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https://www.readbyqxmd.com/read/27918579/a-graph-centric-approach-for-metagenome-guided-peptide-and-protein-identification-in-metaproteomics
#1
Haixu Tang, Sujun Li, Yuzhen Ye
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27901108/survey-of-the-green-picoalga-bathycoccus-genomes-in-the-global-ocean
#2
Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#3
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895636/genomic-and-transcriptomic-evidence-for-carbohydrate-consumption-among-microorganisms-in-a-cold-seep-brine-pool
#4
Weipeng Zhang, Wei Ding, Bo Yang, Renmao Tian, Shuo Gu, Haiwei Luo, Pei-Yuan Qian
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27886631/metagenomics-analysis-reveals-a-new-metallothionein-family-sequence-and-metal-binding-features-of-new-environmental-cysteine-rich-proteins
#5
Antoine Ziller, Rajiv Kumar Yadav, Mercè Capdevila, Mondem Sudhakara Reddy, Laurent Vallon, Roland Marmeisse, Silvia Atrian, Òscar Palacios, Laurence Fraissinet-Tachet
Metallothioneins are cysteine-rich proteins, which function as (i) metal carriers in basal cell metabolism and (ii) protective metal chelators in conditions of metal excess. Metallothioneins have been characterized from different eukaryotic model and cultivable species. Presently, they are categorized in 15 families but evolutionary relationships between these metallothionein families remain unresolved. Several cysteine-rich protein encoding genes that conferred Cd-tolerance in Cd-sensitive yeast mutants have previously been isolated from soil eukaryotic metatranscriptomes...
November 12, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27876823/alignment-free-transcriptomic-and-metatranscriptomic-comparison-using-sequencing-signatures-with-variable-length-markov-chains
#6
Weinan Liao, Jie Ren, Kun Wang, Shun Wang, Feng Zeng, Ying Wang, Fengzhu Sun
The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC)...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872277/an-oligotrophic-deep-subsurface-community-dependent-on-syntrophy-is-dominated-by-sulfur-driven-autotrophic-denitrifiers
#7
Maggie C Y Lau, Thomas L Kieft, Olukayode Kuloyo, Borja Linage-Alvarez, Esta van Heerden, Melody R Lindsay, Cara Magnabosco, Wei Wang, Jessica B Wiggins, Ling Guo, David H Perlman, Saw Kyin, Henry H Shwe, Rachel L Harris, Youmi Oh, Min Joo Yi, Roland Purtschert, Greg F Slater, Shuhei Ono, Siwen Wei, Long Li, Barbara Sherwood Lollar, Tullis C Onstott
Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2 Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs...
November 21, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27857707/bacterial-human-virulence-genes-across-diverse-habitats-as-assessed-by-in-silico-analysis-of-environmental-metagenomes
#8
Ditte A Søborg, Niels B Hendriksen, Mogens Kilian, Jan H Christensen, Niels Kroer
The occurrence and distribution of clinically relevant bacterial virulence genes across natural (non-human) environments is not well understood. We aimed to investigate the occurrence of homologs to bacterial human virulence genes in a variety of ecological niches to better understand the role of natural environments in the evolution of bacterial virulence. Twenty four bacterial virulence genes were analyzed in 46 diverse environmental metagenomic datasets, representing various soils, seawater, freshwater, marine sediments, hot springs, the deep-sea, hypersaline mats, microbialites, gutless worms and glacial ice...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27848951/genetic-deletion-of-the-bacterial-sensor-nod2-improves-murine-crohn-s-disease-like-ileitis-independent-of-functional-dysbiosis
#9
D Corridoni, A Rodriguez-Palacios, G Di Stefano, L Di Martino, D A Antonopoulos, E B Chang, K O Arseneau, T T Pizarro, F Cominelli
Although genetic polymorphisms in NOD2 (nucleotide-binding oligomerization domain-containing 2) have been associated with the pathogenesis of Crohn's disease (CD), little is known regarding the role of wild-type (WT) NOD2 in the gut. To date, most murine studies addressing the role of WT Nod2 have been conducted using healthy (ileitis/colitis-free) mouse strains. Here, we evaluated the effects of Nod2 deletion in a murine model of spontaneous ileitis, i.e., the SAMP1Yit/Fc (SAMP) strain, which closely resembles CD...
