scholarly journals Deep transcriptomic analysis of Chromera velia under Mercury-stress condition

2019 ◽  
Author(s):  
Abdoallah Sharaf ◽  
Roberto De Michele ◽  
Ayush Sharma ◽  
Miroslav Oborník
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Stress Responses ◽  
Control Level ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Biotic And Abiotic Stress ◽  
Terrestrial Plants ◽  
Mercury Stress ◽  
Chromera Velia

The heavy metal pollution in ecosystems is of increasing global concern. The main sources of the metal toxicity are the industrial waste, mining and the use of pesticides containing heavy metals. Out of all heavy metals, mercury (Hg) is considered to be the one, easily accumulated in terrestrial plants as well as aquatic organism. Hg can induce more severe oxidative stress by triggering the production of reactive oxygen species (ROS) and damage macro-molecules. ROS serve not only as dangerous molecules that damage proteins, lipids and DNA but also as signalling molecules in the regulation of biological processes such as biotic and abiotic stress responses, growth and development. This study shows the change in the Chromera velia transcriptome due to Hg stress. C. velia is the recently discovered closest known relative of apicomplexans. Our study shows the first deep transcriptomic analysis of C. velia, specifically focusing on the expression level of the genes involved in detoxification defence systems under heavy metal stress. The results show that in total 1239 genes are differentially expressed. DEGs (Differentially expressed genes) showed overall up-regulation (1,070 genes) and only 169 up-regulated genes in cultures under Mercury stress (Cvel_mer) when compared to the control level (Cvel_cont). The qPCR expression analysis exhibited a positive correlation with the findings of RNA-seq data.

scholarly journals Deep transcriptomic analysis of Chromera velia under Mercury-stress condition

2019 ◽  
Author(s):  
Abdoallah Sharaf ◽  
Roberto De Michele ◽  
Ayush Sharma ◽  
Miroslav Oborník
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Stress Responses ◽  
Control Level ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Biotic And Abiotic Stress ◽  
Terrestrial Plants ◽  
Mercury Stress ◽  
Chromera Velia

The heavy metal pollution in ecosystems is of increasing global concern. The main sources of the metal toxicity are the industrial waste, mining and the use of pesticides containing heavy metals. Out of all heavy metals, mercury (Hg) is considered to be the one, easily accumulated in terrestrial plants as well as aquatic organism. Hg can induce more severe oxidative stress by triggering the production of reactive oxygen species (ROS) and damage macro-molecules. ROS serve not only as dangerous molecules that damage proteins, lipids and DNA but also as signalling molecules in the regulation of biological processes such as biotic and abiotic stress responses, growth and development. This study shows the change in the Chromera velia transcriptome due to Hg stress. C. velia is the recently discovered closest known relative of apicomplexans. Our study shows the first deep transcriptomic analysis of C. velia, specifically focusing on the expression level of the genes involved in detoxification defence systems under heavy metal stress. The results show that in total 1239 genes are differentially expressed. DEGs (Differentially expressed genes) showed overall up-regulation (1,070 genes) and only 169 up-regulated genes in cultures under Mercury stress (Cvel_mer) when compared to the control level (Cvel_cont). The qPCR expression analysis exhibited a positive correlation with the findings of RNA-seq data.

scholarly journals Transcriptomic Analysis Reveals the Roles of Detoxification Systems in Response to Mercury in Chromera velia

Biomolecules ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 647 ◽  
Author(s):  
Sharaf ◽  
De Michele ◽  
Sharma ◽  
Fakhari ◽  
Oborník
Keyword(s):  
Heavy Metal ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Aquatic Organisms ◽  
Heavy Metal Stress ◽  
Transcriptomic Analysis ◽  
Molecular Response ◽  
Sequencing Analysis ◽  
Production Of Hydrogen ◽  
Chromera Velia

Heavy metal pollution is an increasing global concern. Among heavy metals, mercury (Hg) is especially dangerous because of its massive release into the environment and high toxicity, especially for aquatic organisms. The molecular response mechanisms of algae to Hg exposure are mostly unknown. Here, we combine physiological, biochemical, and transcriptomic analysis to provide, for the first time, a comprehensive view on the pathways activated in Chromera velia in response to toxic levels of Hg. Production of hydrogen peroxide and superoxide anion, two reactive oxygen species (ROS), showed opposite patterns in response to Hg2+ while reactive nitrogen species (RNS) levels did not change. A deep RNA sequencing analysis generated a total of 307,738,790 high-quality reads assembled in 122,874 transcripts, representing 89,853 unigenes successfully annotated in databases. Detailed analysis of the differently expressed genes corroborates the biochemical results observed in ROS production and suggests novel putative molecular mechanisms in the algal response to Hg2+. Moreover, we indicated that important transcription factor (TF) families associated with stress responses differentially expressed in C. velia cultures under Hg stress. Our study presents the first in-depth transcriptomic analysis of C. velia, focusing on the expression of genes involved in different detoxification defense systems in response to heavy metal stress.

