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Wei X, Wang X, Zhao Y, Chen W, Nath UK, Yang S, Su H, Wang Z, Zhang W, Tian B, Wei F, Yuan Y, Zhang X. Transcriptome analysis reveals the potential lncRNA-mRNA modules involved in genetic male sterility and fertility of Chinese cabbage (brassica rapa L. ssp. pekinensis). BMC Plant Biol 2024; 24:289. [PMID: 38627624 PMCID: PMC11020818 DOI: 10.1186/s12870-024-05003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene expression vital for the growth and development of plants. Despite this, the role of lncRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) pollen development and male fertility remains poorly understood. RESULTS In this study, we characterized a recessive genic male sterile mutant (366-2 S), where the delayed degradation of tapetum and the failure of tetrad separation primarily led to the inability to form single microspores, resulting in male sterility. To analyze the role of lncRNAs in pollen development, we conducted a comparative lncRNA sequencing using anthers from the male sterile mutant line (366-2 S) and the wild-type male fertile line (366-2 F). We identified 385 differentially expressed lncRNAs between the 366-2 F and 366-2 S lines, with 172 of them potentially associated with target genes. To further understand the alterations in mRNA expression and explore potential lncRNA-target genes (mRNAs), we performed comparative mRNA transcriptome analysis in the anthers of 366-2 S and 366-2 F at two stages. We identified 1,176 differentially expressed mRNAs. Remarkably, GO analysis revealed significant enrichment in five GO terms, most notably involving mRNAs annotated as pectinesterase and polygalacturonase, which play roles in cell wall degradation. The considerable downregulation of these genes might contribute to the delayed degradation of tapetum in 366-2 S. Furthermore, we identified 15 lncRNA-mRNA modules through Venn diagram analysis. Among them, MSTRG.9997-BraA04g004630.3 C (β-1,3-glucanase) is associated with callose degradation and tetrad separation. Additionally, MSTRG.5212-BraA02g040020.3 C (pectinesterase) and MSTRG.13,532-BraA05g030320.3 C (pectinesterase) are associated with cell wall degradation of the tapetum, indicating that these three candidate lncRNA-mRNA modules potentially regulate pollen development. CONCLUSION This study lays the foundation for understanding the roles of lncRNAs in pollen development and for elucidating their molecular mechanisms in regulating male sterility in Chinese cabbage.
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Affiliation(s)
- Xiaochun Wei
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaoqing Wang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yanyan Zhao
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Weiwei Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Shuangjuan Yang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Henan Su
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Zhiyong Wang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Wenjing Zhang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fang Wei
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Yuxiang Yuan
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
| | - Xiaowei Zhang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
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Feng R, Wang L, Chai H, Jiao J, Zhang P, Zheng X, Liu H, Zhang W, Wu S. Systems Pharmacology Strategy for the Investigation of Action Mechanisms of Qin Herb Libanotis Buchtormensis ( Fisch.) DC. in Bone Diseases. Endocr Metab Immune Disord Drug Targets 2024; 24:142-152. [PMID: 37475560 DOI: 10.2174/1871530323666230720143415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/26/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
INTRODUCTION Qin medicines are medicinal plants growing in habitat around the peak of Qinling Mountain. Their unique curative effects on bone metabolic diseases and pain diseases have been favoured by the local people in clinical trials for thousands of years. Libanotis buchtormensis (Fisch.) DC. (LBD), is one of the popular Qin herbs, which has been widely used for the treatment of various diseases, such as osteoporosis, rheumatic, and cardiovascular diseases. However, due to the multiple compounds in LBD, the underlying molecular mechanisms of LBD remain unclear. OBJECTIVE This study aimed to systemically investigate the underlying mechanisms of LBD against bone diseases. METHODS In this study, a systems pharmacology platform included the potential active compound screening, target fishing, and network pharmacological analysis was employed to decipher the action mechanisms of LBD. RESULTS As a result, 12 potential active compounds and 108 targets were obtained. Furthermore, compound-target network and target-pathway network analysis showed that multi-components interacted with multi-targets and multi-pathways, i.e., MARK signalling pathway, mTORC1 signalling pathway, etc., involved in the regulation of the immune system and circulatory system. These results suggested the mechanisms of the therapeutic effects of LBD on various diseases through most compounds targeted by multiple targets. CONCLUSION In conclusion, we successfully predicted the LBD bioactive compounds and potential targets, implying that LBD could be applied as a novel therapeutic herb in osteoporosis, rheumatic, and cardiovascular diseases. This work provides insight into the therapeutic mechanisms of LBD for treating various diseases.
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Affiliation(s)
- Rundong Feng
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Lifang Wang
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Hu Chai
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Jie Jiao
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Peng Zhang
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Xu Zheng
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Haijing Liu
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
| | - Wenjuan Zhang
- Lab for Bone Metabolism, College of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, People's Republic of China
| | - Suli Wu
- Shaanxi Institute for Food and Drug Control, Xi'an, Shaanxi, People's Republic of China
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Nandi A, Nigar T, Das A, Dey YN. Network pharmacology analysis of Plumbago zeylanica to identify the therapeutic targets and molecular mechanisms involved in ameliorating hemorrhoids. J Biomol Struct Dyn 2023:1-15. [PMID: 37948311 DOI: 10.1080/07391102.2023.2280681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Plumbago zeylanica is an important plant used in the Ayurvedic system of medicine for the treatment of hemorrhoids or piles. Despite its clinical uses, its molecular mechanism, for ameliorating hemorrhoids is not yet explored. Hence, the present study evaluated the plausible molecular mechanisms of P. zeylanica in the treatment of hemorrhoids using network pharmacology and other in silico analysis. Network pharmacology was carried out by protein, GO, and KEGG enrichment analysis. Further ADME/T, molecular docking and dynamics studies of the resultant bioactive compounds of P. zeylanica with the regulated proteins were evaluated. Results of the network pharmacology analysis revealed that the key pathways and plausible molecular mechanisms involved in the treatment effects of P. zeylanica on hemorrhoids are cell migration, proliferation, motility, and apoptosis which are synchronized by cancer, focal adhesion, and by signalling relaxin, Rap1, and calcium pathways which indicates the involvement of angiogenesis and vasodilation which are the characteristic features of hemorrhoids. Further, the molecular docking and dynamics studies revealed that the bio active ingredients of P. zeylanica strongly bind with the key target proteins in the ambiance of hemorrhoids. Hence, the study revealed the mechanism of P. zeylanica in ameliorating hemorrhoids.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arijit Nandi
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
| | - Tanzeem Nigar
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
| | - Anwesha Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Palaj, Gandhinagar, Gujarat, India
| | - Yadu Nandan Dey
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
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Dittiger LD, Chaudhary S, Furch ACU, Mithöfer A, Schirawski J. Plant Responses of Maize to Two formae speciales of Sporisorium reilianum Support Recent Fungal Host Jump. Int J Mol Sci 2023; 24:15604. [PMID: 37958588 PMCID: PMC10648682 DOI: 10.3390/ijms242115604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Host jumps are a major factor for the emergence of new fungal pathogens. In the evolution of smut fungi, a putative host jump occurred in Sporisorium reilianum that today exists in two host-adapted formae speciales, the sorghum-pathogenic S. reilianum f. sp. reilianum and maize-pathogenic S. reilianum f. sp. zeae. To understand the molecular host-specific adaptation to maize, we compared the transcriptomes of maize leaves colonized by both formae speciales. We found that both varieties induce many common defense response-associated genes, indicating that both are recognized by the plant as pathogens. S. reilianum f. sp. reilianum additionally induced genes involved in systemic acquired resistance. In contrast, only S. reilianum f. sp. zeae induced expression of chorismate mutases that function in reducing the level of precursors for generation of the defense compound salicylic acid (SA), as well as oxylipin biosynthesis enzymes necessary for generation of the SA antagonist jasmonic acid (JA). In accordance, we found reduced SA levels as well as elevated JA and JA-Ile levels in maize leaves inoculated with the maize-adapted variety. These findings support a model of the emergence of the maize-pathogenic variety from a sorghum-specific ancestor following a recent host jump.
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Affiliation(s)
- Lukas Dorian Dittiger
- Department of Genetics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (L.D.D.); (S.C.)
| | - Shivam Chaudhary
- Department of Genetics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (L.D.D.); (S.C.)
| | - Alexandra Charlotte Ursula Furch
- Department of Plant Physiology, Matthias Schleiden Institute, Friedrich Schiller University Jena, Dornburgerstr. 159, 07743 Jena, Germany;
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany;
| | - Jan Schirawski
- Department of Genetics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (L.D.D.); (S.C.)
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Hua Z, Zhang J, Cheng W, Wang C, Zhao D. Ethanolic Extract from Seed Residues of Sea Buckthorn ( Hippophae rhamnoides L.) Ameliorates Oxidative Stress Damage and Prevents Apoptosis in Murine Cell and Aging Animal Models. Foods 2023; 12:3322. [PMID: 37685254 PMCID: PMC10487224 DOI: 10.3390/foods12173322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Hippophae rhamnoides L. has been widely used in research and application for almost two decades. While significant progress was achieved in the examination of its fruits and seeds, the exploration and utilization of its by-products have received relatively less attention. This study aims to address this research gap by investigating the effects and underlying mechanisms of sea buckthorn seed residues both in vitro and in vivo. The primary objective of this study is to assess the potential of the hydroalcoholic extract from sea buckthorn seed residues (HYD-SBSR) to prevent cell apoptosis and mitigate oxidative stress damage. To achieve this, an H2O2-induced B16F10 cell model and a D-galactose-induced mouse model were used. The H2O2-induced oxidative stress model using B16F10 cells was utilized to evaluate the cellular protective and reparative effects of HYD-SBSR. The results demonstrated the cytoprotective effects of HYD-SBSR, as evidenced by reduced apoptosis rates and enhanced resistance to oxidative stress alongside moderate cell repair properties. Furthermore, this study investigated the impact of HYD-SBSR on antioxidant enzymes and peroxides in mice to elucidate its reparative potential in vivo. The findings revealed that HYD-SBSR exhibited remarkable antioxidant performance, particularly at low concentrations, significantly enhancing antioxidant capacity under oxidative stress conditions. To delve into the mechanisms underlying HYD-SBSR, a comprehensive proteomics analysis was conducted to identify differentially expressed proteins (DEPs). Additionally, a Gene Ontology (GO) analysis and an Encyclopedia of Genes and Genomes (KEGG) pathway cluster analysis were performed to elucidate the functional roles of these DEPs. The outcomes highlighted crucial mechanistic pathways associated with HYD-SBSR, including the PPAR signaling pathway, fat digestion and absorption, glycerophospholipid metabolism, and cholesterol metabolism. The research findings indicated that HYD-SBSR, as a health food supplement, exhibits favorable effects by promoting healthy lipid metabolism, contributing to the sustainable and environmentally friendly production of sea buckthorn and paving the way for future investigations and applications in the field of nutraceutical and pharmaceutical research.