November 16, 2016: Mucosal Immunology
https://www.readbyqxmd.com/read/27822530/moleculo-long-read-sequencing-facilitates-assembly-and-genomic-binning-from-complex-soil-metagenomes
#10
Richard Allen White, Eric M Bottos, Taniya Roy Chowdhury, Jeremy D Zucker, Colin J Brislawn, Carrie D Nicora, Sarah J Fansler, Kurt R Glaesemann, Kevin Glass, Janet K Jansson
Soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87...
May 2016: MSystems
https://www.readbyqxmd.com/read/27818655/prokaryotic-responses-to-ammonium-and-organic-carbon-reveal-alternative-co2-fixation-pathways-and-importance-of-alkaline-phosphatase-in-the-mesopelagic-north-atlantic
#11
Federico Baltar, Daniel Lundin, Joakim Palovaara, Itziar Lekunberri, Thomas Reinthaler, Gerhard J Herndl, Jarone Pinhassi
To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27803690/transparent-dna-rna-co-extraction-workflow-protocol-suitable-for-inhibitor-rich-environmental-samples-that-focuses-on-complete-dna-removal-for-transcriptomic-analyses
#12
Natalie Y N Lim, Constance A Roco, Åsa Frostegård
Adequate comparisons of DNA and cDNA libraries from complex environments require methods for co-extraction of DNA and RNA due to the inherent heterogeneity of such samples, or risk bias caused by variations in lysis and extraction efficiencies. Still, there are few methods and kits allowing simultaneous extraction of DNA and RNA from the same sample, and the existing ones generally require optimization. The proprietary nature of kit components, however, makes modifications of individual steps in the manufacturer's recommended procedure difficult...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27796326/shedding-light-on-cell-compartmentation-in-the-candidate-phylum-poribacteria-by-high-resolution-visualisation-and-transcriptional-profiling
#13
Martin T Jahn, Sebastian M Markert, Taewoo Ryu, Timothy Ravasi, Christian Stigloher, Ute Hentschel, Lucas Moitinho-Silva
Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal...
October 31, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27794040/genomes-online-database-gold-v-6-data-updates-and-feature-enhancements
#14
Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D Thomas, Rida Ali, Kaushal Sharma, Nikos C Kyrpides, T B K Reddy
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects...
October 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27793585/methodologies-for-probing-the-metatranscriptome-of-grassland-soil
#15
Aaron Garoutte, Erick Cardenas, James Tiedje, Adina Howe
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes...
October 25, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27791006/cryptophyte-farming-by-symbiotic-ciliate-host-detected-in-situ
#16
Dajun Qiu, Liangmin Huang, Senjie Lin
Protist-alga symbiosis is widespread in the ocean, but its characteristics and function in situ remain largely unexplored. Here we report the symbiosis of the ciliate Mesodinium rubrum with cryptophyte cells during a red-tide bloom in Long Island Sound. In contrast to the current notion that Mesodinium retains cryptophyte chloroplasts or organelles, our multiapproach analyses reveal that in this bloom the endosymbiotic Teleaulax amphioxeia cells were intact and expressing genes of membrane transporters, nucleus-to-cytoplasm RNA transporters, and all major metabolic pathways...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790194/a-sample-to-sequence-protocol-for-genus-targeted-transcriptomic-profiling-application-to-marine-synechococcus
#17
Frances D Pitt, Andrew Millard, Martin Ostrowski, Suat Dervish, Sophie Mazard, Ian T Paulsen, Mikhail V Zubkov, David J Scanlan
Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27760854/sequence-based-classification-and-identification-of-fungi
#18
David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
https://www.readbyqxmd.com/read/27760570/rumen-metagenome-and-metatranscriptome-analyses-of-low-methane-yield-sheep-reveals-a-sharpea-enriched-microbiome-characterised-by-lactic-acid-formation-and-utilisation
#19
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
https://www.readbyqxmd.com/read/27759035/mdrna-seq-analysis-of-marine-microbial-communities-from-the-northern-red-sea
#20
Shengwei Hou, Ulrike Pfreundt, Dan Miller, Ilana Berman-Frank, Wolfgang R Hess
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5' ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities...
October 19, 2016: Scientific Reports
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