scholarly journals Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256319
Author(s):  
Fernando G. Razo-Mendivil ◽  
Fernando Hernandez-Godínez ◽  
Corina Hayano-Kanashiro ◽  
Octavio Martínez
Keyword(s):  
Secondary Metabolites ◽  
Capsicum Annuum ◽  
Stress Responses ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Tomato Fruit Ripening

Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.

scholarly journals Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6495 ◽  
Author(s):  
Chao Niu ◽  
Min Jiang ◽  
Na Li ◽  
Jianguo Cao ◽  
Meifang Hou ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Marker Genes ◽  
Bioinformatics Analyses ◽  
Soil And Water

Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.

scholarly journals Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 387 ◽  
Author(s):  
Zengkui Lu ◽  
Mingxing Chu ◽  
Qing Li ◽  
Meilin Jin ◽  
Xiaojuan Fei ◽  
...  
Keyword(s):  
Heat Stress ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

scholarly journals Transcriptome Analysis Reveals Cotton (Gossypium hirsutum) Genes That Are Differentially Expressed in Cadmium Stress Tolerance

2019 ◽  
Vol 20 (6) ◽  
pp. 1479 ◽  
Author(s):  
Mingge Han ◽  
Xuke Lu ◽  
John Yu ◽  
Xiugui Chen ◽  
Xiaoge Wang ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Transcriptome Analysis ◽  
Metal Ion ◽  
Molecular Mechanisms ◽  
Reduction Process ◽  
Differentially Expressed ◽  
Cd Tolerance ◽  
Metal Binding Domain ◽  
Cotton Plants

High concentrations of heavy metals in the soil should be removed for environmental safety. Cadmium (Cd) is a heavy metal that pollutes the soil when its concentration exceeds 3.4 mg/kg. Although the potential use of cotton to remediate heavy Cd-polluted soils is known, little is understood about the molecular mechanisms of Cd tolerance. In this study, transcriptome analysis was used to identify Cd tolerance genes and their potential mechanisms in cotton. We exposed cotton plants to excess Cd and identified 4627 differentially expressed genes (DEGs) in the root, 3022 DEGs in the stem and 3854 DEGs in the leaves through RNA-Seq analysis. Among these genes were heavy metal transporter coding genes (ABC, CDF, HMA, etc.), annexin genes and 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 were mainly enriched in two pathways, the influenza A and pyruvate pathway. GhHMAD5, a protein containing a heavy-metal binding domain, was identified in the pathway to transport or to detoxify heavy metal ions. We constructed a GhHMAD5 overexpression system in Arabidopsis thaliana that showed longer roots compared to control plants. GhHMAD5-silenced cotton plants showed more sensitivity to Cd stress. The results indicate that GhHMAD5 is involved in Cd tolerance, which gives a preliminary understanding of the Cd tolerance mechanism in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate soils polluted with Cd and potentially other heavy metals.

scholarly journals Transcriptional responses of Anopheles gambiae s.s mosquito larvae to chronic exposure of cadmium heavy metal

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2173
Author(s):  
Catherine N. Muturi ◽  
Martin K. Rono ◽  
Daniel K. Masiga ◽  
Francis N. Wachira ◽  
Richard Ochieng ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Anopheles Gambiae ◽  
Cadmium Exposure ◽  
Translation Initiation Factor ◽  
Differentially Expressed ◽  
Initiation Factor ◽  
Anopheles Gambiae S.S ◽  
Transcriptional Responses ◽  
Anion Transporter

Background: Anopheles gambiae larvae traditionally thrive in non-polluted environments. We previously documented the presence of the larvae in heavy metal polluted urban aquatic environments and the associated biological cost. The goal of this study was to unravel the molecular dynamics involved in the adaptation of the mosquitoes to the heavy metals. Methods: Total RNA was extracted from third instar larvae of both cadmium treated populations and untreated control populations. The RNA concentrations were normalized and complementary DNAs were prepared. Then annealing control primer (ACP) technology was applied to establish transcriptional responses in An. gambiae larvae following several generational (n=90) chronic exposures to cadmium. Differentially expressed genes were determined by their differential banding patterns on an agarose gel. Gel extraction and purification was then carried out on the DEGs and these were later cloned and sequenced to establish the specific transcripts.    Results: We identified 14 differentially expressed transcripts in response to the cadmium exposure in the larvae. Most (11) of the transcripts were up-regulated in response to the cadmium exposure and were putatively functionally associated with metabolism, transport and protein synthesis processes. The transcripts included ATP-binding cassette transporter, eupolytin, ribosomal RNA, translation initiation factor, THO complex, lysosomal alpha-mannosidase, sodium-independent sulfate anion transporter and myotubularin related protein 2. The down-regulated transcripts were functionally associated with signal transduction and proteolytic activity and included Protein G12, adenylate cyclase and endoplasmic reticulum metallopeptidase. Conclusions: Our findings shed light on pathways functionally associated with the adaptation to heavy metals that can be targeted in integrated vector control programs, and potential An. gambiae larvae biomarkers for assessment of environmental stress or contamination.

