards. And, while there will always be a need for accumulating and storing natural history specimens, digital access represents an increasingly urgent need in the world of research, education and innovation.”

Cornell Chronicle: New cell database paints fuller picture of muscle repair

Cornell Chronicle: New cell database paints fuller picture of muscle repair. “When a muscle becomes injured, it repairs itself using a flurry of cellular activity, with stem cells splitting and differentiating into many types of specialized cells, each playing an important role in the healing process. Biologists have struggled to study rare and transient muscle cells involved in the process, but Cornell engineers have lifted the curtain on these elusive dynamics with the launch of scMuscle, one of the largest single-cell databases of its kind.”

Phys .org: New database of 660,000 assembled bacterial genomes sheds light on the evolution of bacteria

Phys .org: New database of 660,000 assembled bacterial genomes sheds light on the evolution of bacteria. “In a new study, from the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI), researchers standardized all bacterial genome data held in the European Nucleotide Archive (ENA) before 2019, creating a searchable and accessible database of genomic assemblies. In the research, published on 9 November 2021 in PLOS Biology, researchers reviewed all of the bacterial data available as of November 2018 and assembled it into over 660,000 genomes.”

Asahi Shimbun: Social media a boon to finding new animal, plant species

Asahi Shimbun: Social media a boon to finding new animal, plant species. “Satoshi Shimano, a professor of biological taxonomy at Tokyo’s Hosei University, announced the discovery of a new mite species, Choshi hamabe dani, in March. As its scientific name, Ameronothrus twitter, suggests, the arachnid’s existence might not have come to light had it not been for a photo that an amateur photographer posted on Twitter in May 2019. Takamasa Nemoto, a company employee, often snaps photos of mites. But he was unfamiliar with ones he found near a port while out on a fishing trip with his family. His tweet, with the photo of a mite cluster, found its way to Shimano by chance.”

University of Maine: Researchers assess whether open educational resources improved biology instruction

University of Maine: Researchers assess whether open educational resources improved biology instruction. “The National Science Foundation awarded a nearly $2 million collaborative research grant for principal investigators from the University of Nebraska-Lincoln, Cornell University and UMaine to assess the effectiveness of open educational resources in teaching core biology concepts, facilitating student-centered learning and supporting diversity, equity and inclusion. Funding for the five-year project derived from the NSF’s Vision and Change Program.”

The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations (bioRxiv)

bioRxiv: The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations. “Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically-maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static datasets and integration of dynamically-updated databases.”

The Guardian: AI firm DeepMind puts database of the building blocks of life online

The Guardian: AI firm DeepMind puts database of the building blocks of life online. “Last year the artificial intelligence group DeepMind cracked a mystery that has flummoxed scientists for decades: stripping bare the structure of proteins, the building blocks of life. Now, having amassed a database of nearly all human protein structures, the company is making the resource available online free for researchers to use.”