Ontology highlight
ABSTRACT:
PROVIDER: PRJNA557266 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9870320_1.fastq.gz | Fastqsanger.gz | |||
| SRR9870320_2.fastq.gz | Fastqsanger.gz | |||
| SRR9870330_1.fastq.gz | Fastqsanger.gz | |||
| SRR9870330_2.fastq.gz | Fastqsanger.gz | |||
| SRR9870340_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 78 |
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Project description:Total RNA from rumen epithelial tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS)diet were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR.
2017-06-09 | GSE78197 | GEO
Project description:A healthy rumen is crucial for normal growth and improved production performance of ruminant animals. Rumen microbes participate in and regulate rumen epithelial function, and the diverse metabolites produced by rumen microbes are important participants in rumen microbe-host interactions. SCFAs, as metabolites of rumen microbes, have been widely studied, and propionate and butyrate have been proven to promote rumen epithelial cell proliferation. Succinate, as an intermediate metabolite in the citric acid cycle, is a final product in the metabolism of certain rumen microbes, and is also an intermediate product in the microbial synthesis pathway of propionate. However, its effect on rumen microbes and rumen epithelial function has not been studied. It is unclear whether succinate can stimulate rumen epithelial development. Therefore, in this experiment, Chinese Tan sheep were used as experimental animals to conduct a comprehensive analysis of the rumen microbiota community structure and rumen epithelial transcriptome, to explore the role of adding succinate to the diet in the interaction between the rumen microbiota and host.
2023-06-12 | GSE233696 | GEO
Project description:TEMPORAL COLONIZATION OF RICE STRAW BY RUMEN BACTERIA IN VITRO
| PRJEB38732 | ENA
Project description:Straw return is crucial for the sustainable development of rice planting. To investigate the response of rice leaves to rice straw return, we analyzed the physiological index of rice leaves and measured differentially expressed protein (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with no rice straw return, rice straw return significantly decreased the dry weight of rice plants and nonstructural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves under rice straw return, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs and DEMs were mainly involved in various molecular processes, including photosynthesis, carbon fixation in photosynthetic organisms, glycolysis, and the citric acid cycle. Rice straw return promoted the accumulation of osmotic adjustment substances, such as organic acids, amino acids, and other substances, and reduced the material supply and energy production of carbon metabolism, thus inhibiting the growth of rice.
2022-09-12 | PXD035835 | Pride
Project description:Ahmad2017 - Genome-scale metabolic model
(iGT736) of Geobacillus thermoglucosidasius (C56-YS93)
This model is described in the article:
A Genome Scale Model of
Geobacillus thermoglucosidasius (C56-YS93) reveals its
biotechnological potential on rice straw hydrolysate
Ahmad Ahmada, Hassan B. Hartmanb, S.
Krishnakumara, David A. Fellb, Mark G. Poolmanb, Shireesh
Srivastavaa
Journal of Biotechnology
Abstract:
Rice straw is a major crop residue which is burnt in many
countries, creating significant air pollution. Thus,
alternative routes for disposal of rice straw are needed.
Biotechnological treatment of rice straw hydrolysate has
potential to convert this agriculture waste into valuable
biofuel(s) and platform chemicals. Geobacillus
thermoglucosidasius is a thermophile with properties specially
suited for use as a biocatalyst in lignocellulosic
bioprocesses, such as high optimal temperature and tolerance to
high levels of ethanol. However, the capabilities of
Geobacillus thermoglucosidasius to utilize sugars in rice straw
hydrolysate for making bioethanol and other platform chemicals
have not been fully explored. In this work, we have created a
genome scale metabolic model (denoted iGT736) of the organism
containing 736 gene products, 1159 reactions and 1163
metabolites. The model was validated both by purely theoretical
approaches and by comparing the behaviour of the model to
previously published experimental results. The model was then
used to determine the yields of a variety of platform chemicals
from glucose and xylose — two primary sugars in rice
straw hydrolysate. A comparison with results from a model of
Escherichia coli shows that Geobacillus thermoglucosidasius is
capable of producing a wider range of products, and that for
the products also produced by Escherichia coli, the yields are
comparable. We also discuss strategies to utilise arabinose, a
minor component of rice straw hydrolysate, and propose
additional reactions to lead to the synthesis of xylitol, not
currently produced by Geobacillus thermoglucosidasius. Our
results provide additional motivation for the current
exploration of the industrial potential of Geobacillus
thermoglucosidasius and we make our model publicly available to
aid the development of metabolic engineering strategies for
this organism.
This model is hosted on
BioModels Database
and identified by:
MODEL1703060000.
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.
2017-04-12 | MODEL1703060000 | BioModels
Project description:In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high- and low-quality diets. In total, 340, 338, 337, 330, and 328 miRNAs were expressed in the rumen, duodenum, jejunum, liver, and mammary gland tissues, respectively. Some miRNAs were highly correlated with feed and nitrogen efficiency, with target genes involved in transportation and phosphorylation of amino acid (AA). Additionally, low-quality forage diets (corn stover and rice straw) influenced the expression of feed and nitrogen efficiency-associated miRNAs such as miR-99b in rumen, miR-2336 in duodenum, miR-652 in jejunum, miR-1 in liver, and miR-181a in mammary gland. Ruminal miR-21-3p and liver miR-2285f were predicted to regulate AA transportation by targeting ATP1A2 and SLC7A8, respectively. Furthermore, bovine-specific miRNAs regulated the proliferation and morphology of rumen epithelium, as well as the metabolism of liver lipids and branched-chain AAs, revealing bovine-specific mechanisms. Our results suggest that miRNAs expressed in these five tissues play roles in regulating transportation of AA for downstream milk production, which is an important mechanism that may be associated with low milk protein under lowquality forage feed.
2018-07-21 | GSE117441 | GEO
Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ⤠0.0001 and |log2 of the ratio of the RPM values| ⥠2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).
2015-11-22 | E-GEOD-55086 | biostudies-arrayexpress
Project description:THE EFFECT OF CHEMICAL COMPOSITION OF RICE STRAW ON THE IN VITRO COLONIZATION BY RUMEN BACTERIA.
| PRJEB38515 | ENA
Project description:Biodegradation of rice straw with the rumen fluid
| PRJDB14063 | ENA