Ontology highlight
ABSTRACT:
PROVIDER: PRJNA731995 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14621794.fastq.gz | Fastqsanger.gz |
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Project description:Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance is correlated with heritable increase of metal excretion efficiency; less pronounce cadmium induced growth reduction and, over-expression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and cadmium tolerant populations. Many cDNAs responded to cadmium exposure in a reference population. Significantly fewer clones were cadmium responsive in tolerant animals. Analysis of variance revealed transcripts that interact between cadmium exposure and population. Hierarchical clustering of these clones revealed two major groups. The first one contained cDNAs that were up regulated by cadmium in the reference culture, but non-responsive or down regulated in tolerant animals. This cluster was also characterized by elevated constitutive expression in the tolerant population. Gene ontology analysis revealed that these cDNAs were involved in structural integrity of the cuticle, anti-microbial defense, calcium-channel blocking, neurotransmitter transport, chromatin remodeling and, endoplasmatic vesicle activity. The second group consisted of cDNAs down regulated in reference animals but not responding or slightly up regulated in tolerant animals. Their functions involved carbohydrate metabolic processes, Ca2+ dependent stress signaling, proteolysis and digestion. The reference population showed a strong signature of stress-induced genome-wide perturbation of gene expression, whereas the tolerant animals maintained normal gene expression upon cadmium exposure. We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype. Orchesella cincta (Collembola) from the laboratory population (LC) at the department of Animal Ecology, Vrije Universiteit Amsterdam were taken as the reference group. This population originated from a pine forest from the reference area (Roggebotzand, the Netherlands, latitude N = 52 º 34’17’’, longitude E = 5 º 47’56’’) that contains on average < 0.5 μg cadmium per gram litter and humus. Tolerant animals were collected from randomly selected litter samples at two areas of the abandoned, but still heavily polluted lead/zinc mining site of Plombières (Belgium, latitude N = 50˚44’03’’, longitude E = 5˚58’02’’): the locations contain an average cadmium concentration between 10 and 52 μg.g-1 soil (Lock et al. 2003; Sterenborg 2003; Van Straalen et al. 1987). To diminish putative environmental effects from the field the animals were reared in a climate room (20°C, 75% humidity, LD 12 h:12 h) in PVC jars on a moist plaster of Paris layer feeding on algae present on twigs for at least three generations before experimental treatment. Animals were exposed to cadmium (nominal concentration of 112,4 μg cadmium.g-1 dry algae) for 3 days, directly after molting, via algal food. Control groups received the same treatment except that water was spiked into the algal food instead of cadmium solution. The cadmium exposure concentration is two times the no observed effect concentration (NOEC) for reproduction in chronically exposed animals. Total RNA was extracted from times 12 pooled animals per treatment using SV Total RNA Isolation system (Promega) and quantified on a Nanodrop ND-1000 Spectrophotometer (Nanodrop Technologies). Total RNA was visualized on a 1.5% agarose gel to verify its integrity. Each experimental group (pool of 12 animals) was replicated 8 times. Dyes were swapped between biological replicates: 4 Cy-3 labeled replicates and 4 Cy-5 lebeled replicates per experimental group Microarray experiment was designed in a closed loop Lab culture clean vs Cd, Lab culture Cd vs Tolerant culture Cd, Tolerant culture Cd vs Tolerant culture clean, Tolerant culture clean vs lab culture clean
2009-04-01 | E-GEOD-14076 | biostudies-arrayexpress
Project description:For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.
2019-04-25 | GSE126671 | GEO
Project description:Phytoremediation soil polluted by heavy metal has been drawn on a worldwide attention from human society. However, how to improve the efficiency of plant remediation of soil contaminated by cadmium remains unknown. Previous studies showed that nitrogen (N) significantly enhanced cadmium uptake in poplar plants. In order to further explore the key role of N in the detoxification against cadmium stress in plants, this study try to investigate the poplar proteome and phosphoproteome difference between Cd stress and Cd+N treatment. In total, 5838 of the 6573 identified were quantified. With a fold-change threshold >1.3 and p-value<0.05, 375 and 108 proteins were up- and down-regulated by Cd stress when compared to the control, 42 and 89 proteins were up- and down-regulated, respectively, in Cd+N / Cd group, 522 and 127 proteins were up- and down-regulated, respectively, in Cd+N / CK group. In addition, the phosphoproteome data was obtained after the proteomic difference was normalized, and 1471phosphosites in 721 proteins were quantified. Based on a fold-change threshold >1.2, P-value <0.05, the Cd stress up-regulated 8 phosphosites in 8 proteins and down-regulated 69 phosphosites in 58 proteins, whereas N+Cd treatment up-regulated 95 phosphosites in 86 proteins and down-regulated 17 phosphosites in 17 proteins when compared to sole Cd stress. In addition, N+Cd treatment up-regulated 74 phosphosites in 60 proteins and down-regulated 42 phosphosites in 37 proteins when compared to the control.Several putative responses to stress proteins, transcriptional and translational regulation factors were up-regulated by addition ofexogenous nitrogen followed Cd stress at the proteome and phosphoproteome levels. Especially, heat shock protein 70 (HSP70), peroxidase (POD), zinc finger protein (ZFP), ABC transporter protein (ABC), eukaryotic translation initiation factor (elF) and splicing factor 3B subunit 1-like (SF3BI) were up-regulated by Cd+N treatment whether at the proteome or at the phosphoproteome levels, which was need to further study. In a word, taken together of proteome and phosphoproteome data, nitrogen serves a protective role in plants treated with Cd by multiple ways.
2020-05-26 | PXD013360 | Pride
Project description:MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. In the study presented here, four root samples from two contrast soybean cultivars, HX3 (Cd-tolerant) and ZH24 (Cd-sensitive), with or without (Cd) cadmium, harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment, was used to acquire expression profiles of a total of 953 unique genes, leading to the successful construction of supervised.
