Chemistry World: Open access Atlas maps out microbial natural products. “A new open access database of microbial natural products has launched online. The Natural Products Atlas (NPAtlas) is free to use and contains more than 24,000 chemical structures. The tool is based on Fair data principles, making the information within it easier to search and use in secondary analysis.” I don’t put anything in RB unless I can get a basic understanding of what the resource is about. (I have skipped including items because I just didn’t get the underlying discipline or presentation.) In this case I had no idea what microbial natural products are, but I now understand better thanks to PubMed.
EurekAlert: Mapping the ocean’s unseen heroes, one microbe at a time. “Invisible to the naked eye, the health and movement of marine microbes that drift as part of the plankton is difficult to picture even for scientists – let alone everyday citizens. This challenge, to visualise the range of conditions that drifting marine microbes encounter, brought a group of expert scientists and visual designers together on a path to create the online citizen science project Adrift. Adrift is a portal that connects the public with the lives of microscopic marine microbes as they are propelled around the globe by ocean currents, with temperature and nutrient availability changing along the way.”
EurekAlert: The web meets genomics: a DNA search engine for microbes . “The search engine, called Bitsliced Genomic Signature Index (BIGSI), fulfils a similar purpose to internet search engines, such as Google. The amount of sequenced microbial DNA is doubling every two years. Until now, there was no practical way to search this data. This type of search could prove extremely useful for understanding disease. Take, for example, an outbreak of food poisoning, where the cause is a Salmonella strain containing a drug-resistance plasmid (a ‘hitchhiking’ DNA element that can spread drug resistance across different bacterial species). For the first time, BIGSI allows researchers to easily spot if and when the plasmid has been seen before.”
Ars Technica: What’s eating this 400-year-old painting? A whole ecosystem of microbes. “If you could zoom in for a microscopic look at an oil painting on canvas, you would see many thin, overlapping layers of pigments—powdered bits of insects, plants, or minerals—held together with oils or glue made from animal collagens. Many of those pigments and binding materials are surprisingly edible to bacteria and fungi. Each patch of color and each layer of paint and varnish in an oil painting offers a different microbial habitat. So when you look at a painting, you’re not just looking at a work of art; you’re looking at a whole ecosystem.”
Scientific American: Culture Shock: Precious Microbe Collections Languish in Threatened Bio-Libraries. “Freeze-dried and locked away in liquid nitrogen–filled vaults around the world are hundreds of thousands of microbial cultures. In the U.S. these living libraries include 91,000 bacterial and fungal strains in Peoria, Ill., as well as 13,000 fungal strains in Ithaca, N.Y., and 7,500 wild yeasts at the University of California, Davis. Researchers have used strains from such publicly accessible culture collections to develop penicillin as well as the CRISPR gene-editing systems and the PCR (polymerase chain reaction) DNA-amplifying technique. But as government priorities apparently change, and as the federal money that historically created and preserved many of these biological resource repositories in the U.S. dries up, their infrastructure is at risk of deteriorating. “
Now available: a database of DNA viruses and retroviruses. “There are more microbes in, on, and around the planet than there are stars in the Milky Way. Microbes affect food production; air quality; natural breakdown of plants, trees and biomass; soil quality for agriculture; and much more. To work with these microbes, scientists need to learn more about how microbes and viruses interact. Viruses influence microbes’ abilities to work. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute built the largest publicly available database for viruses. This single effort increases the number of known viral genes by a factor of 16. Further, in a series of four articles published in Nucleic Acids Research, DOE Joint Genome Institute researchers report on the latest updates to several other publicly accessible databases and computational tools. These databases and tools will benefit the global community of microbial researchers.”