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Cao J, Yu X, Liu J, Fu J, Wang B, Wu C, Zhang S, Chen H, Wang Z, Xu Y, Sui T, Chang J, Cao X. Ruxolitinib improves the inflammatory microenvironment, restores glutamate homeostasis, and promotes functional recovery after spinal cord injury. Neural Regen Res 2024; 19:2499-2512. [PMID: 38526286 PMCID: PMC11090442 DOI: 10.4103/nrr.nrr-d-23-01863] [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: 11/12/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00030/figure1/v/2024-03-08T184507Z/r/image-tiff The inflammatory microenvironment and neurotoxicity can hinder neuronal regeneration and functional recovery after spinal cord injury. Ruxolitinib, a JAK-STAT inhibitor, exhibits effectiveness in autoimmune diseases, arthritis, and managing inflammatory cytokine storms. Although studies have shown the neuroprotective potential of ruxolitinib in neurological trauma, the exact mechanism by which it enhances functional recovery after spinal cord injury, particularly its effect on astrocytes, remains unclear. To address this gap, we established a mouse model of T10 spinal cord contusion and found that ruxolitinib effectively improved hindlimb motor function and reduced the area of spinal cord injury. Transcriptome sequencing analysis showed that ruxolitinib alleviated inflammation and immune response after spinal cord injury, restored EAAT2 expression, reduced glutamate levels, and alleviated excitatory toxicity. Furthermore, ruxolitinib inhibited the phosphorylation of JAK2 and STAT3 in the injured spinal cord and decreased the phosphorylation level of nuclear factor kappa-B and the expression of inflammatory factors interleukin-1β, interleukin-6, and tumor necrosis factor-α. Additionally, in glutamate-induced excitotoxicity astrocytes, ruxolitinib restored EAAT2 expression and increased glutamate uptake by inhibiting the activation of STAT3, thereby reducing glutamate-induced neurotoxicity, calcium influx, oxidative stress, and cell apoptosis, and increasing the complexity of dendritic branching. Collectively, these results indicate that ruxolitinib restores glutamate homeostasis by rescuing the expression of EAAT2 in astrocytes, reduces neurotoxicity, and effectively alleviates inflammatory and immune responses after spinal cord injury, thereby promoting functional recovery after spinal cord injury.
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Affiliation(s)
- Jiang Cao
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiao Yu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jingcheng Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jiaju Fu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Binyu Wang
- Department of Trauma Surgery, Subei People’s Hospital of Jiangsu, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chaoqin Wu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Sheng Zhang
- Department of Orthopedics, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, China
| | - Hongtao Chen
- Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing, Jiangsu Province, China
| | - Zi Wang
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yinyang Xu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Tao Sui
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jie Chang
- Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing, Jiangsu Province, China
| | - Xiaojian Cao
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
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Aryal YP, Neupane S, Kwak HJ, An CH, Sohn WJ, Yamamoto H, Kwon TY, Min BK, Kim JY, Cho SJ. Unraveling the structure, chemical composition, and conserved signaling in leech teeth. Anim Cells Syst (Seoul) 2024; 28:272-282. [PMID: 38741948 PMCID: PMC11089927 DOI: 10.1080/19768354.2024.2350736] [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: 03/07/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Unlike vertebrates, the number of toothed taxa in invertebrates is very few, with leeches being the only tooth-bearing organisms in the phylum Annelida. Copious studies have been conducted regarding vertebrate teeth; however, studies regarding the structure and function of invertebrate teeth are limited. In this study, the tooth structure of leeches, specifically Hirudo nipponia and Haemadipsa rjukjuana, was revealed, which showed sharp and pointed teeth along the apex of three jaws. Understanding conserved signaling regulations among analogous organs is crucial for uncovering the underlying mechanisms during organogenesis. Therefore, to shed light on the evolutionary perspective of odontogenesis to some extent, we conducted de novo transcriptome analyses using embryonic mouse tooth germs, Hirudo teeth, and Helobdella proboscises to identify conserved signaling molecules involved in tooth development. The selection criteria were particularly based on the presence of tooth-related genes in mice, Hirudo teeth, and Helobdella proboscis, wherein 4113 genes were commonly expressed in all three specimens. Furthermore, the chemical nature of leech teeth was also examined via TEM-EDS to compare the chemical composition with vertebrate teeth. The examination of tissue-specific genetic information and chemical nature between leeches and mice revealed chemical similarities between leech and mice teeth, as well as conserved signaling molecules involved in tooth formation, including Ptpro, Prickle2, and Wnt16. Based on our findings, we propose that leech teeth express signaling molecules conserved in mice and these conserved tooth-specific signaling for dental hard tissue formation in mice would corresponds to the structural formation of the toothed jaw in leeches.