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Affiliation(s)
- Zhongjie Hua
- Beijing Key Laboratory of Plant Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, China
| | - Jiachan Zhang
- Beijing Key Laboratory of Plant Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, China
| | - Wenjing Cheng
- Beijing Key Laboratory of Plant Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, China
| | - Changtao Wang
- Beijing Key Laboratory of Plant Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, China
| | - Dan Zhao
- Beijing Key Laboratory of Plant Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, China
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Ma L, Ling C, Hu S, Ye S, Chen C. High-throughput transcriptome sequencing reveals the protective role of adenosine receptor-related genes in paraquat-exposed Caenorhabditis elegans. Toxicol Res (Camb) 2023; 12:564-573. [PMID: 37663816 PMCID: PMC10470339 DOI: 10.1093/toxres/tfad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 09/05/2023] Open
Abstract
This study sought to identify the genes associated with adenosine's protective action against paraquat (PQ)-induced oxidative stress via the adenosine receptor (ADOR-1) in Caenorhabditis elegans (C. elegans). The C. elegans was divided into 3 groups-2 groups exposed to PQ, one in presence, and one in absence of adenosine-and a control group that was not treated. Each group's total RNA was extracted and sequenced. When the transcriptomes of these groups were analyzed, several genes were found to be differently expressed. These differentially expressed genes were significantly enriched in adenosine-response biological processes and pathways, including gene ontology terms related to neuropeptide and kyoto encyclopedia of genes and genomes pathways associated to cAMP pathway regulator activity. Quantitative reverse-transcription PCR confirmed that G-protein-coupled receptors signaling pathway involving dop-1, egl-30, unc-13, kin-1, and goa-1 genes may play crucial roles in modulating adenosine's protective action. Interestingly, there are no significant variations in the expression of the ador-1 gene across the 3 treatments, thereby indicating that adenosine receptor exerts a consistent and stable influence on its related pathways irrespective of the presence or absence of PQ. Furthermore, the wild-type group with ador-1 gene has higher survival rate than that of the ador-1-/RNA interference group while treated with PQ in the presence of adenosine. Conclusively, our study uncovered a number of novel PQ-response genes and adenosine receptor-related genes in C. elegans, which may function as major regulators of PQ-induced oxidative stress and indicate the possible protective effects of adenosine.
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Affiliation(s)
- Lingmei Ma
- College of Life Sciences, Engineering Training Centre/College of Innovation, China Jiliang University, Hangzhou 310018, China
| | - Chunyan Ling
- College of Life Sciences, Engineering Training Centre/College of Innovation, China Jiliang University, Hangzhou 310018, China
| | - Shuning Hu
- College of Life Sciences, Engineering Training Centre/College of Innovation, China Jiliang University, Hangzhou 310018, China
| | - Sudan Ye
- College of Applied Engineering, Zhejiang Institute of Economics and Trade, Hangzhou 310018, China
| | - Chun Chen
- College of Life Sciences, Engineering Training Centre/College of Innovation, China Jiliang University, Hangzhou 310018, China
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Huang C, Ding L, Ji J, Qiao Y, Xia Z, Shi H, Zhang S, Gan W, Zhang A. Expression profiles and potential roles of serum tRNA‑derived fragments in diabetic nephropathy. Exp Ther Med 2023; 26:311. [PMID: 37273759 PMCID: PMC10236146 DOI: 10.3892/etm.2023.12010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/29/2023] [Indexed: 06/06/2023] Open
Abstract
Diabetic nephropathy (DN) is one of the most important causes of end-stage renal disease and current treatments are ineffective in preventing its progression. Transfer RNA (tRNA)-derived fragments (tRFs), which are small non-coding fragments derived from tRNA precursors or mature tRNAs, have a critical role in various human diseases. The present study aimed to investigate the expression profile and potential functions of tRFs in DN. High-throughput sequencing technology was employed to detect the differential serum levels of tRFs between DN and diabetes mellitus and to validate the reliability of the sequencing results using reverse transcription-quantitative PCR. Ultimately, six differentially expressed (DE) tRFs were identified (P<0.05; |log2fold change| ≥1), including three upregulated (tRF5-GluCTC, tRF5-AlaCGC and tRF5-ValCAC) and three downregulated tRFs (tRF5-GlyCCC, tRF3-GlyGCC and tRF3-IleAAT). Potential functions and regulatory mechanisms of these DE tRFs were further evaluated using an applied bioinformatics-based analysis. Gene ontology analysis revealed that the DE tRFs are mainly enriched in biological processes, including axon guidance, Rad51 paralog (Rad51)B-Rad51C-Rad51D-X-Ray repair cross-complementing 2 complex, nuclear factor of activated T-cells protein binding and fibroblast growth factor-activated receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that they are associated with axon guidance, neurotrophin signaling, mTOR signaling, AMPK signaling and epidermal growth factor receptor family signaling pathways. In conclusion, the present findings indicated that tRFs were DE in DN and may be involved in the regulation of DN pathology through multiple pathways, thereby providing a new perspective for the study of DN therapeutic targets.
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Affiliation(s)
- Chan Huang
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210003, P.R. China
| | - Ling Ding
- Department of Pediatrics, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, P.R. China
| | - Jialing Ji
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210003, P.R. China
| | - Yunyang Qiao
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210003, P.R. China
| | - Zihuan Xia
- School of Pediatrics, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Huimin Shi
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210003, P.R. China
| | - Shiting Zhang
- Department of Pediatrics, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, P.R. China
| | - Weihua Gan
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210003, P.R. China
| | - Aiqing Zhang
- Department of Pediatrics, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, P.R. China
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Shao W, Cai W, Qiao F, Lin Z, Wei L. Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera). BMC Genom Data 2023; 24:5. [PMID: 36782146 PMCID: PMC9925362 DOI: 10.1186/s12863-023-01108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS). RESULTS Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)n, (AC)n, (CAA)n, (AAAC)n, (AACAA)n and (AAACAA)n, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)n, (AC)n, (TAT)n, (TTTA)n, (AACAA)n and (GAGAGG)n, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution. CONCLUSIONS Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.
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Affiliation(s)
- Weiwei Shao
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Wei Cai
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Fen Qiao
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Zhihua Lin
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Li Wei
- College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China.
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Jeyananthan P. SARS-CoV-2 Diagnosis Using Transcriptome Data: A Machine Learning Approach. SN Comput Sci 2023; 4:218. [PMID: 36844504 PMCID: PMC9936926 DOI: 10.1007/s42979-023-01703-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/24/2023] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 pandemic is the big issue of the whole world right now. The health community is struggling to rescue the public and countries from this spread, which revives time to time with different waves. Even the vaccination seems to be not prevents this spread. Accurate identification of infected people on time is essential these days to control the spread. So far, Polymerase chain reaction (PCR) and rapid antigen tests are widely used in this identification, accepting their own drawbacks. False negative cases are the menaces in this scenario. To avoid these problems, this study uses machine learning techniques to build a classification model with higher accuracy to filter the COVID-19 cases from the non-COVID individuals. Transcriptome data of the SARS-CoV-2 patients along with the control are used in this stratification using three different feature selection algorithms and seven classification models. Differently expressed genes also studied between these two groups of people and used in this classification. Results shows that mutual information (or DEGs) along with naïve Bayes (or SVM) gives the best accuracy (0.98 ± 0.04) among these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s42979-023-01703-6.
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Gillani SFA, Rasheed A, Abbasi A, Majeed Y, Abbas M, Hassan MU, Qari SH, Binothman N, Al Kashgry NAT, Tahir MM, Peng Y. Comparative Gene Enrichment Analysis for Drought Tolerance in Contrasting Maize Genotype. Genes (Basel) 2022; 14. [PMID: 36672772 DOI: 10.3390/genes14010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022] Open
Abstract
Drought stress is a significant abiotic factor influencing maize growth and development. Understanding the molecular mechanism of drought tolerance is critical to develop the drought tolerant genotype. The identification of the stress responsive gene is the first step to developing a drought tolerant genotype. The aim of the current research was to pinpoint the genes that are essential for conserved samples in maize drought tolerance. In the current study, inbred lines of maize, 478 and H21, a drought-tolerant and susceptible line, were cultivated in the field and various treatments were applied. The circumstances during the vegetative stage (severe drought, moderate drought and well-watered environments) and RNA sequencing were used to look into their origins. In 478, 68%, 48% and 32% of drought-responsive genes (DRGs) were found, with 63% of DRGs in moderate drought and severe drought conditions in H21, respectively. Gene ontology (GO) keywords were explicitly enriched in the DRGs of H21, which were considerably over-represented in the two lines. According to the results of the GSEA, "phenylpropanoid biosynthesis" was exclusively enriched in H21, but "starch and sucrose metabolism" and "plant hormone signal transduction" were enhanced in both of the two lines. Further investigation found that the various expression patterns of genes linked to the trehalose biosynthesis pathway, reactive oxygen scavenging, and transcription factors, may have a role in maize's ability to withstand drought. Our findings illuminate the molecular ways that respond to lack and offer gene resources for maize drought resistance. Similarly, SNP and correlation analysis gave us noticeable results that urged us to do the same kind of analysis on other crops. Additionally, we isolated particular transcription factors that could control the expression of genes associated to photosynthesis and leaf senescence. According to our findings, a key factor in tolerance is the equilibrium between the induction of leaf senescence and the preservation of photosynthesis under drought.
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Cheng X, Xu X, Zou C, Jiang W. Influence of verapamil on pressure overload-induced ventricular arrhythmias by regulating gene-expression profiles. Cardiovasc J Afr 2022; 33:304-312. [PMID: 35315872 PMCID: PMC10031859 DOI: 10.5830/cvja-2022-010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 02/09/2022] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Life-threatening ventricular arrhythmias can lead to sudden cardiac death in patients. This study aimed to investigate the changes in gene profiles involved when verapamil (VRP) affects increased wall stress (pressure overload)-induced ventricular arrhythmias, thus revealing the potential causative molecular mechanisms and therapeutic targets through gene-expression identification and functional analysis. METHODS Animal models with wall stress-induced ventricular arrhythmias were established. Low (0.5 mg/kg) and high (1 mg/kg) doses of VRP were administered intravenously 10 minutes before transverse aortic constriction, and average ventricular arrhythmia scores were calculated. Next, we evaluated the molecular role of VRP by characterising differential gene-expression profiles between VRP-pretreated (1 mg/kg) and control groups using RNA-sequencing technology. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal molecular function. A protein-protein interaction (PPI) network was then developed. RESULTS VRP exerted its anti-arrhythmic effects in response to increases in left ventricular (LV) afterload. We detected differentially expressed genes (DEGs), of which 36 were upregulated and 1 397 downregulated, between the VRP-pretreated and model groups during acute increases in LV wall stress. GO analysis demonstrated that the DEGs were associated with cytoskeletal protein binding. KEGG analysis showed that enriched pathways were mainly distributed in adherens junctions, actin cytoskeleton regulation and the MAPK signalling pathway. Centralities analysis of the PPI identified Rac1, Grb2, Rbm8a and Mapk1 as hub genes. CONCLUSIONS VRP prevented acute pressure overload-induced ventricular arrhythmias, possibly through the hub genes Rac1, Grb2, Rbm8a and Mapk1 as potential targets of VRP.
