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July 16, 2020

Engagement Webinar: What Can You Do With An Approved CSP Functional Genomics Call Proposal?

Group shot at the IGB, Dec 2019During the JGI Engagement: Accessing Functional Genomics Capabilities Webinar, researchers described how they had availed of JGI’s resources and capabilities through the Community Science Program’s Functional Genomics call for proposals. [Read More]

June 30, 2020

Ray Turner Completes Last Tour of Lab Duty at JGI

For the last 15 years, Ray Turner has been one constant for the Joint Genome Institute. His vigilant stewardship as JGI’s Operations Deputy has come to a close. [Read More]

April 29, 2020

JGI Earth Month: The Unusual Metabolism That Helps Plants Withstand Drought

Karolina Heyduk conducting research in growth chamber in both night and daylight conditions. The following info. is provided by Heyduk 1) I cut leaf samples and use them for RNA analysis. This gives us an idea of what genes are expressed in that tissue at the time I harvested them. 2) I take gas measurements because it tells us when the plant is conducting gas exchange – CO2 into the leaf, water vapour out. For C3 plants, this happens during the day. For CAM plants, gas exchange happens at night. Gas exchange patterns are a way for us to assess whether a plant is C3 or CAM. 3) Green light is needed at night because plant stomata (pores on the leaves that allow for gases to enter and exit) respond to blue and red light. Plants are green to us because they reflect green light back while absorbing red and blue! To avoid stomatal opening, we keep to green lights. A key trait of CAM photosynthesis is that plants take up carbon at night and fix it then, as opposed to doing it during the daytime, like C3 plants. Because CAM is active at night, we have to check for gas exchange and gene expression throughout the day/night cycle to capture both C3 and CAM traits.For JGI Earth Month, Karolina Heyduk, an evolutionary plant biologist at the University of Hawai’i at Mānoa shares how crassulacean acid metabolism, or CAM, helps plants take the heat. [Read More]

April 28, 2020

JGI Earth Month: Wetlands Work in #TenHundredWords

JGI Earth Month graphic orange 1000For JGI Earth Month, graduate student Mo Kaze took on the challenge of explaining her research using the ten hundred most commonly used words in the English language. Her work focuses anthropogenic impacts on wetland microbiome composition and metabolism. The #TenHundredWords Challenge was inspired by Randall Munroe’s xkcd comic “Up Goer Five” and his subsequent book Thing Explainer. [Read More]

April 22, 2020

JGI Earth Month: Lessons in Nature’s Resilience

The oil slick in the Gulf of Mexico from the Deepwater Horizon oil spill as seen on April 29, 2010. (NASA Earth Observatory image created by Jesse Allen, using data provided courtesy of the University of Wisconsin’s Space Science and Engineering Center MODIS Direct Broadcast system)As part of JGI Earth Month, revisiting lessons in Nature’s resilience resulting from studies by Berkeley Lab researchers, including JGI scientists, to understand how the microbial communities in the waters responded to the influx of oil. [Read More]

April 21, 2020

JGI Earth Month: Healthy Streams, Nutritious Microbes?

Grad student Brian Wolff spearheaded samples the Arkansas River.As part of JGI Earth Month, hear from Ed Hall, an ecologist at Colorado State University in Fort Collins. He’s investigating how microbes in the Arkansas River might be influencing the river’s health. [Read More]

April 14, 2020

JGI Earth Month: Kjiersten Fagnan Reflects on Shelter-in-Place Effects

Fagnan JGI Earth MonthIn this brief captioned video, JGI Chief Informatics Officer Kjiersten Fagnan reflects on the personal and environmental impacts of the shelter-in-place order as part of JGI Earth Month. [Read More]

February 21, 2020

Tanja Woyke Elected to American Academy of Microbiology

Tanja Woyke, PhD Microbial Genomics Program Lead, DOE Joint Genome InstituteJGI’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. [Read More]

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? [Read More]

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… [Read More]
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