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Affiliation(s)
- Yam Prasad Aryal
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
| | - Sanjiv Neupane
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Hee-Jin Kwak
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
| | - Chang-Hyeon An
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Wern-Joo Sohn
- Pre-Major of Cosmetics and Pharmaceutics, Daegu Haany University, Gyeongsan, Korea
| | - Hitoshi Yamamoto
- Department of Histology and Developmental Biology, Tokyo Dental College, Tokyo, Japan
| | - Tae-Yub Kwon
- Department of Dental Biomaterials, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Bong-Ki Min
- Center for Research Facilities, Yeungnam University, Gyeongsan, Korea
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
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Wang S, Sun D, Ye B, Xu G, Zou J. Dietary kelp meal improves serum antioxidants, intestinal immunity, and lipid metabolism in hybrid snakehead (Channa maculata ♀ × Channa argus ♂). J Sci Food Agric 2024. [PMID: 38733135 DOI: 10.1002/jsfa.13566] [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] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/28/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Dietary kelp possesses a variety of useful biological qualities but does not have a toxic effect on the host. In this study, we examine how kelp dietary supplementation enhances the serum biochemistry, intestinal immunity, and metabolism of hybrid snakehead. A total of 810 juvenile hybrid snakeheads (Channa maculata ♀ × Channa argus ♂), with an initial average weight of 11.4 ± 0.15 g, were allocated randomly to three treatment groups (three replicates per group). The fish were fed for 60 days with isonitrogenous and isolipidic diets. The groups were the control group (C) (20% high-gluten flour), the medium replacement group (MR) (10% high-gluten flour and 10% kelp meal), and the full replacement group (FR) (0% high-gluten flour and 15% kelp meal). RESULTS The results showed that dietary kelp increased the activity of serum antioxidant enzymes significantly and decreased the content of serum malondialdehyde (MDA) in hybrid snakeheads, with significant changes in the FR group (P < 0.05). The intestinal morphology results showed that dietary kelp helped to increase the specific surface area of intestinal villi, which was beneficial for intestinal digestion and absorption. According to transcriptome and quantitative real-time polymerase chain reaction (qRT-PCR) analysis, dietary kelp can improve the expression of intestinal immunity and metabolism-related pathways. Among them, immune-related genes MHC1 and HSPA1 were significantly up-regulated, and IGH, MHC2, and IL-8 were significantly down-regulated (P < 0.05). Lipid metabolism-related genes DGAT2, FABP2, RXRα, and PLPP1 were all significantly up-regulated (P < 0.05). CONCLUSION Dietary kelp can effectively improve the antioxidant function of hybrid snakeheads, improve intestinal morphology, reduce intestinal inflammation, and promote intestinal lipid synthesis and transportation, thereby improving intestinal immunity and metabolic functions. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shaodan Wang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Di Sun
- Joint Laboratory of Guangdong province and Hong Kong region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Bin Ye
- Joint Laboratory of Guangdong province and Hong Kong region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jixing Zou
- Joint Laboratory of Guangdong province and Hong Kong region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Hao W, Li Y, Guo H, Chen J, Pi F. Co-metabolism of Na +/K + ion regulated physiological enhancement on selenium-accumulation in Saccharomyces yeasts. J Sci Food Agric 2024; 104:4136-4144. [PMID: 38258891 DOI: 10.1002/jsfa.13295] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Selenium is an important nutritional supplement that mainly exists naturally in soil as inorganic selenium. Saccharomyces cerevisiae cells are excellent medium for converting inorganic selenium in nature into organic selenium. RESULTS Under the co-stimulation of sodium selenite (Na2SeO3) and potassium selenite (K2SeO3), the activity of selenophosphate synthetase (SPS) was improved up to about five folds more than conventional Na2SeO3 group with the total selenite salts content of 30 mg/L. Transcriptome analysis first revealed that due to the sharing pathway between sodium ion (Na+) and potassium ion (K+), the K+ largely regulates the metabolisms of amino acid and glutathione under the accumulation of selenite salt. Furthermore, K+ could improve the tolerance performance and selenium-biotransformation yields of Saccharomyces cerevisiae cells under Na2SeO3 salt stimulation. CONCLUSION The important role of K+ in regulating the intracellular selenium accumulation especially in terms of amino acid metabolism and glutathione, suggested a new direction for the development of selenium-enrichment supplements with Saccharomyces cerevisiae cell factory. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Wenhui Hao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, P. R. China
