Berkeley Lab

Predicting metabolic properties using dynamic substrate preference

Exometabolomic profiling was used to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonads and one Bacillus FRC isolates. ENIGMA researchers at Lawrence Berkeley National Lab examined if the first substrates depleted resulted in maximal growth rate, or related to growth medium or biomass composition and found […]

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Digital Droplet Multiple Displacement Amplification

  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 […]

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Stable protein interactome of the model sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough

First demonstration of a highly accurate, genome-wide method for detecting stable protein-protein interactions, without the requirement for genetic manipulation of the organism (prior tagless methodologies have false discovery rates of >85%). Combined with our study of protein complexes published in February 2016, which was based on affinity purification coupled with mass spectroscopy (AP-MS), this experiment […]

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Benchmark properties for highly accurate bacterial protein interactions

SUMMARY Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published […]

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Deutschbauer, Adam

Deputy Director, Biotechnology Development
amdeutschbauer@lbl.gov
(510) 643-5683

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Northen, Trent

Director, Biotechnology Development
trnorthen@lbl.gov
(510) 486-5240

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Auer, Manfred

Principal Investigator
mauer@lbl.gov
(510) 486-7702

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Butland, Gareth

Principal Investigator
gpbutland@lbl.gov
(510) 486-6905

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Siuzdak, Gary

Principal Investigator
siuzdak@scripps.edu
(858) 784-9415

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Walian, Peter

Principal Investigator
pjwalian@lbl.gov
(510) 486-7469

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