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March 10, 2020

Genome Insider Episode 1: Role of Viruses in Releasing Greenhouse Gases? (1/2)

Logo of Genome Insider, podcast of the Joint Genome Institute

Genome Insider is available on Apple Podcasts, Google Play,
Spotify, iHeart Radio , and TuneIn Radio. Subscribe today!

The Genome Insider podcast presents research by Gary Trubl, a virologist at Lawrence Livermore National Lab. He’s using bioinformatics and isotopes to track how viruses in the thawing arctic influence the flow of soil carbon. JGI is a user facility of the Department of Energy (DOE) Office of Science and located at the Lawrence Berkeley National Laboratory in Berkeley, CA.

March 6, 2020

Natural Prodcast – Coming soon!

Natural Prodcast podcast logo

Natural Prodcast is available on Apple Podcasts, Google Play and wherever you listen. Subscribe today!
Check out a teaser of the Joint Genome Institute’s Natural Prodcast, a podcast hosted by Dan Udwary about the science and scientists of secondary metabolism.

February 27, 2020

Genome Insider – Coming soon!

Logo of Genome Insider, podcast of the Joint Genome Institute

A sneak peek of JGI’s Genome Insider podcast with this audio teaser, featuring Gary Trubl, a virologist at Lawrence Livermore National Lab. He answers the question: What sound does a peatland make?

February 21, 2020

Tanja Woyke Elected to American Academy of Microbiology

Tanja Woyke, PhD Microbial Genomics Program Lead, DOE Joint Genome Institute

JGI’s Tanja Woyke has been elected to the American Academy of Microbiology, joining 67 other new Fellows in the Class of 2020. Fellows are selected based on their records of scientific achievement and original contributions that have advanced microbiology.

February 10, 2020

Viruses Reprogram Cells into Different Virocells

How a cell behaves as virocell largely depends on the infecting virus and the genomic similarity between host and virus. Pseudoalteromonas was infected with two unrelated viruses: siphovirus PSA-HS2 and podovirus PSA-HP1. The infections transformed the same bacterial host into two very different virocells, HS2-virocell and HP1-virocell. The HS2 siphovirus genome was much more similar to the host than the genome of HP1 podovirus and had better access to recycle existing host resources. In contrast, the HP1 podovirus needed to work harder at obtaining the resources needed for infection, and reprogrammed multiple host metabolisms. HS2 virocells had a comparatively higher fitness than HP1 virocells. (Figure by Cristina Howard-Varona)

If it looks like a duck and quacks like a duck, so the adage goes, it must be a duck. But if the duck gets infected by a virus so that it no longer looks or quacks like one, is it still a duck? For a team led by researchers from The Ohio State University and the University of Michigan studying how virus infections cause significant metabolic changes in marine microbes, the answer is no. They refer to the infected microbial cells as virocells, a change in name which reflects the metabolic changes they’ve undergone.

February 4, 2020

JGI Scientists Pen Genome Watch Articles

For the May 2019 Genome Watch article by Tanja Woyke. (Credit: Philip Patenall/Springer Nature Limited)

JGI researchers are sharing their expertise in environmental genomics by writing for the column Genome Watch in Nature Reviews Microbiology. In 2018. Tanja Woyke, who leads the Microbial Program at the JGI, received a message from Andrea Du Toit, senior editor for Nature Reviews Microbiology, with an unusual opportunity: would JGI researchers consider regularly writing for the magazine’s column Genome Watch?

January 22, 2020

Here, There and Everywhere: Large and Giant Viruses Abound Globally

Art illustration capturing giant virus genomic diversity. (Zosia Rostomian/Berkeley Lab)

JGI-led team significantly expands the global diversity of large and giant viruses. While the microbes in a single drop of water could outnumber a small city’s population, the number of viruses in the same drop—the vast majority not harmful to humans could be even larger. Viruses infect bacteria, archaea and eukaryotes, and they range in…

January 21, 2020

Inspiring STEM Careers Through a Hands-on Everglades Microbiome Study

Students in the 2018 Boca Raton Community High School A-Level Advanced International Certificate of Education (AICE) Biology class collected samples from the Arthur R. Marshall Loxahatchee National Wildlife Refuge for the pilot project between the class and the JGI. (Image courtesy of Jon Benskin)

Journal publication caps JGI pilot project with fledgling Florida high school scientists. The Florida Everglades evokes images of fanboats skimming over swamps, while alligators peer through the waters and clouds of insects hover just above. Described as a “river of grass” that stretches some 580,000 square miles across southern Florida, they encompass a wide range…

December 23, 2019

Expanding Virophage Diversity

Virophage discovery pipeline. (A) MCP amino acid sequences from reference isolated genomes and published metagenomic contigs were queried against the IMG/VR database with stringent e value cutoffs. All homologous sequences detected were then clustered together to build four independent MCP profiles. (B) The resulting four MCP models were used to recruit additional homologous sequences from the entire IMG/M system. All new sequences were clustered, and models were built creating a final set of 15 unique MCP HMMs. (C) These 15 unique MCP HMMs were then used to search two different databases for homologous sequences: the IMG/M system and a custom assembled human gut database containing 3771 samples from NCBI’s Sequence Read Archive (SRA). (D) The resulting set of 28,294 non-redundant (NR) sequences with stringent e value cutoffs was filtered by size and e by the presence of the four core virophage genes (high-quality genomes; HQ virophages). Finally, completeness of novel metagenomic virophage genomes wsa predicted based on circularity or presence of inverted terminal repeats (ITR). (Figure from Paez-Espino et al. Microbiome (2019) 7:157 https://doi.org/10.1186/s40168-019-0768-5)

Virophages are small viruses with double-stranded DNA genomes that co-infect eukaryotic cells along with giant viruses. Almost all known virophage genomes share only four genes in common: major and minor capsid proteins (MCP and mCP, respectively), ATPase involved in DNA packaging, and PRO, a cysteine protease involved in capsid maturation. Recently reported in Microbiome, researchers…

December 23, 2019

Honey Bee Gut Microbiota Divvy Up Dinner

Honey bees metabolize pollen with the help of their gut microbiota. (Photo by Jason Leung on Unsplash )

Scientists have wondered exactly how the honey bee gut microbial community carries out its helpful metabolism: who’s responsible for what biochemical processes?

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