| | - Ying Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, P. R. China
| | - Hanlin Guo
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, P. R. China
| | - Jian Chen
- Shandong Jiucifang Biotechnology, Co. Ltd, Zibo, P. R. China
| | - Fuwei Pi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, P. R. China
- Shandong Jiucifang Biotechnology, Co. Ltd, Zibo, P. R. China
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Hu S, Du B, Mu G, Jiang Z, Li H, Song Y, Zhang B, Xia J, Rouached H, Zheng L. The transcription factor OsbZIP48 governs rice responses to zinc deficiency. Plant Cell Environ 2024; 47:1526-1542. [PMID: 38251320 DOI: 10.1111/pce.14825] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Nevertheless, despite its primary importance, how rice responds to Zn deficiency remains poorly understood. This study presents genetic evidence supporting the crucial role of OsbZIP48 in regulating rice's response to Zn deficiency, consistent with earlier findings in the model plant Arabidopsis. Genetic inactivation of OsbZIP48 in rice seedlings resulted in heightened sensitivity to Zn deficiency and reduced Zn translocation from roots to shoots. Consistently, OsbZIP48 was constitutively expressed in roots, slightly induced by Zn deficiency in shoots and localized into nuclei induced by Zn deficiency. Comparative transcriptome analysis of the wild-type plants and osbzip48 mutant grown under Zn deficiency enabled the identification of OsbZIP48 target genes, including key Zn transporter genes (OsZIP4 and OsZIP8). We demonstrated that OsbZIP48 controlled the expressions of these genes by directly binding to their promoters, specifically to the Zn deficiency response element motif. This study establishes OsbZIP48 as a critical transcription factor in rice's response to Zn deficiency, offering valuable insights for developing Zn-biofortified rice varieties to combat global Zn limitation.
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Affiliation(s)
- Shubao Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- College of Life sciences, Anqing Normal University, Anqing, China
| | - Binbin Du
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guangmao Mu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zichen Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuxinrui Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baolei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Luqing Zheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Chen L, Dai X. Venous thromboembolism and severe COVID-19: a Mendelian randomization trial and transcriptomic analysis. Front Immunol 2024; 15:1363598. [PMID: 38742101 PMCID: PMC11089160 DOI: 10.3389/fimmu.2024.1363598] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction Venous thromboembolism (VTE) is known to be intricately linked to severe COVID-19 (sCOVID-19) occurrence. Herein, we employed univariable Mendelian randomization (MR) and transcriptome analysis to predict the causal association and associated signaling networks between VTE and sCOVID-19. Methods Potential VTE and sCOVID-19 association was assessed using MR-Egger, weighted median, simple mode, weighted mode, and inverse variance weighted (IVW) regression. We conducted independent univariable analyses involving VTE and sCOVID-19. Using heterogeneity, pleiotropy, and the Leave-One-Out examinations, we performed sensitivity analyses. Thereafter, we performed transcriptome analysis of the GSE164805 dataset to identify differentially expressed genes (DEGs) linked to single nucleotide polymorphisms (SNPs). Lastly, we conducted immune analyses. Results Based on our univariable analysis, VTE was a strong indicator of sCOVID-19 development, and it was intricately linked to sCOVID-19. We further conducted sensitivity analysis to demonstrate the reliability of our results. Using differential analysis, we identified 15 major genes, namely, ACSS2, CEP250, CYP4V2, DDB2, EIF6, GBGT1, GSS, MADD, MAPK8IP1, MMP24, YBPC3, NT5DC3, PROCR, SURF6, and YIPF2, which were strongly connected to suppressive adaptive immune as well as augmented inflammatory cells. In addition, we uncovered strong associations with most differential immunologic gene sets, such as, the Major Histocompatibility Complex (MHC), immunoactivators, and immunosuppressors. Conclusion Herein, we demonstrated we strong association between VTE and enhanced sCOVID-19 risk. We also identified 15 DEGs which potentially contribute to the shared immunologic pathogenesis between VTE and sCOVID-19.