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Affiliation(s)
- Xianfeng Cheng
- Department of Cardiac Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Cardiac Surgery, Weifang People's Hospital, Weifang, Shandong, China
| | - Xue Xu
- Department of Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Cardiology, Peking University People's Hospital, Beijing, China
| | - Chengwei Zou
- Department of Cardiac Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Weidong Jiang
- Department of Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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Gillani SFA, Zhuang Z, Rasheed A, Haq IU, Abbasi A, Ahmed S, Wang Y, Khan MT, Sardar R, Peng Y. Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels. Front Plant Sci 2022; 13:961680. [PMID: 36388543 PMCID: PMC9641234 DOI: 10.3389/fpls.2022.961680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The present study investigated the brassinosteroid-induced drought resistance of contrasting drought-responsive maize genotypes at physiological and transcriptomic levels. The brassinosteroid (BR) contents along with different morphology characteristics, viz., plant height (PH), shoot dry weight (SDW), root dry weight (RDW), number of leaves (NL), the specific mass of the fourth leaf, and antioxidant activities, were investigated in two maize lines that differed in their degree of drought tolerance. In response to either control, drought, or brassinosteroid treatments, the KEGG enrichment analysis showed that plant hormonal signal transduction and starch and sucrose metabolism were augmented in both lines. In contrast, the phenylpropanoid biosynthesis was augmented in lines H21L0R1 and 478. Our results demonstrate drought-responsive molecular mechanisms and provide valuable information regarding candidate gene resources for drought improvement in maize crop. The differences observed for BR content among the maize lines were correlated with their degree of drought tolerance, as the highly tolerant genotype showed higher BR content under drought stress.
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Affiliation(s)
| | - Zelong Zhuang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Adnan Rasheed
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Crop Breeding Department, Jilin Changfa Modern Agricultural Science and Technology Group, co., Ltd., Changchun, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, Pakistan
| | - Shakil Ahmed
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yinxia Wang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Muhammad Tajammal Khan
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Rehana Sardar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yunling Peng
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
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Zhou J, Qiu Y, Zhao J, Wang Y, Zhu N, Wang D, Cui Y, Guo J, Sun T, Ji Y, Wu Z, Zeng P, Li J, Feng X, Hou L, Liu J. The Network of Interactions between the Porcine Epidemic Diarrhea Virus Nucleocapsid and Host Cellular Proteins. Viruses 2022; 14:2269. [PMID: 36298827 DOI: 10.3390/v14102269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Host–virus protein interactions are critical for intracellular viral propagation. Understanding the interactions between cellular and viral proteins may help us develop new antiviral strategies. Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe damage to the global swine industry. Here, we employed co-immunoprecipitation and liquid chromatography-mass spectrometry to characterize 426 unique PEDV nucleocapsid (N) protein-binding proteins in infected Vero cells. A protein–protein interaction network (PPI) was created, and gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses revealed that the PEDV N-bound proteins belong to different cellular pathways, such as nucleic acid binding, ribonucleoprotein complex binding, RNA methyltransferase, and polymerase activities. Interactions of the PEDV N protein with 11 putative proteins: tripartite motif containing 21, DEAD-box RNA helicase 24, G3BP stress granule assembly factor 1, heat shock protein family A member 8, heat shock protein 90 alpha family class B member 1, YTH domain containing 1, nucleolin, Y-box binding protein 1, vimentin, heterogeneous nuclear ribonucleoprotein A2/B1, and karyopherin subunit alpha 1, were further confirmed by in vitro co-immunoprecipitation assay. In summary, studying an interaction network can facilitate the identification of antiviral therapeutic strategies and novel targets for PEDV infection.
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Fan M, Zhang G, Xie M, Liu X, Zhang Q, Wang L. Siglec-15 as a New Perspective Therapy Target in Human Giant Cell Tumor of Bone. Curr Oncol 2022; 29:7655-71. [PMID: 36290882 DOI: 10.3390/curroncol29100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/13/2023] Open
Abstract
The main features of a giant cell tumor of bone (GCTB) are frequent recurrence and aggressive osteolysis, which leads to a poor prognosis in patients. Although the treatment methods for a GCTB, such as scraping and resection, effectively inhibit the disease, the tendency toward malignant transformation remains. Therefore, it is important to identify new treatment methods for a GCTB. In this study, we first found high Siglec-15 expression in GCTB tissues, which was significantly associated with Campanacci staging and tumor recurrence. In Spearman's analysis, Siglec-15 expression was significantly correlated with Ki-67 levels in tumor tissues. In vitro, the mRNA and protein levels of Siglec-15 were high in GCTB stromal cells (Hs737. T), and Siglec-15 knockdown inhibited the biological characteristics of GCTB stromal cells. The RNA sequencing results enabled a prediction of the downstream genes by using the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and MCODE analyses, and the findings showed that CXCL8 was significantly regulated by Siglec-15 and might be a promising downstream target gene of Siglec-15. Therefore, Siglec-15 may be a potential immunotherapy target for a GCTB.
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Tang B, Xie L, Yang H, Li X, Chen Y, Zou X, Liu F, Dai X. Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress. Front Plant Sci 2022; 13:852511. [PMID: 35599873 PMCID: PMC9116226 DOI: 10.3389/fpls.2022.852511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.
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Affiliation(s)
- Bingqian Tang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Lingling Xie
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Huiping Yang
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xiumin Li
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Ying Chen
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Feng Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xiongze Dai
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
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Pradeepkumara N, Sharma PK, Munshi AD, Behera TK, Bhatia R, Kumari K, Singh J, Jaiswal S, Iquebal MA, Arora A, Rai A, Kumar D, Bhattacharya RC, Dey SS. Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber. Genomics 2022; 114:110273. [PMID: 35092817 DOI: 10.1016/j.ygeno.2022.110273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Affiliation(s)
- N Pradeepkumara
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jogendra Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - R C Bhattacharya
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Zhu F, Zuo L, Hu R, Wang J, Yang Z, Qi X, Feng L. A ten-genes-based diagnostic signature for atherosclerosis. BMC Cardiovasc Disord 2021; 21:513. [PMID: 34688276 PMCID: PMC8540101 DOI: 10.1186/s12872-021-02323-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/12/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Atherosclerosis is the leading cause of cardiovascular disease with a high mortality worldwide. Understanding the atherosclerosis pathogenesis and identification of efficient diagnostic signatures remain major problems of modern medicine. This study aims to screen the potential diagnostic genes for atherosclerosis. METHODS We downloaded the gene chip data of 135 peripheral blood samples, including 57 samples with atherosclerosis and 78 healthy subjects from GEO database (Accession Number: GSE20129). The weighted gene co-expression network analysis was applied to identify atherosclerosis-related genes. Functional enrichment analysis was conducted by using the clusterProfiler R package. The interaction pairs of proteins encoded by atherosclerosis-related genes were screened using STRING database, and the interaction network was further optimized with the cytoHubba plug-in of Cytoscape software. RESULTS The logistic regression diagnostic model was constructed to predict normal and atherosclerosis samples. A gene module which included 532 genes related to the occurrence of atherosclerosis were screened. Functional enrichment analysis basing on the 532 genes identified 235 significantly enriched GO terms and 44 significantly enriched KEGG pathways. The top 50 hub genes of the protein-protein interaction network were identified. The final logistic regression diagnostic model was established by the optimal 10 key genes, which could distinguish atherosclerosis samples from normal samples. CONCLUSIONS A predictive model based on 10 potential atherosclerosis-related genes was obtained, which should shed light on the diagnostic research of atherosclerosis.
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Affiliation(s)
- Feng Zhu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Department of Traditional Chinese Medicine, Hebei North University, Zhangjiakou City, Hebei Province, China.,Department of Cardiology, Tianjin Union Medical Center, Tianjin, China
| | - Lili Zuo
- Department of Neonatal, ZiBo Maternal and Child Health Hospital, Zibo City, Shandong Province, China
| | - Rui Hu
- Center for Drug Monitoring and Evaluation Department, Center for Drug Monitoring and Evaluation in Zhangjiakou, Zhangjiakou City, Hebei Province, China
| | - Jin Wang
- Department of Cardiovascular Disease, ZiBo Hospital of Traditional Chinese Medicine, Zibo City, Shandong Province, China
| | - Zhihua Yang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xin Qi
- Department of Cardiology, Tianjin Union Medical Center, Tianjin, China
| | - Limin Feng
- Department of Cardiology, The Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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Vatanparast M, Park Y. Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress. Genes (Basel) 2021; 12:genes12101610. [PMID: 34681004 PMCID: PMC8535336 DOI: 10.3390/genes12101610] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022] Open
Abstract
Solenopsis japonica, as a fire ant species, shows some predatory behavior towards earthworms and woodlice, and preys on the larvae of other ant species by tunneling into a neighboring colony's brood chamber. This study focused on the molecular response process and gene expression profiles of S. japonica to low (9 °C)-temperature stress in comparison with normal temperature (25 °C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. The results were 81 GO subgroups and 18 EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) keywords. Differentially expressed genes (DEGs) with log2fold change (FC) > 1 and log2FC < -1 with p-value ≤ 0.05 were screened for cold stress temperature. We found 215 unigenes up-regulated and 115 unigenes down-regulated. Comparing transcriptome profiles for differential gene expression resulted in various DE proteins and genes, including fatty acid synthases and lipid metabolism, which have previously been reported to be involved in cold resistance. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings facilitate the basis for the future understanding of the adaptation mechanisms of S. japonica and the molecular mechanisms underlying the response to low temperatures.
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Tang F, Zhang L, Xu L, Zou Q, Feng H. The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis. Brief Bioinform 2021; 22:6295810. [PMID: 34113984 DOI: 10.1093/bib/bbab227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/24/2021] [Indexed: 12/16/2022] Open
Abstract
Cancerlectins, lectins linked to tumor progression, have become the focus of cancer therapy research for their carbohydrate-binding specificity. However, the specific characterization for cancerlectins involved in tumor progression is still unclear. By taking advantage of the g-gap tripeptide and tetrapeptide composition feature descriptors, we increased the accuracy of the classification model of cancerlectin and lectin to 98.54% and 95.38%, respectively. About 36 cancerlectin and 135 lectin features were selected for functional characterization by P/N feature ranking method, which particularly selects the features in positive samples. The specific protein domains of cancerlectins are found to be p-GalNAc-T, crystal and annexin by comparing with lectins through the exclusion method. Moreover, the combined GO analysis showed that the conserved cation binding sites of cancerlectin specific domains are covered by selected feature peptides, suggesting that the capability of cation binding, critical for enzyme activity and stability, could be the key characteristic of cancerlectins in tumor progression. These results will help to identify potential cancerlectin and provide clues for mechanism study of cancerlectin in tumor progression.
