Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18679338_1.fastq.gz | Fastqsanger.gz | |||
| SRR18679338_2.fastq.gz | Fastqsanger.gz | |||
| SRR18679339_1.fastq.gz | Fastqsanger.gz | |||
| SRR18679339_2.fastq.gz | Fastqsanger.gz | |||
| SRR18679340_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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: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: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:Parascedosporium putredinis NO1 was grown for 4 days on six lignocellulosic substrates: Kraft Lignin (LI), Sugar Cane Bagasse (SC), Rice Straw (RS), Wheat Straw (WS), Wheat Bran (WB), and Empty Fruit Bunches from Palm Oil (EF). Proteins were harvested from the culture supernatant and from the insoluble fraction using a biotin-labelling approach to target the proteins bound to the lignocellulosic substrates.
2023-06-08 | MSV000092129 | MassIVE
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.
2015-11-22 | GSE55086 | GEO
Project description:Total RNA from duodenum, jejunum, liver and mammary gland 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 and SAS software.
2020-03-05 | GSE78524 | GEO
Project description:Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.
2019-10-15 | GSE131173 | GEO
Project description:Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean and wheat straws) revealed a highly overlapping group of 430 genes, the Biomass commonly Induced Core Set (BICS). A large proportion of induced carbohydrate-active-enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also up-regulated under no-carbon conditions, the remaining 252 genes were defined as the Biomass Regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the Biomass Unique Set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. Conidia of Neurospora crass wild type were inoculated at 10^6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/w) ground crop straws, barley straw, corn straw, rice straw, soybean straw and wheat straw respectively for 30 h or 2% sucrose for 16 h. Then, mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000 platform.
2015-01-21 | E-GEOD-60986 | biostudies-arrayexpress