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To identify and study the regulation of cellulosic enzymes in a biomass degrading gut fungal isolate from horse (Piromyces sp. finn)

ABSTRACT: Here, we develop a systems-level approach leveraging powerful next generation sequencing, proteomics and phenotypic studies to rapidly obtain an integrated view of lignocellulose degradation in the earliest free living fungi RNA-seq of Piromyces grown on Glucose, Cellulose, Cellulobiose, Avicel, Filter paper, and time-course of transient glucose pulse (catabolite repression). N>=2

ORGANISM(S): Piromyces sp. Finn

SUBMITTER: Michelle OâMalley

PROVIDER: E-GEOD-64834 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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To identify and study the regulation of cellulosic enzymes in a biomass degrading gut fungal isolate from horse (Piromyces sp. finn)

Project description:Here, we develop a systems-level approach leveraging powerful next generation sequencing, proteomics and phenotypic studies to rapidly obtain an integrated view of lignocellulose degradation in the earliest free living fungi

2016-02-12 | GSE64834 | GEO

Gene Expression Defines Natural Changes in Mammalian Lifespan

Project description:Mammals differ more than hundred fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life history traits, and identified the processes and pathways involved. These findings provide direct insights into how Nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages. RNA-seq gene expression profiling in normal liver, kidney and brain of 33 mammalian species.

2015-02-17 | E-GEOD-43013 | biostudies-arrayexpress

Developmental gene expression of Hymenochirus boettgeri

Project description:RNA-seq experiments to construct Hymenochirus bettgeri transcripts Collect mRNA from whole eggs/embryos/tadpoles, with poly-A enrichment method

2016-10-24 | E-GEOD-76089 | biostudies-arrayexpress

Spatial Regulation Dominates Gene Function in the Ganglia Chain

Project description:Spatial regulation analysis across multiple condition comparisons revealed distinct patterns of gene expression. We combined these transcriptome data with spatial CNS data to produce the spatio-transcripto map of the ganglia chain. The Hirudo Medicinalis set of transcripts generated here provides a resource for gene discovery and gene regulation within the nervous system. In addition, the strategy for de novo assembly of transcriptome data presented here may be helpful in other similar transcriptome studies. Examination of 3 different ganglia in 3 different leeches.

2013-12-04 | E-GEOD-45569 | biostudies-arrayexpress

Tumour-associated antigenic peptides are present in the HLA class I ligandome of cancer cell line derived extracellular vesicles.

Project description:The recent success of monoclonal antibody checkpoint inhibitor therapies that enhance the ability of CD8+ T cells to detect cancer-related antigenic peptides has refocused the need to fully understand the repertoire of peptides being presented to the immune system. Whilst the peptide ligandome presented by cell surface HLA class I molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles remains poorly defined. Here we report the HLA class I ligandome of both cell surface and extracellular vesicles from eight breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-453, HCC 1806, HCC 1395, and HCC 1954), and additionally the melanoma cell line ESTDAB-056 and the multiple myeloma line RPMI 8226. Utilising HLA class I immunoisolation and mass spectrometry we detected a total of 6574 peptides from the cell surface and 2461 peptides from the extracellular vesicles of the cell lines studied. Within the extracellular vesicle HLA class I ligandome we identified 150 peptides derived from tumour associated antigenic proteins, of which 19 peptides have been shown to elicit T cell responses in previous studies. Our data thus confirms for the first time the presence of clinically relevant tumour-associated antigenic peptides in the HLA class I ligandome present on EV.

2022-04-01 | PXD025345 | Pride

Transcription profiling by high throughput sequencing of liver from SHR/OlaIpcv and BN-Lx/Cub rats (SOLiD 4 paired-end)

Project description:Liver RNA sequencing of BN-Lx/Cub, SHR/OlaIpcv

2012-04-04 | E-MTAB-1069 | biostudies-arrayexpress

Rat_RNASeq_WBrain_BNLx_SHR

Project description:Whole brain RNA sequencing of BN-Lx/Cub, SHR/OlaIpcv and their hybrids

2012-04-04 | E-MTAB-1070 | biostudies-arrayexpress

Transcriptome analysis and molecular marker discovery in red pepper, Capsicum annuum L. TF68

Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. 1 sample TF68 accession examined

2011-09-08 | E-GEOD-29215 | biostudies-arrayexpress

Biomass-degrading glycoside hydrolases of archaeal origin.

Project description:During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.

| S-EPMC7469102 | biostudies-literature

Transcriptional responses to cold in five Pooideae species

Project description:To investigate the evolution of cold response in Pooideae, five species spanning early to later diverging lineages were sampled before and after subjecting them to a drop in temperature (17C to 6C), shorter days (12 to 8 hours of light) and less intensive light. Short-term response was sampled in the afternoon 8 hours after drop in temperature but 24 hours after the respective control sample to control for diurnal rhythm. Long-term response was sampled after 4 and 9 weeks in the morning directly after lights were turned on with a respective control sample also taken in the morning on the day before the temperature drop.

2016-12-12 | E-MTAB-5300 | biostudies-arrayexpress

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