scholarly journals Liver Transcriptome Changes of Hyla Rabbit in Response to Chronic Heat Stress

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1141
Author(s):  
Zhou-Lin Wu ◽  
Xue Yang ◽  
Shi-Yi Chen ◽  
Fei-Long Deng ◽  
Xian-Bo Jia ◽  
...  
Keyword(s):  
Heat Stress ◽  
Metabolic Process ◽  
Pcr Analysis ◽  
P Value ◽  
Biological Processes ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Liver Transcriptome ◽  
Quality Filtering ◽  
Gene Expression Levels

Rabbit is an economically important farm animal in China and also is a widely used animal model in biological researches. Rabbits are very sensitive to the environmental conditions, therefore we investigated the liver transcriptome changes in response to chronic heat stress in the present study. Six Hyla rabbits were randomly divided into two groups: chronic heat stress (HS) and controls without heat stress (CN). Six RNA-Seq libraries totally yielded 380 million clean reads after the quality filtering. Approximately 85.07% of reads were mapped to the reference genome. After assembling transcripts and quantifying gene expression levels, we detected 51 differentially expressed genes (DEGs) between HS and CN groups with thresholds of the adjusted p-value < 0.05 and |log2(FoldChange)| > 1. Among them, 33 and 18 genes were upregulated and downregulated, respectively. Gene ontology analyses further revealed that these DEGs were mainly associated with metabolism of lipids, thyroid hormone metabolic process, and cellular modified amino acid catabolic process. The upregulated ACACB, ACLY, LSS, and CYP7A1 genes were found to be inter-related through biological processes of thioester biosynthetic process, acyl-CoA biosynthetic process, acetyl-CoA metabolic process, and others. Six DEGs were further validated by quantitative real-time PCR analysis. The results revealed the candidate genes and biological processes that will potentially be considered as important regulatory factors involved in the heat stress response in rabbits.

scholarly journals A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 22 ◽  
Author(s):  
Dong Xue ◽  
Yun Chen ◽  
Jiang Li ◽  
Jiahui Han ◽  
Zhengfu Zhou ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Environmental Stress ◽  
Noncoding Rna ◽  
Deinococcus Radiodurans ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Rna Seq ◽  
Environmental Stress Response ◽  
Heat Stress Response

Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

2018 ◽  
Vol 30 (6) ◽  
pp. 3103-3119 ◽  
Author(s):  
Sze-Wan Poong ◽  
Kok-Keong Lee ◽  
Phaik-Eem Lim ◽  
Tun-Wen Pai ◽  
Chiew-Yen Wong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Chlorella Sp

scholarly journals Transcriptome Analysis of a Jujube (Ziziphus Jujuba Mill.) Cultivar Response to Heat Stress

2021 ◽  
Author(s):  
Lei Yang ◽  
Juan Jin ◽  
Ding-yu Fan ◽  
Qing Hao ◽  
Jianxin Niu
Keyword(s):  
Gene Ontology ◽  
Heat Stress ◽  
Stress Response ◽  
Heat Resistance ◽  
Molecular Mechanism ◽  
Cdna Libraries ◽  
Biological Processes ◽  
Rna Seq ◽  
Ziziphus Jujuba ◽  
Growth And Reproduction

Abstract Background: Heat stress (HS) is a common stress and influences the growth and reproduction of plant species. We found and bred a putative heat-resistant jujube (Ziziphus jujuba Mill.) cultivar (JHR17) in previous study. Results: In the current study, we made the seedlings of ‘JHR17’ cultivar to be under HS (45°C) for 0, 1, 3, 5 and 7 days, respectively, and the leaf samples (HR0, HR1, HR3, HR5 and HR7) were collected accordingly. Fifteen cDNA libraries from ‘JHR17’ leaves were built with a transcriptome assay. The RNA sequencing (RNA-seq) and transcriptome comparisons were performed, and the results indicated that 1642, 4080, 5160 and 2119 differentially expressed genes (DEGs) were identified in HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0 and HR7 vs. HR0, respectively. Gene Ontology (GO) analyses of the DEGs from these comparisons were implemented. Conclusion: It revealed that a series of biological processes, involved in stress response, photosynthesis and metabolism, were enriched successfully, suggesting that lowering or up-regulating these genes of processes might play important roles in response to HS. This study may contribute to understand the molecular mechanism of ‘JHR17’ cultivar response to HS, and be beneficial for developing jujube cultivars to improve heat resistance.

scholarly journals Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinhuan Dou ◽  
Angela Cánovas ◽  
Luiz F. Brito ◽  
Ying Yu ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Metabolic Pathways ◽  
Adrenal Glands ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Mammal Species ◽  
Heat Stress Response ◽  
Sprague Dawley Rats

Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; CT) and 42°C for 30 min (H30), 60 min (H60), and 120 min (H120), RNA-sequencing (RNA-Seq) assays were performed for blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120). A total of 53, 1,310, and 1,501 differentially expressed genes (DEGs) were significantly identified in the blood (P &lt; 0.05 and |fold change (FC)| &gt;2), liver (P &lt; 0.01, false discovery rate (FDR)–adjusted P = 0.05 and |FC| &gt;2) and adrenal glands (P &lt; 0.01, FDR-adjusted P = 0.05 and |FC| &gt;2), respectively. Of these, four DEGs, namely Junb, P4ha1, Chordc1, and RT1-Bb, were shared among the three tissues in CT vs. H120 comparison. Functional enrichment analyses of the DEGs identified in the blood (CT vs. H120) revealed 12 biological processes (BPs) and 25 metabolic pathways significantly enriched (FDR = 0.05). In the liver, 133 BPs and three metabolic pathways were significantly detected by comparing CT vs. H30, H60, and H120. Furthermore, 237 BPs were significantly (FDR = 0.05) enriched in the adrenal glands, and no shared metabolic pathways were detected among the different heat-stressed groups of rats. Five and four expression patterns (P &lt; 0.05) were uncovered by 73 and 91 shared DEGs in the liver and adrenal glands, respectively, over the different comparisons. Among these, 69 and 73 genes, respectively, were proposed as candidates for regulating heat stress response in rats. Finally, together with genome-wide association study (GWAS) results in cattle and phenome-wide association studies (PheWAS) analysis in humans, five genes (Slco1b2, Clu, Arntl, Fads1, and Npas2) were considered as being associated with heat stress response across mammal species. The datasets and findings of this study will contribute to a better understanding of heat stress response in mammals and to the development of effective approaches to mitigate heat stress response in livestock through breeding.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

2020 ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
The Philippines ◽  
Differentially Expressed ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab ◽  
Heat Response

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Transcriptome Assembly ◽  
The Philippines ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Data Set ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab

Abstract Background The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mustafa Sibai ◽  
Cüneyd Parlayan ◽  
Pelin Tuğlu ◽  
Gürkan Öztürk ◽  
Turan Demircan
Keyword(s):  
Wound Healing ◽  
Statistical Power ◽  
Limb Regeneration ◽  
Ambystoma Mexicanum ◽  
Integrative Analysis ◽  
Pcr Analysis ◽  
P Value ◽  
Rna Seq ◽  
Study Designs ◽  
Merging Method

AbstractAxolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and restoration of amputated limbs, which makes it a powerful experimental model for regenerative biology and medicine. Previous studies have utilized microarrays and RNA-Seq technologies for detecting differentially expressed (DE) genes in different phases of the axolotl limb regeneration. However, sufficient consistency may be lacking due to statistical limitations arising from intra-laboratory analyses. This study aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs using the “merging” method. A total of 351 genes were found DE in regenerative samples compared to the control in data of both technologies, showing an adjusted p-value < 0.01 and log fold change magnitudes >1. Downstream analyses illustrated consistent correlations of the directionality of DE genes within and between data of both technologies, as well as concordance with the literature on regeneration related biological processes. qRT-PCR analysis validated the observed expression level differences of five of the top DE genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.

scholarly journals Genome-wide identification of Hsp70/110 genes in rainbow trout and their regulated expression in response to heat stress

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10022
Author(s):  
Fang Ma ◽  
Lintong Luo
Keyword(s):  
Heat Stress ◽  
Rainbow Trout ◽  
Gene Family ◽  
Cold Water ◽  
Functional Characterization ◽  
Head Kidney ◽  
Rna Seq ◽  
Systematic Analysis ◽  
Heat Stress Response ◽  
Shock Proteins

Heat shock proteins (Hsps) play an important role in many biological processes. However, as a typical cold water fish, the systematic identification of Hsp70/110 gene family of rainbow trout (Oncorhynchus mykiss) has not been reported, and the role of Hsp70/110 gene in the evolution of rainbow trout has not been described systematically. In this study, bioinformatics methods were used to analyze the Hsp70/110 gene family of rainbow trout. A total of 16 hsp70/110 genes were identified and classified into ten subgroups. The 16 Hsp70/110 genes were all distributed on chromosomes 2, 4, 8 and 13. The molecular weight is ranged from 78.93 to 91.39 kD. Gene structure and motif composition are relatively conserved in each subgroup. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of four out of 16 genes were significantly upregulated in liver under heat stress, and a total of seven out of 16 genes were significantly upregulated in head kidney. RT-qPCR was carried out on these gene, and the result were consistent with those of RNA-seq. The significantly regulated expressions of Hsp70/110 genes under heat stress indicats that Hsp70/110 genes are involved in heat stress response in rainbow trout. This systematic analysis provided valuable information about the diverse roles of Hsp70/110 in the evolution of teleost, which will contribute to the functional characterization of Hsp70/110 genes in further research.

Sign in / Sign up

Export Citation Format

Share Document