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Affiliation(s)
- Furong Tang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen 518000, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen 518172, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen 518000, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hailin Feng
- School of Information Engineering Zhejiang A&F University, Key Laboratory of Forestry Intelligent Monitoring and Information Technology of Zhejiang Province, Hangzhou, Zhejiang 311300, China
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Zhou P, Xiang CX, Wei JF. The clinical significance of spondin 2 eccentric expression in peripheral blood mononuclear cells in bronchial asthma. J Clin Lab Anal 2021; 35:e23764. [PMID: 33998076 PMCID: PMC8183911 DOI: 10.1002/jcla.23764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Bronchial asthma (BA) was a heterogeneous disease characterized by chronic airway inflammation. Spondin 2 (SPON2) was reported to be implicated in the integrin pathway, protein metabolism, and drug‐induced lupus erythematosus. The purpose of this study was to evaluate the significance of SPON2 in BA diagnosis and treatment. Methods Peripheral blood samples were obtained from 137 BA pediatric patients (61 mild‐to‐moderate BA and 76 severe BA) and 59 healthy children. Subject's information, clinical indexes, pulmonary ventilation functions were recorded in the two groups. Peripheral blood mononuclear cells (PBMCs) were isolated from patients’ samples. qRT‐PCR and ELISA assays were employed to examine the levels of SPON2 and inflammatory cytokines, respectively. Pearson's correlation analysis confirmed the association between SPON2 and inflammatory cytokines. Receiver operating characteristic (ROC) analysis was used to evaluate the potentials of SPON2 in terms of BA detection and discriminating against the severity of BA. Results Bioinformatics analysis showed that SPON2, OLFM4, XIST, and TSIX were significantly upregulated, while KDM5D and RPS4Y1 were reduced in BA. GO analysis verified that these six genes were mainly involved in neutrophil degranulation, neutrophil activation involved in immune response, neutrophil activation, and neutrophil‐mediated immunity. After isolating PBMCs, we found that SPON2 was remarkably increased in BA pediatric group compared with healthy children, and the relative levels of SPON2 were related to the severity of BA. The receiver operating characteristic (ROC) analysis revealed the high potentials of SPON2 in BA diagnosis (AUC was 0.8080) and severity distinctions (AUCs were 0.7341 and 0.8541, respectively). Also, we found that there were significant differences in fractional exhaled nitric oxide (FeNO), forced expiratory volume in 1 s (FEV1)%, FEV1/ forced vital capacity (FVC)%, immunoglobulin E (IgE), serum eosinophils, and serum neutrophils between mild‐to‐moderate BA group and severe BA group. Finally, SPON2 was negatively correlated with IL‐12 while positively associated with IL‐4, IL‐13, and IL‐17A. Conclusions SPON2 was a viable biomarker for diagnosing and degree of severity in BA, providing more insight into exploring BA and treatment's pathogenesis.
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Affiliation(s)
- Peng Zhou
- Department of Pediatric, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Shengzhou, China
| | - Cai-Xia Xiang
- Department of Pediatric, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Shengzhou, China
| | - Jin-Feng Wei
- Department of Respiratory, Hangzhou Children's Hospital, Hangzhou, China
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21
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Zhai Z, Tao X, Alami MM, Shu S, Wang X. Network Pharmacology and Molecular Docking Combined to Analyze the Molecular and Pharmacological Mechanism of Pinellia ternata in the Treatment of Hypertension. Curr Issues Mol Biol 2021; 43:65-78. [PMID: 34062719 DOI: 10.3390/cimb43010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 12/13/2022] Open
Abstract
Hypertension is a cardiovascular disease that causes great harm to health and life, affecting the function of important organs and accompanied by a variety of secondary diseases, which need to be treated with drugs for a long time. P. ternata alone or combination with western medicine has played an important role in traditional Chinese medicine. Although P. ternata is used clinically to treat hypertension, its functional molecular mechanism and pharmacological mechanism have not been elucidated. Therefore, in this study, the potentially effective components, and targets of P. ternata in the treatment of hypertension were screened by the method of network pharmacology, and the mechanism of P. ternata in the treatment of hypertension was analyzed by constructing a component-target relationship network, PPI interaction network, targets’ function analysis, and molecular docking. In the study, 12 potentially effective components and 88 targets were screened, and 3 potential protein modules were found and analyzed after constructing a PPI network using targets. In addition, 10 targets were selected as core targets of the PPI network. After that, the targets were analyzed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, the molecular docking method is used to study the interaction between the targets and the active components. The above evidence shows that the mechanism of P. ternata in the treatment of hypertension is complicated, as it acts in many ways, mainly by affecting nerve signal transmission, cell proliferation, and apoptosis, calcium channels, and so on. The binding between targets and active components mainly depends on Pi bonds and hydrogen bonds. Using the method of network pharmacology and molecular docking to analyze the mechanism of P. ternata in the treatment of hypertension will help to provide a better scientific basis for the combined use of traditional Chinese medicine and western medicine, and will better help to improve the quality of P. ternata and point out its direction.
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Grummer JA, Whitlock MC, Schulte PM, Taylor EB. Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss). BMC Ecol Evol 2021; 21:63. [PMID: 33888062 PMCID: PMC8063319 DOI: 10.1186/s12862-021-01795-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01795-9.
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Affiliation(s)
- Jared A Grummer
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Michael C Whitlock
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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Wu Y, Ding Y, Wang J, Wang X. Determination of the key ccRCC-related molecules from monolayer network to three-layer network. Cancer Genet 2021; 256-257:40-7. [PMID: 33887693 DOI: 10.1016/j.cancergen.2021.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 03/08/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC), with an increasing incidence rate, is one of the ubiquitous cancers. Its pathogenic factors are complicated and the molecular mechanism is not clear. It is essential to analyze the potential key genes related to ccRCC carcinogenesis. In this study, the differentially expressed mRNAs, miRNAs and lncRNAs (DEmRNAs, DEmiRNAs and DElncRNAs) of ccRCC were screened from TCGA database. Then the miRNA-mRNA network, lncRNA-miRNA network and lncRNA-mRNA network were constructed by online database or WGCNA algorithm. Topology attributes of these monolayer networks showed that hsa-mir-155, hsa-mir-200c, hsa-mir-122, hsa-mir-506, hsa-mir-216b, hsa-mir-141, lncRNA AC137723.1 and AC021074.3 are the crucial genes related with the regulatory effects on the proliferation, metastasis and invasion of ccRCC cells. Subsequently, these three monolayer networks were integrated into a lncRNA-miRNA-mRNA multilayer network. Considering node degree, closeness centrality and betweenness centrality, we found hsa-mir-122 is screened out as the only crucial gene in three-layer network. In order to better illustrate the effect of hsa-mir-122 on ccRCC, the lncRNA-hsa-mir-122-mRNA network was constructed with hsa-mir-122 as the center. Pathway analysis of the unique target gene GALNT3 linked to hsa-mir-122 showed that GALNT3 influenced the metabolic process of mucin type O-Glycan biosynthesis. LncRNA AC090377.1 is the unique gene that has target genes among lncRNAs with clinical significance that linked to hsa-mir-122 in the lncRNA-hsa-mir-122-mRNA network. Pathway analysis of AC090377.1 suggested that GUCY2F enriched in phototransduction pathway associated with retina. From monolayer network to three-layer network, hsa-mir-122 is identified as an important molecule in the oncogenesis and progression of ccRCC, offering new strategies to further study of the carcinogenic mechanism of ccRCC.
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Yao MD, Zhu Y, Zhang QY, Zhang HY, Li XM, Jiang Q, Yan B. CircRNA expression profile and functional analysis in retinal ischemia-reperfusion injury. Genomics 2021; 113:1482-1490. [PMID: 33771636 DOI: 10.1016/j.ygeno.2021.03.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/09/2021] [Accepted: 03/21/2021] [Indexed: 12/30/2022]
Abstract
Retinal ischemia-reperfusion (I/R) is involved in the pathogenesis of many vision-threatening diseases. circRNAs act as key players in gene regulation and human diseases. However, the global circRNA expression profile in retinal I/R injury has not been fully uncovered. Herein, we established a murine model of retinal I/R injury and performed circRNA microarrays to identify I/R-related circRNAs. 1265 differentially expressed circRNAs were identified between I/R retinas and normal retinas. Notably, the detection of cWDR37 level in aqueous humor could discriminate glaucoma patients from cataract patients (AUC = 0.9367). cWdr37 silencing protected against hypoxic stress- or oxidative stress-induced retinal ganglion cell (RGC) injury. cWdr37 silencing alleviated IR-induced retinal neurodegeneration as shown by increased NeuN staining, reduced retinal reactive gliosis, and decreased retinal apoptosis. Collectively, this study provides a novel insight into the pathogenesis of retinal I/R injury. cWdr37 is a promising target for the diagnosis or treatment of I/R-related ocular diseases.
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Affiliation(s)
- Mu-Di Yao
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Zhu
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qiu-Yang Zhang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Hui-Ying Zhang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China; The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China.
| | - Biao Yan
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, China; Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, China.
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25
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Wu X, Yang W, Gou XH, Xu XY, Lu N, Jian SN, Han YJ, Lv TS, Luo LZ. A study of the proteomic expression in patients with complicated parapneumonic pleural effusion. Arch Med Sci 2021; 19:1270-1280. [PMID: 37732066 PMCID: PMC10507766 DOI: 10.5114/aoms/132885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/27/2021] [Indexed: 09/22/2023] Open
Abstract
Introduction The present study aimed to investigate the differences in the proteomic expression between uncomplicated parapneumonic pleural effusion (UPPE) and complicated parapneumonic pleural effusion (CPPE). Material and methods There were 10 patients with UPPE and 10 patients with CPPE. These patients were combined due to the complication of pleural effusion and further divided into group A and group B. An LC-MS analysis was conducted with the extraction of high-abundance proteins, and proteins with 1.5-fold or higher difference multiples were identified as differential proteins. Then, gene ontology (GO) and KEGG analyses were conducted on the differential proteins between the groups. Results Compared with the UPPE group, there were 38 upregulated proteins and 29 downregulated proteins in the CPPE group. The GO analysis revealed that the CPPE group had enhanced expressions in monosaccharide biosynthesis, glucose catabolism, fructose-6-phosphate glycolysis, glucose-6-phosphate glycolysis, and NADH regeneration as well as reduced expressions in fibrinogen complexes, protein polymerization, and coagulation. Moreover, the KEGG analysis showed that the CPPE group had enhanced expressions in amino acid synthesis, the HIF-1 signalling pathway, and glycolysis/glycoisogenesis and decreased expressions in platelet activation and complement activation. Conclusions In pleural effusion in patients with CPPE, there are enhanced expressions of proteins concerning glucose and amino acid metabolism, NADH regeneration, and HIF-1 signalling pathways together with decreased expressions of proteins concerning protein polymerization, blood coagulation, platelet activation, and complement activation.
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Affiliation(s)
- Xin Wu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Wei Yang
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Hua Gou
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Yun Xu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Na Lu
- Department of Respiration, Lixian County Hospital, HeBei, China
| | - Shi-Ning Jian
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Yu-Jie Han
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Tong-Shuai Lv
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Li-Zhu Luo
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
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Liang HB, Li R, Yao JC, Qin GF, Zhang H, Zhang GM. [Mechanism of Shouhui Tongbian Capsules in treating constipation based on network pharmacology and molecular docking]. Zhongguo Zhong Yao Za Zhi 2021; 46:511-519. [PMID: 33645014 DOI: 10.19540/j.cnki.cjcmm.20201117.406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To explore the mechanism of Shouhui Tongbian Capsules in treating constipation by means of network pharmacology and molecular docking approach. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) and Bioinfoematics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine(BATMAN) were applied to obtain chemical components and potential targets of eight herbs in Shouhui Tongbian Capsules according to the screening principles of oral availability(OB)≥30% and drug-like property(DL)≥0.18. Disease targets relating to constipation were screened out through GeneCards, PharmGkb and other databases, drug targets were integrated with disease targets, and intersection targets were exactly the potential action targets of Shouhui Tongbian Capsules for treating constipation; PPI network of potential targets was constructed using STRING platform, and GO(gene ontology) analysis and KEGG(Kyoto encyclopedia of genes and genomes) pathway data were obtained to conduct enrichment analysis and predict its mechanism of action. Cytoscape 3.6.1 was used to construct a network of "medicinal materials-chemical components-drug targets", and the network topology analysis was carried out on the PPI network to obtain its main components and key targets. Molecular docking between components and key targets of Shouhui Tongbian Capsules verified the accuracy of network pharmacological analysis results. The PPI network analysis showed 92 chemical components, including quercetin, stigmaste-rol, aloe-emodin, rhein, and key targets for instance AKT1, MAPK1, IL6, JUN, TNF and TP53. The enrichment analysis of KEGG screened out 157 signal pathways(P<0.01), mainly involving interleukin 17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, thyroid hormone signaling pathway. Quercetin, resveratrol and lysine with top degree value had a rational conformation in docking site of protein crystal complexes. This study preliminarily showed that various active ingredients in Shouhui Tongbian Capsules could regulate multiple signaling pathways, increase intestinal smoothness and peristalsis function, ensure smooth intestinal lumen, and play a role in treating constipation by acting on key targets, such as AKT1, MAPK1, IL6 and JUN.
