scholarly journals Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

2021 ◽  
Author(s):  
Biao Xuan ◽  
Jongbin Park ◽  
Sukjung Choi ◽  
Inhwan You ◽  
Bo-Hye Nam ◽  
...  
Keyword(s):  
Global Warming ◽  
Heat Stress ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Enrichment Analysis ◽  
Economic Resource ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Muscle Tissues

Abstract Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5 °C) versus warm (HT, 23 °C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO : 0008610, P < 0.001) and regulation of apoptotic process (GO : 0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO : 0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO : 0001666, P < 0.05), transcription regulator activity (GO : 0140110, P < 0.001) and calcium-release channel activity (GO : 0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO : 0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

scholarly journals Draft Genome of the Korean smelt (Hypomesus nipponensis) and its transcriptomic responses to heat stress in the liver and muscle

2021 ◽  
Author(s):  
Biao Xuan ◽  
Jongbin Park ◽  
Sukjung Choi ◽  
Inhwan You ◽  
Bo-Hye Nam ◽  
...  
Keyword(s):  
Global Warming ◽  
Heat Stress ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Enrichment Analysis ◽  
Economic Resource ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Muscle Tissues

Backgrounds: Hypomesus nipponensis is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming. Aim of the study: Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. Methods: We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. Results: We observed a total of 1,987 contigs, with N50 of 0.46 Gbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KO (KEGG Orthology). In the missing and gained genes analysis, we detected 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes with coverage less than 10% and for gained genes found from alignment to other species that human, zebrafish and salmon, respectively, we observed 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes with coverage less than 10% compared with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs, adjusted p-value < 0.05) were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. Conclusion: The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and be useful for better survival of the smelt and its closely related species under global warming.

scholarly journals Molecular Targets and Associated Potential Pathways of Danlu Capsules in Hyperplasia of Mammary Glands Based on Systems Pharmacology

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Jihan Huang ◽  
Haitao Tang ◽  
Sumin Cao ◽  
Yingchun He ◽  
Yibin Feng ◽  
...  
Keyword(s):  
Hormonal Regulation ◽  
Molecular Mechanisms ◽  
Clinical Symptoms ◽  
Molecular Targets ◽  
Enrichment Analysis ◽  
Mammary Glands ◽  
Systems Pharmacology ◽  
Analgesic Effects ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Hyperplasia of mammary glands (HMG) is common in middle-aged women. Danlu capsules (DLCs) can effectively relieve pain and improve clinical symptoms and are safe for treating HMG. However, the active substances in DLCs and the molecular mechanisms of DLCs in HMG remain unclear. This study identified the bioactive compounds and delineated the molecular targets and potential pathways of DLCs by using a systems pharmacology approach. The candidate compounds were retrieved from the traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform. Each candidate’s druggability was analyzed according to its oral bioavailability and drug-likeness indices. The candidate proteins and genes were extracted in the TCMSP and UniProt Knowledgebase, respectively. The potential pathways associated with the genes were identified by performing gene enrichment analysis with DAVID Bioinformatics Resources 6.7. A total of 603 compounds were obtained from DLCs, and 39 compounds and 66 targets associated with HMG were obtained. Gene enrichment analysis yielded 10 significant pathways with 34 targets. The integrated HMG pathway revealed that DLCs probably act in patients with HMG through multiple mechanisms of anti-inflammation, analgesic effects, and hormonal regulation. This study provides novel insights into the mechanisms of DLCs in HMG, from the molecular level to the pathway level.

scholarly journals Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

2021 ◽  
Vol 22 (5) ◽  
pp. 2481
Author(s):  
Jodi Callwood ◽  
Kalpalatha Melmaiee ◽  
Krishnanand P. Kulkarni ◽  
Amaranatha R. Vennapusa ◽  
Diarra Aicha ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Stomatal Closure ◽  
Enrichment Analysis ◽  
Leaf Size ◽  
Vaccinium Corymbosum ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Transcriptomic Changes ◽  
Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

scholarly journals Effect of flapless osteoperforation-assisted tooth movement on atrophic alveolar ridge: Histomorphometric and gene-enrichment analysis

2017 ◽  
Vol 88 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Ji-Won Lee ◽  
Jung-Yul Cha ◽  
Ki-Ho Park ◽  
Yoon-Goo Kang ◽  
Su-Jung Kim
Keyword(s):  
Signaling Pathway ◽  
Tooth Movement ◽  
Osteoclast Differentiation ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Tissue Response ◽  
Alveolar Ridge ◽  
Mineral Density ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

ABSTRACT Objective: To investigate the effect of flapless osteoperforation on the tissue response of the atrophic alveolar ridge affected by orthodontic tooth movement (OTM). Materials and Methods: An atrophic alveolar ridge model was established in the mandibular quadrants of eight beagle dogs. As a split-mouth design, the quadrants were randomly divided into group C (OTM only) and group OP (OTM with flapless osteoperforation). The rate of OTM for 10 weeks was compared between groups, and micro-CT-based histomorphometric analysis and RNA-sequencing-based gene-enrichment analysis were performed targeting the atrophic ridge. Results: Group OP displayed more rapid tooth movement with lower bone mineral density and higher trabecular fraction in the atrophic ridge than did group C, showing no intergroup difference of total ridge volume. As contributing biological functional pathways in group OP, the genes related to osteoclast differentiation and TNF signaling pathway were up-regulated and those associated with Wnt signaling pathway and AMPK signaling pathway were down-regulated. Conclusions: Flapless osteoperforation facilitated the rate of OTM toward the atrophic ridge, maintaining low bone density, whereas it did not increase the volume of the atrophic ridge.

