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Full-Text Articles in Life Sciences
An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble
An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble
OES Faculty Publications
In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …
Baseline Microbial Characterizations Of An Imperiled Aquatic Diversity Hotspot: Ash Meadows National Wildlife Refuge, Jessica Newburn, Jim Bruckner, Jenny C. Fisher, Duane P. Moser
Baseline Microbial Characterizations Of An Imperiled Aquatic Diversity Hotspot: Ash Meadows National Wildlife Refuge, Jessica Newburn, Jim Bruckner, Jenny C. Fisher, Duane P. Moser
Undergraduate Research Opportunities Program (UROP)
Located in the discharge zone of the Death Valley Flow System, Ash Meadows National Wildlife Refuge is a spring-fed desert oasis and biodiversity hotspot about 90 miles northwest of Las Vegas. These critical wetlands are potentially threatened by groundwater pumping, exotic species invasions, and climate change. Although a major component of the lower food web, very little is known about the microbial makeup of this ecosystem. As a first step towards understanding the microbial and biogeochemical aspects of this system, a detailed molecular-based characterization of microbial communities, baseline chemistry, and physical characteristics of various springs of Ash Meadows will be …
Changes In The Sea-Ice Brine Community During The Spring-Summer Transition, Mcmurdo Sound, Antarctica .2. Phagotrophic Protists, Diane K. Stoecker, Kurt R. Buck, Mary Putt
Changes In The Sea-Ice Brine Community During The Spring-Summer Transition, Mcmurdo Sound, Antarctica .2. Phagotrophic Protists, Diane K. Stoecker, Kurt R. Buck, Mary Putt
OES Faculty Publications
The land-fast sea-ice brine contains a diverse phagotrophic protist assemblage consisting of < 5 mum heterotrophic flagellates, Cryothecomonas spp., heterotrophic dinoflagellates, and heterotrophic and mixotrophic ciliates. Fine-scale horizontal spatial variability is a feature of this assemblage; samples taken within 1 m of each other can be dominated by different heterotrophic protists. Many of the larger heterotrophic protists found in the brine are also found in the water column. The photosynthetic ciliate Mesodinium rubrum is also common. In mid to late austral spring, the heterotrophic assemblage accounts for ca 10% of the total protist biomass in the brine and is dominated by Cryothecomonas spp. This flagellate …