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Affiliation(s)
- Hong-Bao Liang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd. Linyi 276006, China
| | - Rui Li
- Shandong New Time Pharmaceutical Co., Ltd. Linyi 276006, China
| | - Jing-Chun Yao
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd. Linyi 276006, China
| | - Guo-Fei Qin
- Shandong New Time Pharmaceutical Co., Ltd. Linyi 276006, China
| | - Hao Zhang
- Shandong New Time Pharmaceutical Co., Ltd. Linyi 276006, China
| | - Gui-Min Zhang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd. Linyi 276006, China
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Singh P, Mishra AK, Singh CM. Genome-wide identification and characterization of Lectin receptor-like kinase (LecRLK) genes in mungbean (Vigna radiata L. Wilczek). J Appl Genet 2021; 62:223-234. [PMID: 33469874 DOI: 10.1007/s13353-021-00613-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/26/2020] [Accepted: 01/11/2021] [Indexed: 11/28/2022]
Abstract
Lectins are a diverse group of proteins found throughout plant species. Numerous lectins are involved in many important processes such as organogenesis, defense mechanism, signaling, and stress response. Although the mungbean whole genome sequence has been published, distribution, diversification, and gene structure of lectin genes in mungbean are still unknown. A total of 73 putative lectin genes with kinase domain have been identified through BLAST and HMM profiling. Furthermore, these sequences could be classified into three families, such as G-type, L-type, and C-type VrLecRLKs. 59 out of 73 VrLecRLKs were distributed on to 11 chromosomes, whereas rest could not be anchored onto any specific chromosome. Gene structure analysis revealed a varying number of exons in 73 VrLecRLK genes. Gene ontology annotations were grouped into three categories like biological processes, cellular components and molecular functions, which were associated with signaling pathways, defense responses, transferase activity, binding activity, and kinase activity. The comprehensive and systematic studies of LecRLK genes family provides a reference and foundation for further functional analysis of VrLecRLK genes in mungbean.
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Affiliation(s)
- Poornima Singh
- Department of Biotechnology, School of Life Sciences, Mahatma Gandhi Central University, Motihari, Bihar, 845401, India
| | | | - Chandra Mohan Singh
- Department of Genetics and Plant Breeding, College of Agriculture, Banda University of Agriculture and Technology, Banda, Uttar Pradesh, 210 001, India.
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Wang P, Yang X, Zhou N, Wang J, Li Y, Liu Y, Xu X, Wei W. Identifying a Potential Key Gene, TIMP1, Associated with Liver Metastases of Uveal Melanoma by Weight Gene Co-Expression Network Analysis. Onco Targets Ther 2020; 13:11923-11934. [PMID: 33239893 PMCID: PMC7682792 DOI: 10.2147/ott.s280435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Uveal melanoma (UM) is a primary intraocular tumor in adults, with a high percentage of metastases to the liver. Identifying potential key genes may provide information for early detection and prognosis of UM metastasis. Patients and Methods Differentially expressed genes (DEGs) were identified using the GSE22138 dataset. Weighted gene co-expression network analysis was used to construct co-expression modules. Functional enrichment analysis was performed for DEGs and genes of key modules. Hub genes were screened by co-expression network and protein–protein interaction network (PPI), and validated by survival analysis in The Cancer Genome Atlas database. Gene set enrichment analysis (GSEA) was used to explore the potential metastasis mechanism of UM. Transient transfection was used to investigate the effect of TIMP1 on the proliferation, migration, and invasion of UM cells. Results In total, 552 DEGs were identified between primary and metastatic UM and mainly enriched in extracellular matrix, cellular senescence and focal adhesion pathway. A weighted gene co‑expression network was built to identify key gene modules associated with UM metastasis (n=36). The turquoise module is positively correlated with metastasis and genes in this module were mainly enriched in peptidyl-tyrosine autophosphorylation and regulation of organ growth. The hub gene TIMP1 was screened out by co-expression network and PPI analysis. High expression of TIMP1 was related to p53 pathway by GSEA and short overall survival time. Experimental results indicated that overexpression of TIMP1 inhibited the proliferation and migration, while it had no significant effect on invasion of UM cells. Conclusion Our study indicates that TIMP1 might be associated with metastasis in UM, which might have important significance for identifying patients with high risk of metastasis and predicting the prognosis of UM.
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Affiliation(s)
- Ping Wang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Xuan Yang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Nan Zhou
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Jinyuan Wang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Yang Li
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Yueming Liu
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Xiaolin Xu
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
| | - Wenbin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, People's Republic of China
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Zheng WQ, Zhang Y, Chen B, Wei M, Wang XW, Du L. [Identification and Characterization of circRNAs in the Developing Stem Cambium of Poplar Seedlings]. Mol Biol (Mosk) 2020; 54:802-812. [PMID: 33009790 DOI: 10.31857/s0026898420050134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/05/2020] [Indexed: 11/24/2022]
Abstract
Non-coding RNAs are a class of RNAs with multiple roles in plant life. Covalently closed circular RNA molecules (circRNAs) have been recently shown to be a group of RNA isoforms that show widespread tissue-specific expression in plants, often cooperating with the corresponding linear mRNAs to regulate gene function. However, no previous study of poplar has identified circRNAs in the cambium and determined their potential roles in the cambium or xylem development. In the present study, we sequenced RNAs in the cambium of poplar seedlings at two developmental stages, and identified and characterized 4912 circRNAs. Alternative back-splicing circularization events for 87 genes were identified among the circRNAs derived from different chromosomes. A total of 1138 circRNAs originated from 928 host genes, which were classified among the three major functional categories by GO analysis. Thirty-nine circRNAs were differentially expressed between cambium samples of stems at two developmental stages. Twenty-four DEcircRNAs interacted with 98 miRNAs as targets, of which some were associated with cambium growth and development. The results suggest that circRNAs play important roles in the cambium in relation to the regulation of stem growth and development in poplar seedlings.
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Affiliation(s)
- W Q Zheng
- Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 China
| | - Y Zhang
- Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 China
| | - B Chen
- Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 China
| | - M Wei
- COFCO Nutrition and Health Research Institute, Beijing, 102209 China
| | - X W Wang
- Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 China
| | - L Du
- Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 China.,
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Sun YN, Liu B, Wang JJ, Li XM, Zhu JY, Liu C, Yao J, Zhong YL, Jiang Q, Yan B. Identification of aberrantly expressed circular RNAs in hyperlipidemia-induced retinal vascular dysfunction in mice. Genomics 2020; 113:593-600. [PMID: 32991963 DOI: 10.1016/j.ygeno.2020.09.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Hyperlipidemia-induced retinal vascular dysfunction is a complex pathological process. circRNAs are important regulators of biological processes and disease progression. However, the expression pattern of circRNAs in hyperlipidemia-induced retinal vascular dysfunction remains unclear. Herein, we used a murine model of hyperlipidemia and identified 317 differentially expressed circRNAs between hyperlipidemic retinas and normolipidemic retinas by circRNA microarrays. GO analysis indicated that the host genes of dysregulated circRNAs were targeted to cell differentiation (ontology: biological process), cytoplasm (ontology: cellular component), and protein binding (ontology: molecular function). Pathway analysis revealed that circRNAs-mediated network was mostly enriched in focal adhesion signaling. Notably, circLDB1 was significantly up-regulated in the serum of coronary artery disease patients and aqueous humor of age-related macular degeneration patients. circLDB1 regulated endothelial cell viability, proliferation, and apoptosis in vitro. Thus, circRNAs are the promising targets for the prediction and diagnosis of hyperlipidemia-induced vascular diseases.
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Affiliation(s)
- Ya-Nan Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Ban Liu
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jia-Jian Wang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Xiu-Miao Li
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Jun-Ya Zhu
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Chang Liu
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Jin Yao
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yu-Ling Zhong
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.
| | - Biao Yan
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China; NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai 200031, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai 200031, China.
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Song SQ, Ma WW, Zeng SX, Zhang CL, Yan J, Sun CC, Li X, Wang RM, Li ZQ. Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing. Biosci Rep 2019; 39:BSR20192144. [PMID: 31755521 DOI: 10.1042/BSR20192144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022] Open
Abstract
RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology.
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Li H, Huang X, Li W, Lu Y, Dai X, Zhou Z, Li Q. MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation. Plant Cell Rep 2020; 39:1199-1217. [PMID: 32577818 DOI: 10.1007/s00299-020-02559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/12/2020] [Indexed: 05/22/2023]
Abstract
MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.
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Affiliation(s)
- Hui Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanfeng Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Zaizhi Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Abstract
BACKGROUND The mechanism of diabetes and cataracts is complicated. Considering our increasing acknowledge of exosomes, exosomal miRNAs isolated from aqueous humour (AH) may play an important role in the mechanism of diabetes and cataracts. Our study aimed to isolate exosomes from human aqueous humour and study the functions of exosomal miRNAs on human lens epithelial cells (HLECs). RESULTS MiRNA sequencing revealed that 295 miRNAs were upregulated and 138 miRNAs were downregulated in exosomes of the diabetes and cataracts group (DMC) compared with the age-related cataracts group (ARC), among which miR-551b was highly expressed with a log2 fold change of 5.99. GO and KEGG analyses indicated that the predicted genes were mainly involved in cadherin binding, proteoglycans in cancer and AGE-RAGE signalling pathway in diabetic complications. We then examined the function of miR-551b and found that miR-551b reduced the viability and increased the apoptosis of HLECs by downregulating CRYAA expression. CONCLUSIONS Exosomes isolated from human aqueous humour contained abundant miRNAs. A highly expressed miRNA, miR-551b, could regulate the functions of HLEC by targeting CRYAA. METHODS We pooled all the aqueous humour of each group into one sample and isolated exosomes from human aqueous humour by ultracentrifugation, measured the size and concentration of exosomes by nanoparticle tracking analysis (NTA), observed the morphology of exosomes by transmission electron microscopy (TEM), and sequenced exosomal miRNAs. We performed bioinformatic analysis of the sequencing results, including GO analysis and KEGG pathway enrichment. We then examined CRYAA mRNA expression levels and protein levels by quantitative real-time PCR and Western blot. Cell Counting Kit-8 and flow cytometry were applied to examine cell viability, proliferation and apoptosis.
