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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List

Grants

Courtesy of Wiebke Mohr, close-up of a combustion furnace for automated protein isotope ratio analysis

Harvard University, Department of Earth and Planetary Sciences

Fingerprinting the stable isotope patterns of microbial proteins

In support of developing new analytical methods to examine, at an unprecedented level of detail, the natural stable isotope patterns of microbial proteins. When linked to bacterial, archaeal and microeukaryote diversity information, these patterns will illuminate microbial metabolisms and functions unable to be detected previously.

Title: Fingerprinting the stable isotope patterns of microbial proteins
Date Awarded: Oct 2011
Amount: $716,186
Term: 42 months
Grant ID: GBMF3131
Funding Area: Science, Marine Microbiology Initiative
 

Abstract:

Microbial communities in the ocean are complex, harboring thousands of species.  Some of these species are producers, while other species are consumers.  Like a prairie or savannah ecosystem, they are believed to interact with complex ecology, exchanging resources and nutrients in a network of consumption and recycling. Unlike in macroecology, however, it is difficult to measure how networks of single-celled species interact, because they generally cannot be observed or measured as individuals.  The goal of this project is to develop an automated analytical approach to track the flow of carbon and nutrients through marine microbial communites, thereby understanding their modes of interaction.

Although DNA sequencing has accelerated the discovery of species, there has been slower progress in linking taxonomic diversity to the functions, resource utilization, and ecological niches occupied by these many species.  This work will develop a novel application of isotope geochemistry and will apply it in the field of biochemical oceanography as a first step toward tackling these challenges.  The goal of the project is to combine natural isotope ratio data with proteomics.  Different metabolic processes yield different ratios of the stable isotopes of carbon and nitrogen; and by measuring these ratios on specific proteins with simultaneous sequencing, these natural isotope signals can attribute biogeochemical processes (functions) to specific microbes (taxonomic and genetic information).  The approach will be called P-SIF (protein stable isotope fingerprinting). The project is focused on the twin goals of achieving high throughput and automation. The first step is a multidimensional separation of whole proteins.  We use a Spooling Wire Microcombustion (SWiM) irMS system and micro-autosampler to measure isotope ratios of the resulting separated aliquots.  Subsequently, the parent proteins and their phylogenetic origins are determined on peptide digests of the remainder of each aliquot. The specific project first will aim to analyze pure cultures and a model system.  We then will attempt to analyze a natural marine sample.

 

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