Ontology highlight
ABSTRACT:
PROVIDER: PRJNA523859 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8627510_1.fastq.gz | Fastqsanger.gz | |||
| SRR8627510_2.fastq.gz | Fastqsanger.gz | |||
| SRR8627520_1.fastq.gz | Fastqsanger.gz | |||
| SRR8627520_2.fastq.gz | Fastqsanger.gz | |||
| SRR8627511_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
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Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater biological and metabolic contributions to rumen function remain largely undescribed. Here, we have leveraged (meta)genome-centric metaproteome datasets from rumen fluid samples originating from both cows and goats fed contrasting diets, to detail the specific metabolic niches that E. caudatum occupies in the context of its bacterial and archaeal co-habitants. Initial proteome estimations via total protein counts and label free quantification highlight that E. caudatum populations comprise an extensive fraction of the total rumen metaproteome. Our analysis also suggested increased microbial predation and volatile fatty acid metabolism by E. caudatum to occur in high methane emitting animals, although with no apparent direct metabolic link to methanogenesis. Despite E. caudatum having a well-established reputation of digesting starch, it was unexpectedly less active in low methane emitting animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation. Collectively, our results illuminate the substantial metabolic influence under-explored eukaryotic populations have in the rumen, with greater implications towards both digestion and methane metabolism.
2025-11-13 | PXD034779 | Pride
Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater biological and metabolic contributions to rumen function remain largely undescribed. Here, we have leveraged (meta)genome-centric metaproteome datasets from rumen fluid samples originating from both cows and goats fed contrasting diets, to detail the specific metabolic niches that E. caudatum occupies in the context of its bacterial and archaeal co-habitants. Initial proteome estimations via total protein counts and label free quantification highlight that E. caudatum populations comprise an extensive fraction of the total rumen metaproteome. Our analysis also suggested increased microbial predation and volatile fatty acid metabolism by E. caudatum to occur in high methane emitting animals, although with no apparent direct metabolic link to methanogenesis. Despite E. caudatum having a well-established reputation of digesting starch, it was unexpectedly less active in low methane emitting animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation. Collectively, our results illuminate the substantial metabolic influence under-explored eukaryotic populations have in the rumen, with greater implications towards both digestion and methane metabolism.
2025-11-13 | PXD034544 | Pride
Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors. Three biological replicates from each condition (inhibitors, no inhibitors) were analyzed.
2012-10-18 | E-GEOD-41659 | biostudies-arrayexpress
Project description:Peptidases from Spilostethus pandurus
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Project description:Martins2013 - True and apparent inhibition of
amyloid fribril formation
This model is described in the article:
True and apparent inhibition
of amyloid fibril formation.
Martins PM.
Prion 2013 Mar-Apr; 7(2): 136-139
Abstract:
A possible therapeutic strategy for amyloid diseases
involves the use of small molecule compounds to inhibit protein
assembly into insoluble aggregates. According to the recently
proposed Crystallization-Like Model, the kinetics of amyloid
fibrillization can be retarded by decreasing the frequency of
new fibril formation or by decreasing the elongation rate of
existing fibrils. To the compounds that affect the nucleation
and/or the growth steps we call true inhibitors. An apparent
inhibition mechanism may however result from the alteration of
thermodynamic properties such as the solubility of the
amyloidogenic protein. Apparent inhibitors markedly influence
protein aggregation kinetics measured in vitro, yet they are
likely to lead to disappointing results when tested in vivo.
This is because cells and tissues media are in general much
more buffered against small variations in composition than the
solutions prepared in lab. Here we show how to discriminate
between true and apparent inhibition mechanisms from
experimental data on protein aggregation kinetics. The goal is
to be able to identify false positives much earlier during the
drug development process.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000561.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000561 | BioModels
Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.
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Project description:Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.
2024-09-30 | GSE270124 | GEO
Project description:Colletotrichum caudatum 103
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