Ontology highlight
ABSTRACT:
PROVIDER: PRJNA862313 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20787443.fastq.gz | Fastqsanger.gz | |||
| SRR20787444.fastq.gz | Fastqsanger.gz | |||
| SRR20787445.fastq.gz | Fastqsanger.gz |
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Project description:Furans (furfural and 5-hydroxymethylfurfural (HMF)), phenolic aldehydes (4-hydroxybenzaldehyde, syringaldehyde, and vanillin), and weak acids (acetic acid and formic acid) are the main degradation products of lignocellulose pretreatment process and seriously inhibit the cellullas enzyme activity and the fermentation process.
2022-07-21 | GSE208427 | GEO
Project description:Coal is a major energy source that generates diverse environmental impacts through its production, primarily by the release of coal dust particles. An aqueous coal dust extract was obtained from a mineral sample taken from one of the largest coal mines in Colombia (La Loma, Cesar), trace elements by ICP/MS were measured, and its toxicity evaluated using the zebrafish (Danio rerio) vertebrate model. In this study, zebrafish embryos were exposed to different concentrations of aqueous coal extract (0, 0.1, 1, 10, 100 and 1000 parts per million (ppm; μg/mL) to establish acute toxicity, as well as morphological and transcriptome alterations. Trace elements within the coal extract yielding the highest concentrations included Sr, Zn, Ba, As, Cu, Se, Li, Ni, Sb, Rb, Co, and Cr. In addition, Cd and Pb were found in lower concentrations. No significant difference in mortality was observed with survival near 90% in all treatments. A significant decrease in rate of hatching was observed in the 0.1 and 1000 ppm treatment groups at 72 hpf. Furthermore, no significant differences in total body length, head length, or head diameter was observed in any of the treatment groups. Transcriptomic results of zebrafish larvae revealed alterations in 77, 61, and 1,376 genes in the 1, 10, and 100 ppm treatments, respectively. Gene ontology analysis revealed gene alterations associated with hematological system development and function, tissue morphology and development, connective tissue development and function, and embryonic development. Overall, these findings are the first to identify gene expression alterations in response to a developmental aqueous coal dust residue from coal mining.
2017-11-30 | GSE94997 | 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:Renewables-based biotechnology depends on enzymes to degrade plant lignocellulose to simple sugars that are converted to fuels or high-value products. Identification and characterization of such lignocellulose degradative enzymes could be fast-tracked by availability of an enzyme activity measurement method that is fast, label-free, uses minimal resources and allows direct identification of generated products. We developed such a method by applying carbohydrate arrays coupled with MALDI-ToF mass spectrometry to identify reaction products of carbohydrate active enzymes (CAZymes) of the filamentous fungus Aspergillus niger. We describe the production and characterization of plant polysaccharide-derived oligosaccharides and their attachment to hydrophobic self-assembling monolayers on a gold target. We verify effectiveness of this array for detecting exo- and endo-acting glycoside hydrolase activity using commercial enzymes, and demonstrate how this platform is suitable for detection of enzyme activity in relevant biological samples, the culture filtrate of A. niger grown on wheat straw. In conclusion, this versatile method is broadly applicable in screening and characterisation of activity of CAZymes, such as fungal enzymes for plant lignocellulose degradation with relevance to biotechnological applications as biofuel production, the food and animal feed industry.
2018-10-26 | PXD005699 | Pride
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
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.
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2017-04-12 | MODEL1703060000 | BioModels