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Affiliation(s)
- Chao Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Fan Fan
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Xin Liu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Jianing Yang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Xiyue Zhou
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Hengjun Mei
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Xiaolei Lin
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
| | - Yi Luo
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University , Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University , Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality , Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission , Shanghai, China
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Pathak RK, Baunthiyal M, Pandey D, Kumar A. Computational analysis of microarray data of Arabidopsis thaliana challenged with Alternaria brassicicola for identification of key genes in Brassica. J Genet Eng Biotechnol 2020; 18:17. [PMID: 32607787 PMCID: PMC7326868 DOI: 10.1186/s43141-020-00032-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/30/2020] [Indexed: 11/10/2022]
Abstract
Background Alternaria blight, a recalcitrant disease caused by Alternaria brassicae and Alternaria brassicicola, has been recognized for significant losses of oilseed crops especially rapeseed-mustard throughout the world. Till date, no resistance source is available against the disease; hence, plant breeding methods cannot be used to develop disease-resistant varieties. Therefore, in the present study, efforts have been made to identify resistance and defense-related genes as well as key components of JA-SA-ET-mediated pathway involved in resistance against Alternaria brasscicola through computational analysis of microarray data and network biology approach. Microarray profiling data from wild type and mutant Arabidopsis plants challenged with Alternaria brassicicola along with control plant were obtained from the Gene Expression Omnibus (GEO) database. The data analysis, including DEGs extraction, functional enrichment, annotation, and network analysis, was used to identify genes associated with disease resistance and defense response. Results A total of 2854 genes were differentially expressed in WT9C9; among them, 1327 genes were upregulated and 1527 genes were downregulated. A total of 1159 genes were differentially expressed in JAM9C9; among them, 809 were upregulated and 350 were downregulated. A total of 2516 genes were differentially expressed in SAM9C9; among them, 1355 were upregulated and 1161 were downregulated. A total of 1567 genes were differentially expressed in ETM9C9; among them, 917 were upregulated and 650 were downregulated. Besides, a total of 2965 genes were differentially expressed in contrast WT24C24; among them, 1510 genes were upregulated and 1455 genes were downregulated. A total of 4598 genes were differentially expressed in JAM24C24; among them, 2201 were upregulated and 2397 were downregulated. A total of 3803 genes were differentially expressed in SAM24C24; among them, 1819 were upregulated and 1984 were downregulated. A total of 4164 genes were differentially expressed in ETM24C24; among them, 1895 were upregulated and 2269 were downregulated. The upregulated genes of Arabidopsis thaliana were mapped and annotated with CDS sequences of Brassica rapa obtained from PlantGDB database. Additionally, PPI network of these genes were constructed to investigate the key components of hormone-mediated pathway involved in resistance during pathogenesis. Conclusion The obtained information from present study can be used to engineer resistance to Alternaria blight caused by Alternaria brasscicola through molecular breeding or genetic manipulation-based approaches for improving Brassica oilseed productivity.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, 246194, India
| | - Mamta Baunthiyal
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand, 246194, India.
| | - Dinesh Pandey
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, 263145, India
| | - Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, 284003, India.
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Yang YJ, Wang Z, Zheng RX, Li Y, Wang L, Liu YM, Wang X, Su R, Dai QH, Liu C. DNA microarray analysis of dendritic cells infected by enterovirus 71. J BIOL REG HOMEOS AG 2020; 34:577-583. [PMID: 32549552 DOI: 10.23812/19-409-l-52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Y J Yang
- Graduate School, Tianjin Medical University, Tianjin, China.,Department of Infectious Diseases, Tianjin Second People's Hospital, Tianjin, China
| | - Z Wang
- Department of Infectious Diseases, Tianjin Second People's Hospital, Tianjin, China
| | - R X Zheng
- Department of Pediatric, Tianjin Medical University General Hospital, Tianjin, China
| | - Y Li
- Department of Infectious Diseases, Tianjin Second People's Hospital, Tianjin, China
| | - L Wang
- Department of Pharmacy, Tianjin Second People's Hospital, Tianjin, China
| | - Y M Liu
- Department of Infectious Diseases, Tianjin Second People's Hospital, Tianjin, China
| | - X Wang
- Department of Infectious Diseases, Tianjin Second People's Hospital, Tianjin, China
| | - R Su
- Viral immunology Laboratory, Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, China
| | - Q H Dai
- Viral immunology Laboratory, Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, China
| | - C Liu
- Viral immunology Laboratory, Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, China
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Xu J, Liao K, Fu Z, Xiong Z. Screening differentially expressed genes of pancreatic cancer between Mongolian and Han people using bioinformatics technology. BMC Cancer 2020; 20:298. [PMID: 32272917 PMCID: PMC7147062 DOI: 10.1186/s12885-020-06722-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 03/06/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND To screen and analyze differentially expressed genes in pancreatic carcinoma tissues taken from Mongolian and Han patients by Affymetrix Genechip. METHODS Pancreatic ductal cell carcinoma tissues were collected from the Mongolian and Han patients undergoing resection in the Second Affiliated Hospital of Nanchang University from March 2015 to May 2018 and the total RNA was extracted. Differentially expressed genes were selected from the total RNA qualified by Nanodrop 2000 and Agilent 2100 using Affymetrix and a cartogram was drawn; The gene ontology (GO) analysis and Pathway analysis were used for the collection and analysis of biological information of these differentially expressed genes. Finally, some differentially expressed genes were verified by real-time PCR. RESULTS Through the microarray analysis of gene expression, 970 differentially expressed genes were detected by comparing pancreatic cancer tissue samples between Mongolian and Han patients. A total of 257 genes were significantly up-regulated in pancreatic cancer tissue samples in Mongolian patients; while a total of 713 genes were down-regulated. In the Gene Ontology database, 815 differentially expressed genes were identified with clear GO classification, and CPB1 gene showed the highest increase in expression level (multiple difference: 31.76). The pathway analysis detected 28 signaling pathways that included these differentially expressed genes, involving a total of 178 genes. Among these pathways, the enrichment of differentially expressed genes in the FAK signaling pathway was the strongest and COL11A1 gene showed the highest multiple difference (multiple difference: 5.02). The expression of differentially expressed genes CPB1, COL11A1、ITGA4、BIRC3、PAK4、CPA1、CLPS、PIK3CG and HLA-DPA1 determined by real-time PCR were consistent with the results of gene microarray analysis. CONCLUSIONS The results of microarray analysis of gene expression profiles showed that there are a large number of differentially expressed genes in pancreatic cancer tissue samples comparing Mongolian and Han population. These genes are closely related to the cell proliferation, differentiation, invasion, metastasis and multi-drug resistance in pancreatic cancer. They are also involved in the regulation of multiple important signaling pathways in organisms.
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Affiliation(s)
- Jiasheng Xu
- Department of Pathology, the First Affiliated Hospital of Nanchang University, No.17 YONGWAIZHENG Street, Nanchang, 330006, Jiangxi, China
| | - Kaili Liao
- Department of Clinical Laboratory, the Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Zhonghua Fu
- Department of Burns, the First Affiliated Hospital of Nanchang University, No.17 YONGWAIZHENG Street, Nanchang, 330006, Jiangxi, China.
| | - Zhenfang Xiong
- Department of Pathology, the First Affiliated Hospital of Nanchang University, No.17 YONGWAIZHENG Street, Nanchang, 330006, Jiangxi, China.
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Polei M, Günther J, Koczan D, Fürbass R. Trophoblast cell differentiation in the bovine placenta: differentially expressed genes between uninucleate trophoblast cells and trophoblast giant cells are involved in the composition and remodeling of the extracellular matrix and O-glycan biosynthesis. BMC Mol Cell Biol 2020; 21:1. [PMID: 31952476 PMCID: PMC6969411 DOI: 10.1186/s12860-020-0246-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/10/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In the bovine placenta, intimate fetomaternal contacts are restricted to discrete placentomes. Here, widely branched fetal chorionic villi interdigitate with corresponding maternal caruncular crypts. The fetal trophoblast epithelium covering the chorionic villi consists of approximately 80% uninucleate trophoblast cells (UTCs) and 20% binuclear trophoblast giant cells (TGCs). The weakly invasive TGCs migrate toward the caruncle epithelium and eventually fuse with individual epithelial cells to form short-lived fetomaternal hybrid cells. In this way, molecules of fetal origin are transported across the placental barrier and released into the maternal compartment. The UTC/TGC ratio in the trophoblast remains almost constant because approximately as many new TGCs are produced from UTCs as are consumed by the fusions. The process of developing TGCs from UTCs was insufficiently understood. Therefore, we aimed to detect differentially expressed genes (DEGs) between UTCs and TGCs and identify molecular functions and biological processes regulated by DEGs. RESULTS We analyzed gene expression patterns in virtually pure UTC and TGC isolates using gene arrays and detected 3193 DEGs (p < 0.05; fold change values < - 1.5 or > 1.5). Of these DEGs, 1711 (53.6%) were upregulated in TGCs and 1482 (46.4%) downregulated. Gene Ontology (GO) analyses revealed that molecular functions and biological processes regulated by DEGs are related to the extracellular matrix (ECM) and its interactions with cellular receptors, cell migration and signal transduction. Furthermore, there was some evidence that O-glycan biosynthesis in TGCs may produce sialylated short-chain O-glycans (Tn antigen, core 1 O-glycans), while the synthesis of other O-glycan core structures required for the formation of complex (i.e., branched and long-chain) O-glycans appears to be decreased in TGCs. CONCLUSION The differentiation of UTCs into TGCs particularly regulates genes that enable trophoblast cells to interact with their environment. Significant differences between UTCs and TGCs in ECM composition indicate reduced anchoring of TGCs in the surrounding matrix, which might contribute to their migration and their weakly invasive interaction with the maternal endometrium. Furthermore, increased expression of sialylated short chain O-glycans by TGCs could facilitate the modulation of maternal immune tolerance.
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Affiliation(s)
- Marina Polei
- Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Juliane Günther
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Dirk Koczan
- Institute of Immunology, University of Rostock, 18057, Rostock, Germany
| | - Rainer Fürbass
- Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
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Lei Z, Wu J, Zhang D, Liu T, Zhao S, Wang J, Zhang X. Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ). Animals (Basel) 2020; 10:E150. [PMID: 31963250 DOI: 10.3390/ani10010150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Amino acid composition is among the important indexes of the nutritional composition of meat nutrients. In this study, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using isobaric tags for a relative and absolute quantification (iTRAQ) approach. Seventeen amino acids were detected in tenderloin and flank steaks, including seven essential amino acids and 10 non-essential amino acids. A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs). Furthermore, 27 DEPs (p < 0.05) were subjected to Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Abstract Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.
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Tang B, Xie L, Yi T, Lv J, Yang H, Cheng X, Liu F, Zou X. Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L. Int J Mol Sci 2019; 21:E269. [PMID: 31906076 DOI: 10.3390/ijms21010269] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/26/2019] [Accepted: 12/28/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial transcription termination factors (mTERFs) regulate the expression of mitochondrial genes and are closely related to the function of the mitochondrion and chloroplast. In this study, the mTERF gene family in capsicum (Capsicum annuum L.) was identified and characterized through genomic and bioinformatic analyses. Capsicum was found to possess at least 35 mTERF genes (CamTERFs), which were divided into eight major groups following phylogenetic analysis. Analysis of CamTERF promoters revealed the presence of many cis-elements related to the regulation of cellular respiration and photosynthesis. In addition, CamTERF promoters contained cis-elements related to phytohormone regulation and stress responses. Differentially expressed genes in different tissues and developmental phases were identified using RNA-seq data, which revealed that CamTERFs exhibit various expression and co-expression patterns. Gene ontology (GO) annotations associated CamTERFs primarily with mitochondrion and chloroplast function and composition. These results contribute towards understanding the role of mTERFs in capsicum growth, development, and stress responses. Moreover, our data assist in the identification of CamTERFs with important functions, which opens avenues for future studies.