scholarly journals Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joon-Yung Cha ◽  
Sang-Ho Kang ◽  
Imdad Ali ◽  
Sang Cheol Lee ◽  
Myung Geun Ji ◽  
...  
Keyword(s):  
Heat Stress ◽  
Humic Acid ◽  
Heat Shock ◽  
Stress Tolerance ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Heat Stress Tolerance

Abstract Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.

scholarly journals Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

2008 ◽  
Vol 36 (7) ◽  
pp. e43-e43 ◽  
Author(s):  
K. De Preter ◽  
R. Barriot ◽  
F. Speleman ◽  
J. Vandesompele ◽  
Y. Moreau
Keyword(s):  
High Resolution ◽  
Enrichment Analysis ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Gene Sets

scholarly journals A Network Pharmacology Approach to Uncover the Multiple Mechanisms of Hedyotis diffusa Willd. on Colorectal Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Xinkui Liu ◽  
Jiarui Wu ◽  
Dan Zhang ◽  
Kaihuan Wang ◽  
Xiaojiao Duan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Network Analysis ◽  
Chinese Herb ◽  
Endocrine System ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Hedyotis Diffusa

Background. As one of the most frequently diagnosed cancer diseases globally, colorectal cancer (CRC) remains an important cause of cancer-related death. Although the traditional Chinese herb Hedyotis diffusa Willd. (HDW) has been proven to be effective for treating CRC in clinical practice, its definite mechanisms have not been completely deciphered. Objective. The aim of our research is to systematically explore the multiple mechanisms of HDW on CRC. Methods. This study adopted the network pharmacology approach, which was mainly composed of active component gathering, target prediction, CRC gene collection, network analysis, and gene enrichment analysis. Results. The network analysis showed that 10 targets might be the therapeutic targets of HDW on CRC, namely, HRAS, PIK3CA, KRAS, TP53, APC, BRAF, GSK3B, CDK2, AKT1, and RAF1. The gene enrichment analysis implied that HDW probably benefits patients with CRC by modulating pathways related to cancers, infectious diseases, endocrine system, immune system, nervous system, signal transduction, cellular community, and cell motility. Conclusions. This study partially verified and predicted the pharmacological and molecular mechanism of HDW against CRC from a holistic perspective, which will also lay a foundation for the further experimental research and clinical rational application of HDW.

scholarly journals Network pharmacology-based elucidation of the molecular mechanism underlying the anti-migraine effect of Asari Radix et Rhizoma

2021 ◽  
Vol 18 (10) ◽  
pp. 2067-2074
Author(s):  
Yun-Bin Jiang ◽  
Mei Zhong ◽  
Ting Huang ◽  
Zhong-Hua Dai ◽  
Xing-Bao Tao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Scientific Basis ◽  
Network Pharmacology ◽  
Overlapping Genes ◽  
Hub Genes ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Tnf Gene

Purpose: To determine the molecular mechanism involved in the anti-migraine effect of Asari Radix et Rhizoma (ARR) using network pharmacology. Methods: The compounds present in ARR were identified through information retrieval from literature and public databases, and were screened based on absorption, distribution, metabolism, excretion and toxicity. Target genes related to the selected compounds and migraine were identified or predicted from public databases. Hub genes in ARR against migraine were identified through analysis of interactions in overlapping genes between compounds and migraine target genes, based on STRING database. Gene enrichment analysis of overlapping genes was performed using Database for Annotation, Visualization and Integrated Discovery. Results: A total of 138 compounds were selected as potential bioactive compounds in ARR. Target genes related to the selected compounds (611 genes) and migraine (278 genes) were obtained, including 71 overlapping genes. The hub genes in the anti-migraine effect of ARR were BDNF, IL6, COMT, APP and TNF. Gene enrichment analysis showed the top 10 biological processes or pathways involved in the mechanism of anti-migraine action of ARR. The tissue source of the overlapping genes was not limited to the brain. The results from gene enrichment analysis revealed that the effect of ARR on migraine was holistic, which is characteristic of traditional Chinese medicines. Conclusion: Network pharmacology has been used to decipher the molecular mechanism involved in the action of ARR against migraine. The results provide a scientific basis for the clinical effect of ARR on migraine.

scholarly journals From Protein Variations to Biological Processes and Pathways with NET-GE

2017 ◽  
Vol 3 (3) ◽  
pp. 45 ◽  
Author(s):  
Samuele Bovo ◽  
Pietro Di Lena ◽  
Pier Luigi Martelli ◽  
Piero Fariselli ◽  
Rita Casadio
Keyword(s):  
Biological Networks ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Obsessive Compulsive ◽  
Compulsive Disorder ◽  
Hyperactivity Disorder ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Common Technique

Gene enrichment analysis is a common technique for highlighting molecular pathways and biological processes of a phenotype. Such technique has recently evolved exploiting the information contained in biological networks. We developed NET-GE, a web server for network-based gene enrichment analyses. NET-GE defines functional associations between a list of genes/proteins and biological processes or pathways by identifying function-specific modules in a molecular interaction network. The peculiarity of NET-GE is the possibility to enrich terms not detectable by standard enrichment procedure. Here, we highlight with two specific applications the performances of NET-GE by computing which functional phenotypes can be associated with two different sets of genes related to Attention Deficit Hyperactivity Disorder and to an Obsessive-compulsive disorder, respectively.

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