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Affiliation(s)
- Liang Chen
- Department of Infectious Diseases, Taikang Xianlin Drum Tower Hospital, Affiliated Hospital of Medical College of Nanjing University, Nanjing, China
| | - Xiaoting Dai
- Department of Infectious Diseases, Nanjing Lishui People’s Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
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Yang L, Peng J, Tang T. [Transcriptional analysis of the molecular response of Arabidopsis to manganese stress and recovery]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1138-1156. [PMID: 38658154 DOI: 10.13345/j.cjb.230516] [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] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Manganese (Mn) is an essential element for plants and plays a role in various metabolic processes. However, excess manganese can be toxic to plants. This study aimed to analyze the changes in various physiological activities and the transcriptome of Arabidopsis under different treatments: 1 mmol/L MnCl2 treatment for 1 day or 3 days, and 1 day of recovery on MS medium after 3 days of MnCl2 treatment. During the recovery phase, minor yellowing symptoms appeared on the leaves of Arabidopsis, and the content of chlorophyll and carotenoid decreased significantly, but the content of malondialdehyde and soluble sugar increased rapidly. Transcriptome sequencing data shows that the expression patterns of differentially expressed genes exhibit three major models: initial response model, later response model, recovery response model. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis identified several affected metabolic pathways, including plant hormone signal transduction mitosolysis activates protein kinase (MAPK) phytohormone signaling, phenylpropanoid biosynthesis, ATP binding cassette transporters (ABC transporter), and glycosphingolipid biosynthesis. Differential expressed genes (DEGs) involved in phenylpropanoid biosynthesis, ABC transporter, and glycosphingolipid biosynthesis, were identified. Sixteen randomly selected DEGs were validated through qRT-PCR and showed consistent results with RNA-seq data. Our findings suggest that the phenylpropanoid metabolic pathway is activated to scavenge reactive oxygen species, the regulation of ABC transporter improves Mn transport, and the adjustment of cell membrane lipid composition occurs through glycerophospholipid metabolism to adapt to Mn stress in plants. This study provides new insights into the molecular response of plants to Mn stress and recovery, as well as theoretical cues for cultivating Mn-resistant plant varieties.
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Affiliation(s)
- Li Yang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411100, Hunan, China
| | - Jiashi Peng
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411100, Hunan, China
| | - Ting Tang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411100, Hunan, China
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Qin X, He X, Chen L, Han Y, Yun Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of adipose tissue in grazing cattle: Identifying key regulators of fat metabolism. Open Life Sci 2024; 19:20220843. [PMID: 38681730 PMCID: PMC11049749 DOI: 10.1515/biol-2022-0843] [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: 12/20/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024] Open
Abstract
The taste and tenderness of meat are the main determinants of carcass quality in many countries. This study aimed to discuss the mechanisms of intramuscular fat deposition in grazing and house-breeding cattle. We performed transcriptome analysis to characterize messenger RNA and microRNA (miRNA) expression profiles. A total of 456 and 66 differentially expressed genes (DEGs) and differentially expressed (DE) miRNAs were identified in the adipose tissue of grazing and house-breeding cattle. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the association of DEGs with fatty acid metabolism, fatty acid degradation, peroxisome proliferator-activated receptors signaling pathway, adenosine monophosphate-activated protein kinase signaling pathway, adipocytokine signaling pathway, and the association of DE miRNAs with mitogen-activated protein kinase signaling pathway. Apolipoprotein L domain containing 1, pyruvate dehydrogenase kinase 4, and sphingosine-1-phosphate lyase 1 genes may be the key regulators of fat metabolism in grazing cattle. Finally, we found that miR-211 and miR-331-5p were negatively correlated with the elongation of very long-chain fatty acids protein 6 (ELOVL6), and miR-331-5p might be the new regulator involved in fat metabolism. The results indicated that ELOVL6 participated in various functions and pathways related to fat metabolism. Meanwhile, miR-331-5p, as a new regulator, might play an essential role in this process. Our findings laid a more in-depth and systematic research foundation for the formation mechanism and characteristics of adipose tissue in grazing cattle.