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Wang L, Tang S, Wang Z, Chen H, Rajcha SS, Qian J. The administration of dexmedetomidine changes microRNA expression profiling of rat hearts. Biomed Pharmacother 2019; 120:109463. [PMID: 31541882 DOI: 10.1016/j.biopha.2019.109463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Dexmedetomidine is widely used for perioperative and ICU patients. microRNAs (miRNAs) function as regulators of gene expression. The aim of the study was to assay expression profiling of microRNA in rat hearts following administration of dexmedetomidine. METHODS In this study 6 rats were randomly divided into two groups (n = 3): dexmedetomidine group and control group. The rats of dexmedetomidine group were intraperitoneally given dexmedetomidine in a dose of 100 μg/kg whereas the rats in control group were administered normal saline intraperitoneally. The hearts were excised 30 min after the administration of dexmedetomidine or normal saline under anesthesia. The samples were analyzed for differentially expressed microRNAs with Exiqon miRNA Array. The differentially expressed microRNAs were confirmed by using qRT-PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to find the target genes and signaling pathways of the aberrantly expressed miRNAs. RESULTS Six microRNAs were identified to be significantly expressed, among of which, five microRNAs (miRNA-434-3p, miRNA-3596d, miRNA-496-5p, miRNA-7a-2-3p and miRNA-702-3p) were up-regulated and 1 microRNA (miRNA-208b-3p) down-regulated compared to those of control group. The aberrantly expressed microRNAs were further validated by Quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). GO and KEGG analyses were used to identify target genes and the signaling pathways. CONCLUSIONS The use of dexmedetomidine is associated with differentially expressed microRNAs which may be involved in cardioprotection following administration of dexmedetomidine.
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Affiliation(s)
- Lingyan Wang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Shumiao Tang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhuoran Wang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Hongmei Chen
- Department of Anesthesiology, Kunming Angel Women's & Children's Hospital, Kunming, Yunnan Province, China
| | - Shiva Sunder Rajcha
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Jinqiao Qian
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China.
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He F, Wang X, Ren H, Yuan M, Sun L. Association between ACE gene polymorphism and carotid stenosisand and construction of related gene regulatory networks. Saudi J Biol Sci 2019; 26:2000-2005. [PMID: 31889785 PMCID: PMC6923473 DOI: 10.1016/j.sjbs.2019.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 11/16/2022] Open
Abstract
Objective To investigate the association between DD, ID and II genotypes of ACE gene and carotid stenosis, and to construct a network of ACE-related genes regulating carotid stenosis. Approaches Meta-analysis was used to study the association between three genotypes DD, ID and II of carotid stenosis susceptibility gene ACE; functional annotation of ACE gene was conducted by GO analysis; and a network of ACE-related genes that regulate the mechanisms of carotid stenosis was established. Results Meta-analysis showed that DD and II genotypes of ACE gene were associated with carotid stenosis. GO analysis showed that the main biological processes involved in ACE include: the process of transforming angiotensinogen into mature angiotensin; angiotensin’s mediation of the brain's response to alcohol consumption and thirst control; any chemical reaction involving the regulation of angiotensin; and the process of catalyzing the release of a C-terminal dipeptide from a polypeptide chain. A network of ACE gene regulation of carotid stenosis was constructed in combination with KEGG analysis. Conclusion The ACE gene is a susceptibility gene for carotid stenosis. Through the functional annotation and pathway analysis of ACE gene, an ACE gene-involved carotid stenosis regulatory mechanisms network was constructed.
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Affiliation(s)
- Feng He
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Xiying Wang
- Department of Nursing, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Huimin Ren
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Min Yuan
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Laiguang Sun
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
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Adilijiang A, Hirano M, Okuno Y, Aoki K, Ohka F, Maeda S, Tanahashi K, Motomura K, Shimizu H, Yamaguchi J, Wakabayashi T, Natsume A. Next Generation Sequencing-Based Transcriptome Predicts Bevacizumab Efficacy in Combination with Temozolomide in Glioblastoma. Molecules 2019; 24:molecules24173046. [PMID: 31443404 PMCID: PMC6749405 DOI: 10.3390/molecules24173046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/18/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022] Open
Abstract
Glioblastoma (GBM), the most common and malignant brain tumor, is classified according to its isocitrate dehydrogenase (IDH) mutation status in the 2016 World Health Organization (WHO) brain tumor classification scheme. The standard treatment for GBM is maximal resection, radiotherapy, and Temozolomide (TMZ). Recently, Bevacizumab (Bev) has been added to basic therapy for newly diagnosed GBM, and monotherapy for recurrent GBM. However, the effect of IDH1 mutation on the combination of Bev and TMZ is unknown. In this study, we performed transcriptomic analysis by RNA sequencing with next generation sequencing (NGS), a newly developed powerful method that enables the quantification of the expression level of genome-wide genes. Extracellular matrix and immune cell migration genes were mainly upregulated whereas cell cycle genes were downregulated in IDH1-mutant U87 cells but not in IDH1-wildtype U87 cells after adding Bev to TMZ. In vitro and in vivo studies were conducted for further investigations to verify these results, and the addition of Bev to TMZ showed a significant antitumor effect only in the IDH1-mutant GBM xenograft model. Further studies of gene expression profiling in IDH1 mutation gliomas using NGS will provide more genetic information and will lead to new treatments for this refractory disease.
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Affiliation(s)
- Alimu Adilijiang
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Masaki Hirano
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya 4668560, Japan
| | - Kosuke Aoki
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Kuniaki Tanahashi
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Hiroyuki Shimizu
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Toshihiko Wakabayashi
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 4668550, Japan.
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Lu P, Magwanga RO, Kirungu JN, Dong Q, Cai X, Zhou Z, Wang X, Xu Y, Hou Y, Peng R, Wang K, Liu F. Genome-wide analysis of the cotton G-coupled receptor proteins (GPCR) and functional analysis of GTOM1, a novel cotton GPCR gene under drought and cold stress. BMC Genomics 2019; 20:651. [PMID: 31412764 PMCID: PMC6694541 DOI: 10.1186/s12864-019-5972-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/12/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The efficient detection and initiation of appropriate response to abiotic stresses are important to plants survival. The plant G-protein coupled receptors (GPCRs) are diverse membranous proteins that are responsible for signal transduction. RESULTS In this research work, we identified a novel gene of the GPCR domain, transformed and carried out the functional analysis in Arabidopsis under drought and cold stresses. The transgenic lines exposed to drought and cold stress conditions showed higher germination rate, increased root length and higher fresh biomass accumulation. Besides, the levels of antioxidant enzymes, glutathione (GSH) and ascorbate peroxidase (APX) exhibited continuously increasing trends, with approximately threefold higher than the control, implying that these ROS-scavenging enzymes were responsible for the detoxification of ROS induced by drought and cold stresses. Similarly, the transgenic lines exhibited stable cell membrane stability (CMS), reduced water loss rate in the detached leaves and significant values for the saturated leaves compared to the wild types. Highly stress-responsive miRNAs were found to be targeted by the novel gene and based on GO analysis; the protein encoded by the gene was responsible for maintaining an integral component of membrane. In cotton, the virus-induced gene silencing (VIGS) plants exhibited a higher susceptibility to drought and cold stresses compared to the wild types. CONCLUSION The novel GPCR gene enhanced drought and cold stress tolerance in transgenic Arabidopsis plants by promoting root growth and induction of ROS scavenging enzymes. The outcome showed that the gene had a role in enhancing drought and cold stress tolerance, and can be further exploited in breeding for more stress-resilient and tolerant crops.
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Affiliation(s)
- Pu Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
- School of Physical and Biological Sciences (SPBS), Main campus, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210-40601, Bondo, Kenya
| | - Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Qi Dong
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Renhai Peng
- Research Base in Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Anyang Institute of technology, Anyang, 455000 Henan China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, 455000 Henan China
- School of Agricultural Sciences, Zhengzhou University, 450001 Henan China
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Hua QQ, Liu Y, Liu CH, Liu L, Meng DL. Revealing synergistic mechanism of multiple components in Stauntonia brachyanthera Hand.-Mazz. for gout by virtual screening and system pharmacological approach. Bioorg Chem 2019; 91:103118. [PMID: 31344517 DOI: 10.1016/j.bioorg.2019.103118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/30/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
Stauntonia brachyanthera Hand.-Mazz. (SB), reported as a traditional Chinese medicine, displays a wide spectrum of interesting bioactivities, such as anti-inflammatory and analgesia. It is noteworthy that anti-gout effects of the components in SB have been reported. Hence, this study contributes to the prediction of promising active compounds and mechanisms for the treatment of gout. The active compounds with better oral bioavailability, and drug-likeness of SB were selected for further investigation by the approach of network pharmacology, molecular docking, gene ontology (GO) analysis, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis, respectively. A total of 34 predicted targets and 98 compounds in SB were obtained. Sorted by structure types of compounds, phenylethanoid glycosides exhibited the best anti-gout activity, followed by phenolics and flavonoids. What's more, it was shown in the network analysis that Serine/threonine-protein kinase mTOR (mTOR), Mitogen-activated protein kinase 12 (MAPK12), tumor necrosis factor (TNF-α), Integrin alpha-4 (ITGA4) and Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma (PIK3CG) were the key targets with intensely interaction, which should be attached more attention for further study. The functional enrichment analysis indicated that SB probably produced the anti-gout effects by synergistically regulating many biological pathways, such as MAPK signaling pathway, PI3K-Akt signaling pathway, Toll-like receptor signaling pathway and NOD-like receptor signaling pathway, etc. In addition, C61, C67, C68 and C81 might be promising leading compounds with good molecular docking score. As a consequence, the active constituents and mechanisms based on data analysis were holistically illuminated, which was of vital importance to the development of new drugs for gout.
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Affiliation(s)
- Qiong-Qiong Hua
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China; Beijing Shijitan Hospital, Capital Medical University, Beijing Key Laboratory of Bio-characteristic Profiling for Evaluation of Rational Drug Use, Beijing 100038, PR China
| | - Ying Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Cai-Hong Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Li Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Da-Li Meng
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China; Beijing Shijitan Hospital, Capital Medical University, Beijing Key Laboratory of Bio-characteristic Profiling for Evaluation of Rational Drug Use, Beijing 100038, PR China.
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Hong M, Jiang A, Li N, Li W, Shi H, Storey KB, Ding L. Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 2019; 7:e6538. [PMID: 30923649 PMCID: PMC6431541 DOI: 10.7717/peerj.6538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/29/2019] [Indexed: 01/27/2023] Open
Abstract
The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I, COX1; cytochrome c oxidase subunit III, COX3; cytochrome b, CYTb; cytochrome P450 17A1, CYP17A1) were up-regulated with the increase of gene expression associated with lipid metabolism (apolipoprotein E precursor, APoE; coenzyme Q-binding protein, CoQ10; high-density lipoprotein particle, SAA) and carbohydrate metabolism (HK, MIP). These findings improve our understanding of the underlying molecular mechanisms involved in salinity adaptation and provide general guidance to illuminate the invasion potential of T. s. elegans into saline environments.
