Project description:Analysis of bacterial fraction collected on GF/F filters post pre-filtration on 1um filter. 15L were filtered from Bering Strait (BSt) surface water and Chukchi Sea (station 2) bottom waters.
Project description:A genetic engineering strategy for editing near-infrared-II fluorophores. The labeled albumin proteins were digested using suspension trapping (STrap) approach with in-house packed glass fiber filters. The LC-MS/MS analysis was performed on a nanoLC-Q Exactive MS system. The protein identification was performed using Proteome Discoverer (version 2.3) and MaxQuant (version 1.6.3.4).
Project description:<p>Findings from recent studies suggest that the community of microbes residing in the human body is important in disease etiology; however, it remains unclear whether personal factors modulate human microbial composition. Studies based on animal models indicate that differences in composition might be attributed to sex-mediated effects. We analyzed the relationship of sex, adiposity, and dietary fiber intake with gut microbial composition using fecal samples from human subjects. We explored the associations of these factors with metrics of community composition and specific taxon abundances. We found that men and women had significantly different microbial community composition and that women had reduced abundance of a major phylum. Adiposity was associated with gut microbiome composition and specifically in women but not in men. Fiber from fruits and vegetables and fiber from beans were each associated with increased abundance of specific bacterial taxa. These findings provide initial indications that sex, adiposity, and dietary fiber might play important roles in influencing the human gut microbiome. Better understanding of these factors may have significant implications for gastrointestinal health and disease prevention.</p>
Project description:This dataset consists of 20 metaproteomic analyses of the Western Atlantic Ocean aboard the R/V Knorr KN210-04 DeepDOM expedition in 2013. Samples were collected by McLane pumps on GFF or GF75 filters, split, and frozen until analyses. Expedition metadata and co-sampled datasets are available at: https://www.bco-dmo.org/deployment/59057
Project description:Skeletal muscle fiber composition and muscle energetics are not static and change in muscle disease. This study was performed to determine if a mitochondrial myopathy is associated with adjustments in skelatal fiber type composition. These effects of drug induced mitochondrial dysfunction on skeletal muscle fiber type composition were analyzed in an animal model.
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition. Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.
Project description:We examined phytotoxic potential of diploid potato hybrids from 15-1 population. Individuals were bulked in bulks C and D. Both bulks characterized low total glycoalkaloids content and differ phytotoxic potential. Water extract prepared from leaves of individuals of bulk C inhibited growth of test plant - mustard in 40%, while in bulk D no inhibition was observed. To evaluate cause of expression of phytotoxic potential in bulk C, we examined glycoalklaoids composition in leaf water extract (mass spectrometry), compared gene (deep RNA sequencing - BGISEQ) and protein expression (nano-LC-MS-MS/MS) profiles between the bulks. Bulks differed in glycoalkaloids composition, bulk C contained alpha-solasonine which wasn't detected in bulk D. We concluded, alpha-solasonine may act together with alpha-solamargine and increases phytotoxic potential of leave extract of bulk C. Comparison of gene expression profiles indicating on contribution of genes, not directly involved in glycoalkaloids biosynthesis to express phytotoxic potential of C bulk. We have found 3 proteins characteristic for C bulk and 2 proteins characteristic for D bulk. We found one protein threonine dehydratase biosynthetic, which is more abundant in D bulk and his abundance corresponds with gene transcripts found in RNA-seq experiment.
Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.