2013-08-31 | E-GEOD-50388 | biostudies-arrayexpress
Project description:Ecotoxicological tests may be biased by the use of laboratory strains that usually contain very limited genetic diversity. It is therefore essential to study how genetic variation influences stress tolerance relevant for toxicity outcomes. To that end we studied sensitivity to cadmium in two distinct genotypes of the parthogenetic soil ecotoxicological model organism Folsomia candida. Clonal lines of both genotypes (TO1 and TO2) showed divergent fitness responses to cadmium exposure; TO2 reproduction was 20% less affected by cadmium. Statistical analyses revealed significant differences between the cadmium-affected transcriptomes; i) the number of genes affected by cadmium in TO2 was only minor (~22%) compared to TO1; ii) 97 genes showed a genotype M-CM-^W cadmium interaction and their response to cadmium showed globally larger fold changes in TO1 when compared to TO2; iii) the interaction genes showed a concerted manner of expression in TO1 while a less coordinated pattern was observed in TO2. We conclude that (1) there is genetic variation in parthenogenetic populations of F. candida, and (2) this variation affects life-history and molecular endpoints relative to cadmium toxicity. This sheds new light on the sources of biological variability in test results, even when the test organisms are thought to be genetically homogeneous because of their parthenogenetic reproduction. Gene expression was measured in two different clones (TO1 and TO2) of the springtail Folsomia candida, after exposure of 2 days to soil containing cadmium (Cd+) and non-spiked (Cd-) soil. A 2 x 2 factorial analysis was performed, to examine the effect of clone (TO1, TO2), of treatment (Cd+, Cd-), and the clone x treatment interaction.
2012-12-21 | E-GEOD-34167 | biostudies-arrayexpress
Project description:Verbena bonariensis is a species with excellent garden plant, good environmental adaptability and great potential for future development.Cadmium has caused serious heavy metal pollution in the soil, which has posed a great threat to plant growth. In this study, Illumina sequencing technology was used to sequence the transcriptome of Verbena bonariensis leaf under normal and Cd stress, respectively. In total, 95,013 transcripts and 63021 genes with an average length of 923 bp and 1,246 bp were constructed from the clean sequence reads, respectively. And 1037 DEGs were found in response to cadmium treatment, of which 10 were selected for qRT-PCR. In conclusion, this study first identified the Verbena bonariensis as a heavy metal tolerant plant and provided the first large-scale transcriptional data set in response to cadmium stress. Our research will help to understand the mechanism of resistance to Cd in the Verbena bonariensis and provide clues for further studies on the relationships between plants and heavy metals in other Verbenaceae plants.
2018-01-18 | GSE101600 | GEO
Project description:Pseudomonas aeruginosa san ai resists a high concentration of up to 7.2 mM of cadmium. Leaving biomass of P. aeruginosa san ai exposed to sub-lethal concentration of cadmium (0.9 mM) adsorbed 75% of added cadmium after 48 hours, while remaining 25% in culture supernatant was adsorbed by exopollysaccaryde, implying a large biosorption potential of leaving biomass and its exopollysaccaryde. Inner cell response on the protein level was investigated by shotgun proteomics approach based on liquid chromatography and tandem mass spectrometry coupled with bioinformatics to identify proteins in complex protein fractions obtained by size exclusion chromatography used to preserve native forms of metalloproteins and protein complexes. Using this approach a total of 59 proteins were observed as up-regulated in cadmium- amended culture. Almost a third of the total number of up-regulated were metalloproteins. P. aeruginosa san ai developed a complex mechanism to adapt to cadmium, based on: extracellular biosorption, bioaccumulation, the formation of biofilm, controlled siderophore production, enhanced respiration and modified protein profile. An increased abundance of proteins involved in cell energy metabolism, amino acid metabolism, cell motility and posttranslational modifications, primarily based on thiol-disulfide exchange, were observed. Enhanced oxygen consumption of biomass in cadmium- amended culture versus control was found. Our results signify that P. aeruginosa san ai has a great potential for application in bioremediation of cadmium polluted sites.
2022-05-19 | PXD008020 | Pride
Project description:MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24.
2013-08-31 | GSE50388 | GEO
Project description:Petroleum hydrocarbons are recalcitrant contaminants, which has caused most serious environmental problems. Acinetobacter calcoaceticus Aca13 was isolated from petroleum polluted soil for petroleum biodegradation. Hexadecane and naphthalene were used to incubate with Acinetobacter calcoaceticus Aca13. After incubation, the whole transcriptome was obtained from treated groups and control groups, and then used for RNA sequence and analysis. Obtained data in this project will help us understand the biodegradation mechanism of hexadecane and naphthalene, and will be helpful for the bioremediation of petroleum hydrocarbons.
2024-06-30 | GSE235642 | GEO
Project description:Background: Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant, which not only causes permanent and irreversible health problems for humans, but also causes a significant reduction in crop yields. Results: This study examined the chemical forms of Cd in the roots of two wheat varieties (M1019 and Xinong20) by continuous extraction and analyzed differences in distribution characteristics of Cd in the root cell wall, cytoplasm, and organelles by elemental content determination and subcellular separation. Furthermore, we conducted proteomics analysis of the roots of the two varieties under Cd pollution using mass spectrometry quantitative proteomics techniques. A total of 11,651 proteins were identified, of which 10,532 proteins contained quantitative information. In addition, the differentially expressed proteins in the two varieties were related to DNA replication and repair, protein metabolism, and the glutathione metabolism pathway. Conclusion: The results of this study improve our understanding of the mechanism of plant responses to Cd stress.
2020-03-30 | PXD018179 | Pride