Dorsk Alexander

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Dorsk
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Alexander
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  • Preprint
    Needles in the blue sea : sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome
    ( 2015-03-27) Saito, Mak A. ; Dorsk, Alexander ; Post, Anton F. ; McIlvin, Matthew R. ; Rappe, Michael S. ; DiTullio, Giacomo R. ; Moran, Dawn M.
    Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8+1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13+15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ~4x107, 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.
  • Presentation
    Dataset to DOI using SWORD [poster]
    ( 2012-03-12) Devenish, Ann ; Chandler, Cynthia L. ; Dorsk, Alexander ; Raymond, Lisa ; Work, Tobias
    This poster describes the tools and processes by which datasets are deposited in an institutional repository (IR) and digital object identifiers (DOI) are acquired. The Marine Biological Laboratory/Woods Hole Oceanographic Institution (MBLWHOI) Library and the Biological and Chemical Oceanography Data Management Office (BCO-DMO) have developed tools and processes to automate the ingestion of datasets and metadata from BCO-DMO for deposit into the Woods Hole Open Access Server (WHOAS) institutional repository. The system also incorporates functionality for BCO-DMO to request a DOI from the Library and streamlines the process by which XML files are generated for DOI deposit with CrossRef, a DOI registration agency. This partnership allows the Library to work with a trusted data repository to ensure high quality data while the data repository utilizes library services and is assured of a permanent archive of the copy of the data extracted from the repository database. This research is being conducted by a team of librarians, data managers and scientists that are collaborating with representatives from the Scientific Committee on Oceanic Research (SCOR) and the International Oceanographic Data and Information Exchange (IODE) of the Intergovernmental Oceanographic Commission (IOC).