scholarly journals Transcriptional responses of Anopheles gambiae s.s mosquito larvae to chronic exposure of cadmium heavy metal

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 2173
Author(s):  
Catherine N. Muturi ◽  
Martin K. Rono ◽  
Daniel K. Masiga ◽  
Francis N. Wachira ◽  
Richard Ochieng ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Anopheles Gambiae ◽  
Cadmium Exposure ◽  
Translation Initiation Factor ◽  
Differentially Expressed ◽  
Initiation Factor ◽  
Anopheles Gambiae S.S ◽  
Transcriptional Responses ◽  
Anion Transporter

Background: Anopheles gambiae larvae traditionally thrive in non-polluted environments. We previously documented the presence of the larvae in heavy metal polluted urban aquatic environments and the associated biological cost. The goal of this study was to unravel the molecular dynamics involved in the adaptation of the mosquitoes to the heavy metals. Methods: Total RNA was extracted from third instar larvae of both cadmium treated populations and untreated control populations. The RNA concentrations were normalized and complementary DNAs were prepared. Then annealing control primer (ACP) technology was applied to establish transcriptional responses in An. gambiae larvae following several generational (n=90) chronic exposures to cadmium. Differentially expressed genes were determined by their differential banding patterns on an agarose gel. Gel extraction and purification was then carried out on the DEGs and these were later cloned and sequenced to establish the specific transcripts.    Results: We identified 14 differentially expressed transcripts in response to the cadmium exposure in the larvae. Most (11) of the transcripts were up-regulated in response to the cadmium exposure and were putatively functionally associated with metabolism, transport and protein synthesis processes. The transcripts included ATP-binding cassette transporter, eupolytin, ribosomal RNA, translation initiation factor, THO complex, lysosomal alpha-mannosidase, sodium-independent sulfate anion transporter and myotubularin related protein 2. The down-regulated transcripts were functionally associated with signal transduction and proteolytic activity and included Protein G12, adenylate cyclase and endoplasmic reticulum metallopeptidase. Conclusions: Our findings shed light on pathways functionally associated with the adaptation to heavy metals that can be targeted in integrated vector control programs, and potential An. gambiae larvae biomarkers for assessment of environmental stress or contamination.

Making the life of heavy metal-stressed plants a little easier

2005 ◽  
Vol 32 (6) ◽  
pp. 481 ◽  
Author(s):  
Priscila L. Gratão ◽  
Andrea Polle ◽  
Peter J. Lea ◽  
Ricardo A. Azevedo
Keyword(s):  
Heavy Metals ◽  
Reactive Oxygen Species ◽  
Heavy Metal ◽  
Toxic Metals ◽  
Stress Responses ◽  
Environmental Problem ◽  
Oxygen Species ◽  
Cellular Stress Responses ◽  
Contamination Of Soils

The contamination of soils and water with metals has created a major environmental problem, leading to considerable losses in plant productivity and hazardous health effects. Exposure to toxic metals can intensify the production of reactive oxygen species (ROS), which are continuously produced in both unstressed and stressed plants cells. Some of the ROS species are highly toxic and must be detoxified by cellular stress responses, if the plant is to survive and grow. The aim of this review is to assess the mode of action and role of antioxidants in protecting plants from stress caused by the presence of heavy metals in the environment.

INFLUENCE OF THE ECOLOGICAL STATE OF THE SEREPOK RIVER (VIETNAM) ON ACCUMULATION OF HEAVY METALS IN ORGANS OF FISH

2017 ◽  
pp. 98-105
Author(s):  
Ngo The Cuong ◽  
Tran Hoan Quoc ◽  
Svetlana Vasilievna Zolotokopova
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
River Water ◽  
Bottom Sediments ◽  
Heavy Metal Concentration ◽  
Industrial Areas ◽  
Industrial Regions ◽  
Cadmium Lead ◽  
Sarotherodon Galilaeus ◽  
Water Bottom

The article focuses on the study of change of containing heavy metals (zinc, copper, iron, cadmium, lead, arsenic) in the abiotic and biotic components of the Serepok river (Vietman) influenced by wastewater discharge from industrial areas. Heavy metal content was determined in the river water and bottom sediments in the four zones: above and within the boundaries of industrial regions Xoa Phu and Tam Thang and in two water reservoirs situated below the boundaries of those industrial areas. Tilapia Galilean ( Sarotherodon galilaeus ), Hemibagrus ( Hemibagrus ), and sazan ( Cyprinus carpio ) caught in these areas were the hydrobionts under study in which liver, gills, skeleton and muscles accumulation of heavy metals was detected. In the organs of fish caught in the river within industrial region, heavy metals concentration was 3-7 times higher. The greatest concentration of heavy metals was found in the liver and gills of fish caught in the boundaries of industrial regions, the least concentration was in the muscles. In most cases, significant correlation between heavy metal concentration in organs of fishes and in river water, bottom sediments has been revealed.

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