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Affiliation(s)
- Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Aiping Jiang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Na Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Weihao Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
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Klemm P, Frommolt P, Kornfeld JW. s ·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data. BMC Genomics 2019; 20:85. [PMID: 30678634 PMCID: PMC6346532 DOI: 10.1186/s12864-018-5396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/18/2018] [Indexed: 11/24/2022] Open
Abstract
Background Next-Generation Sequencing (NGS) has been widely accepted as an essential tool in molecular biology. Reduced costs and automated analysis pipelines make the use of NGS data feasible even for small labs, yet the methods for interpreting the data are not sophisticated enough to account for the amount of information. Results We propose s ·nr, a Visual Analytics tool that provides simple yet powerful visual interfaces for displaying and querying NGS data. It allows researchers to explore their own data in the context of experimental data deposited in public repositories, as well as to extract specific data sets with similar gene expression signatures. We tested s ·nr on 1543 RNA-Seq based mouse differential expression profiles derived from the public ArrayExpress platform. We provide the repository of processed data with this paper. Conclusion s ·nr, easily deployable utilizing its containerized implementation, empowers researchers to analyze and relate their own RNA-Seq as well as to provide interactive and contextual crosstalk with data from public repositories. This allows users to deduce novel and unbiased hypotheses about the underlying molecular processes. Demo Login demo/demo: snr.sf.mpg.de (Tested with Google Chrome) Electronic supplementary material The online version of this article (10.1186/s12864-018-5396-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Klemm
- Max Planck Institute for Metabolism Research, Gleuler Str. 50, Cologne, 50931, Germany.
| | - Peter Frommolt
- Indivumed Group, Falkenried 88, Bldg. D, Hamburg, D-20251, Germany
| | - Jan-Wilhelm Kornfeld
- University of Southern Denmark, Department of Biochemistry and Molecular Biology, Campusvej 55, Odense, DK-5230, Denmark
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Yang LX, Yang LK, Zhu J, Chen JH, Wang YH, Xiong K. Expression signatures of long non-coding RNA and mRNA in human traumatic brain injury. Neural Regen Res 2019; 14:632-641. [PMID: 30632503 PMCID: PMC6352599 DOI: 10.4103/1673-5374.247467] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play a key role in craniocerebral disease, although their expression profiles in human traumatic brain injury are still unclear. In this regard, in this study, we examined brain injury tissue from three patients of the 101st Hospital of the People’s Liberation Army, China (specifically, a 36-year-old male, a 52-year-old female, and a 49-year-old female), who were diagnosed with traumatic brain injury and underwent brain contusion removal surgery. Tissue surrounding the brain contusion in the three patients was used as control tissue to observe expression characteristics of lncRNAs and mRNAs in human traumatic brain injury tissue. Volcano plot filtering identified 99 lncRNAs and 63 mRNAs differentially expressed in frontotemporal tissue of the two groups (P < 0.05, fold change > 1.2). Microarray analysis showed that 43 lncRNAs were up-regulated and 56 lncRNAs were down-regulated. Meanwhile, 59 mRNAs were up-regulated and 4 mRNAs were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed 27 signaling pathways associated with target genes and, in particular, legionellosis and influenza A signaling pathways. Subsequently, a lncRNA-gene network was generated, which showed an absolute correlation coefficient value > 0.99 for 12 lncRNA-mRNA pairs. Finally, quantitative real-time polymerase chain reaction confirmed different expression of the five most up-regulated mRNAs within the two groups, which was consistent with the microarray results. In summary, our results show that expression profiles of mRNAs and lncRNAs are significantly different between human traumatic brain injury tissue and surrounding tissue, providing novel insight regarding lncRNAs’ involvement in human traumatic brain injury. All participants provided informed consent. This research was registered in the Chinese Clinical Trial Registry (registration number: ChiCTR-TCC-13004002) and the protocol version number is 1.0.
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Affiliation(s)
- Li-Xiang Yang
- Department of Neurosurgery, 101st Hospital of People's Liberation Army, Wuxi, Jiangsu Province, China
| | - Li-Kun Yang
- Department of Neurosurgery, 101st Hospital of People's Liberation Army, Wuxi, Jiangsu Province, China
| | - Jie Zhu
- Department of Neurosurgery, 101st Hospital of People's Liberation Army, Wuxi, Jiangsu Province, China
| | - Jun-Hui Chen
- Department of Neurosurgery, 101st Hospital of People's Liberation Army, Wuxi, Jiangsu Province, China
| | - Yu-Hai Wang
- Department of Neurosurgery, 101st Hospital of People's Liberation Army, Wuxi, Jiangsu Province, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
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Jaramillo ML, Guzman F, da Fonseca GC, Margis R, Müller YMR, Ammar D, Nazari EM. microRNAs in Macrobrachium olfersii embryos: Identification, their biogenesis components and potential targets. Comput Biol Chem 2019; 78:205-16. [PMID: 30576966 DOI: 10.1016/j.compbiolchem.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022]
Abstract
In embryonic development, microRNAs (miRNAs) regulate the complex gene expression associated with the complexity of embryogenesis. Today, few studies have been conducted on the identification of miRNAs and components of miRNA biogenesis on embryonic development in crustaceans, especially in prawns. In this context, the aim of this study was to identify in silico components of miRNA biogenesis, and miRNAs and potential target genes during embryonic development in the prawn Macrobrachium olfersii through small RNAs and transcriptome analyses. Using the miRDeep2 program, we identified 17 miRNA precursors in M. olfersii, which seven (miR-9, miR-10, miR-92, miR-125, miR-305, miR-1175, and miR-2788) were reported in the miRBase database, indicating high evolutionary conservation of these sequences among animals. The other 10 miRNAs of M. olfersii were novel miRNAs and only similar to Macrobrachium niponnense miRNAs, indicating genus-specific miRNAs. In addition, eight key components of miRNA biogenesis (DROSHA, PASHA/DGCR8, XPO5, RAN, DICER, TRBP2, AGO, and PIWI) were identified in M. olfersii embryos unigenes. In the annotation of miRNA targets, 516 genes were similar to known sequences in the GenBank database. Regarding the conserved miRNAs, we verified that they were differentially expressed during embryonic development in M. olfersii. In conclusion, this is the first study that identifies conserved and novel miRNAs in the prawn M. olfersii with some miRNA target genes involved in embryonic development. Our results will allow further studies on the function of these miRNAs and miRNA biogenesis components during embryonic development in M. olfersii and other prawns of commercial interest.
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Zhang W, Huai Y, Miao Z, Chen C, Shahen M, Rahman SU, Alagawany M, El-Hack MEA, Zhao H, Qian A. Systems pharmacology approach to investigate the molecular mechanisms of herb Rhodiola rosea L. radix. Drug Dev Ind Pharm 2018; 45:456-464. [PMID: 30449200 DOI: 10.1080/03639045.2018.1546316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rhodiola rosea L. radix (RRL) is one of the most popular medical herb which has been widely used for the treatment of different diseases effectively, including cardiovascular diseases and nerve system diseases. However, due to the multiple compounds in RRL, the underlying molecular mechanisms of RRL are remained unclear. To decipher the action mechanisms of RRL from a systematic perspective, a systems pharmacology approach integrated absorption, distribution, metabolism, and excretion (ADME) system, drug targeting, and network analysis was introduced. First, by the ADME screening system and the target fishing process, 56 potential active compounds and 62 targets were obtained, respectively. In addition, compound-target network demonstrated that most compounds interacted with multiple targets, indicating that RRL may enhance its therapeutic effects probably through hitting on multiple targets in a holistic level. Moreover, target-pathway network and gene ontology analysis showed that multiple targets of RRL were involved in several biological pathways, i.e. Neuroactive ligand-receptor interaction, calcium signaling pathway, adrenergic signaling in cardiomyocytes, and VEGF signaling pathway, which dissecting the therapeutic effects of RRL on various diseases, such as cardiovascular diseases, depression, adaptation diseases, etc. In summary, this work successfully explains the potential active compounds and the multi-scale curative action mechanisms of RRL for treating various diseases; meanwhile, it implies that RRL could be applied as a novel therapeutic agent in arthritic diseases. Most importantly, this work provides an in silico strategy to understand the action mechanisms of herbal medicines from molecular/system levels, which will promote the new drug development of traditional Chinese medicine.
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Affiliation(s)
- Wenjuan Zhang
- a Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences , Northwestern Polytechnical University , Xi'an , People's Republic of China
| | - Ying Huai
- a Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences , Northwestern Polytechnical University , Xi'an , People's Republic of China
| | - Zhiping Miao
- a Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences , Northwestern Polytechnical University , Xi'an , People's Republic of China
| | - Chu Chen
- b Clinical Laboratory of Honghui Hospital , Xi'an JiaoTong University College of Medicine , Xi'an , Shaanxi , People's Republic of China
| | - Mohamed Shahen
- c Zoology Department, Faculty of Science , Tanta University , Tanta , Egypt
| | - Siddiq Ur Rahman
- d College of Life Sciences , Northwest A & F University , Yangling , Shaanxi , People's Republic of China
| | - Mahmoud Alagawany
- e Department of Poultry, Faculty of Agriculture , Zagazig University , Zagazig , Egypt
| | - Mohamed E Abd El-Hack
- e Department of Poultry, Faculty of Agriculture , Zagazig University , Zagazig , Egypt
| | - Heping Zhao
- b Clinical Laboratory of Honghui Hospital , Xi'an JiaoTong University College of Medicine , Xi'an , Shaanxi , People's Republic of China
| | - Airong Qian
- a Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences , Northwestern Polytechnical University , Xi'an , People's Republic of China
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Tian Y, Xu Y, Wang H, Shu R, Sun L, Zeng Y, Gong F, Lei Y, Wang K, Luo H. Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer. Funct Integr Genomics 2019; 19:311-27. [PMID: 30446877 DOI: 10.1007/s10142-018-0641-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/04/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022]
Abstract
Increasing data demonstrate that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) play important roles in tumorigenesis. However, the mechanisms in colorectal cancer (CRC) remain unclear. Here, hundreds of significantly expressed circRNAs, and thousands of lncRNAs as well as mRNAs were identified. By qRT-PCR, one abnormal circRNA, lncRNA, and three mRNAs were verified in 24 pairs of tissues and blood samples, respectively. Then, by GO analysis, we found that the gene expression profile of linear counterparts of upregulated circRNAs in human CRC tissues preferred positive regulation of GTPase activity, cellular protein metabolic process, and protein binding, while that of downregulated circRNAs of CRC preferred positive regulation of cellular metabolic process, acetyl-CoA metabolic process, and protein kinase C activity. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that p53 signaling pathway was an important pathway in upregulated protein-coding genes, whereas cyclic guanosine monophosphate-protein kinase G (cGMP–PKG) signaling pathway was the top enriched KEGG pathway for downregulated transcripts. Furthermore, lncRNA–mRNA co-expression analysis demonstrated that downregulated lncRNA uc001tma.3 was negatively with CDC45 and positively with ELOVL4, BVES, FLNA, and HSPB8, while upregulated lncRNA NR_110882 was positively with FZD2. In addition, lncRNA–transcription factor (TF) co-expression analysis showed that the most relevant TFs were forkhead box protein A1 (FOXA1), transcription initiation factor TFIID submint 7 (TAF7), and adenovirus early region 1A(E1A)-associated protein p300 (EP300). Our findings offer a fresh view on circRNAs and lncRNAs and provide the foundation for further study on the potential roles of circRNAs and lncRNAs in colorectal cancer.
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