Lab Microbiology Team Archives

DuBSEQ functional characterization Nature Communications

January 18, 2019 By Astrid Terry

ENIGMA researchers release DuBSEQ, a tool for broader use in microbial functional characterization and which allows for high throughput manipulation of specific strain libraries in Nature Communications. A multi-disciplinary team of bench scientists and computational scientists collaborated to generate the large data set and analyses that confirm known functional genes and identify interesting genes of […]

Robustness of a model microbial community emerges from population structure among single cells of a clonal population

May 1, 2017 By Astrid Terry

Robustness of a model microbial community emerges from population structure among single cells of a clonal population Thompson, A.W, Turkarslan S., Arens, C.E, López García de Lomana, A., Raman, A., Stahl, D.A., Baliga, N.S. Environmental Microbiology, 10.1111/1462-2920.13764

ENIGMA Researchers Uncover Factors in Microbial Community Collapse

April 7, 2017 By Astrid Terry

Serdar Turkarslan, a Senior Research Scientist at the Institute for Systems Biology in Seattle, Washington; along with a team of researchers has developed a framework to quantify microbial community resilience in the face of environmental changes. This framework will be invaluable for observing the behavior of microbial communities under simulations of current and projected environmental conditions. Their […]

Metabolizing Data in the Cloud

January 20, 2017 By Astrid Terry

ENIGMA researchers at Scripps Research Institute have developed tools with available data to enable microbial and environmental research. ENIGMA’s XCMS Online systems biology data processing and the METLIN database represent a successful model of how community oriented cloud-computing can be implemented on a global scale. This free, cloud-based platform provides users with processing tools, data streaming, […]

Rapid Detection of Microbial Cell Abundance in Aquatic Systems

November 15, 2016 By Astrid Terry

ENIGMA post doctoral fellow developed the application of ACEK-enhanced capacitive sensing technology as a rapid screening tool for the detection and quantification of microbial abundance in aquatic environments, such as groundwater wells at our Oak Ridge field site. As a proof of principle, she applied the tool to samples from ORNL and the Great Australian Bight. […]

Digital Droplet Multiple Displacement Amplification

May 31, 2016 By Astrid Terry

The ddMDA technique enabled significantly lower bias and non-specific amplification than conventional MDA thus achieving more uniform coverage of amplification over the entire genome This technique can be a powerful tool for genomic studies where DNA samples are limited such as single cells, microaggregates, and uncultured microbes from many different environments Digital Droplet Multiple […]

Nitrite Reduction Assay for Whole Pseudomonas Cells

May 20, 2016 By Astrid Terry

ENIGMA researchers at University of Georgia developed and published a rapid high-throughput assay for whole cell nitrite reductase activity. Such activity assays will be key for future ENIGMA endeavors to relate biological activities of individual microorganisms and their communities to the environment. A rapid high-throughput assay was constructed to measure whole cell nitrite reductase activity. […]

Post Doc Lauren Lui profiled by Berkeley Lab for her Public Service and contribution to Women in Science

March 15, 2016 By Astrid Terry

During March- Women’s History Month, Berkeley Lab recognizes and celebrates the diverse and historic accomplishments of women by honoring those who have shaped America’s history and its future through their public service and government leadership. http://diversity.lbl.gov/2016/03/14/berkeley-lab-celebrates-women-in-science-and-public-service/ Lauren Lui, an ENIGMA post doctoral fellow in Adam Arkin’s Lab, was one of three women profiled by the […]

Are free-living bacteria optimized by natural selection?

December 15, 2015 By Astrid Terry

Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level […]

David Stahl selected as EMSL Chief Scientist

August 21, 2015 By Astrid Terry

David Stahl, an environmental microbiologist at the University of Washington, has been selected to serve as Chief Scientist for the EMSL user program. David will fill this position as a dual appointment and maintain his teaching and research at the UW. As Chief Scientist, he will lead efforts to build user communities in EMSL’s science […]

Lara Rajeev Stars in video demonstrating DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems

July 21, 2014 By Astrid Terry

Rajeev, L., E. G. Luning and A. Mukhopadhyay (2014). DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. Journal of Visualized Experiments (89). Epub 2014/08/01. doi:3791/51715. PMID:25079303 http://www.jove.com/video/51715/dna-affinity-purified-chip-dap-chip-method-to-determine-gene-targets#.VR3XCenZIek.google_plusone_share In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of […]