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Affiliation(s)
- Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
- Pharmacy and Materials School, Huainan Union University, Huainan232038, China
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yunfei Han
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yueying Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Jindi Wu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
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Ding X, Tian Y, Qiu Y, Duan P, Wang X, Li Z, Li L, Liu Y, Wang L. Effects of Long-Term Cryopreservation on the Transcriptomes of Giant Grouper Sperm. Genes (Basel) 2024; 15:523. [PMID: 38674457 PMCID: PMC11050297 DOI: 10.3390/genes15040523] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The giant grouper fish (Epinephelus lanceolatus), one of the largest and rarest groupers, is a fast-growing economic fish. Grouper sperm is often used for cross-breeding with other fish and therefore sperm cryopreservation is important. However, freezing damage cannot be avoided. Herein, we performed a transcriptome analysis to compare fresh and frozen sperm of the giant grouper with frozen storage times of 0, 23, 49, and 61 months. In total, 1911 differentially expressed genes (DEGs), including 91 in El-0-vs-El-23 (40 upregulated and 51 downregulated), 251 in El-0-vs-El-49 (152 upregulated and 69 downregulated), and 1569 in El-0-vs-El-61 (984 upregulated and 585 downregulated), were obtained in the giant grouper sperm. DEGs were significantly increased at 61 months of cryopreservation (p < 0.05). GO and KEGG enrichment analyses of the DEGs revealed significant enrichment in the pilus assembly, metabolic process, MAPK signaling pathway, apoptosis, and P53 signaling pathway. Time-series expression profiling of the DEGs showed that consistently upregulated modules were also significantly enriched in signaling pathways associated with apoptosis. Four genes, scarb1, odf3, exoc8, and atp5f1d, were associated with mitochondria and flagella in a weighted correlation network analysis. These genes may play an important role in the response to sperm freezing. The experimental results show that long-term cryopreservation results in freezing damage to the giant grouper sperm. This study provides rich data for studies of the mechanism underlying frozen fish sperm damage as well as a technical reference and evaluation index for the long-term cryopreservation of fish sperm.
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Affiliation(s)
- Xiaoyu Ding
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
| | - Yongsheng Tian
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
| | - Yishu Qiu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
| | - Pengfei Duan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
| | - Xinyi Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
| | - Zhentong Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
| | - Linlin Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
| | - Yang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
| | - Linna Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.D.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
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Liu Q, Li H, Shi R, Wei W, Yuan X, Cao YM, Liu S. Investigation into the Synthesis, Bioactivity, and Mechanism of Action of the Novel 6-Pyrazolyl-2-picolinic Acid as a Herbicide. J Agric Food Chem 2024; 72:8840-8848. [PMID: 38570314 DOI: 10.1021/acs.jafc.3c08517] [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] [Indexed: 04/05/2024]
Abstract
A series of new 4-amino-3,5-dicholo-6-(5-aryl-substituted-1H-pyrazol-1-yl)-2-picolinic acid compounds were designed and prepared to discover herbicidal molecules. The inhibitory activities of all new compounds against the root growth ofArabidopsis thaliana were assayed. On the whole, the new synthesized compounds displayed good inhibition effects and had excellent herbicidal activities on root growth of weed at 500 μM. Importantly, a selection of compounds demonstrated comparable herbicidal properties to picloram. At the dosage of 250 g/ha, most of the compounds showed a 100% postemergence herbicidal activity to control Chenopodium album and Amaranthus retroflexus. Using compound V-2, the mechanism of action was investigated based on a phenotype study using AFB5-deficient Arabidopsis thaliana. It was found that the novel 6-pyrazolyl-2-picolinic acids were auxinic compounds. In addition, it was proposed that V-2 may be an immune activator due to its upregulation of defense genes and the increased content of jasmonic acid.
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Affiliation(s)
- Qing Liu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Huiting Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Rongchuan Shi
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Wei Wei
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiao Yuan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yi-Ming Cao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Shangzhong Liu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
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11
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Guo Y, Abou Daya F, Le HD, Panda S, Melkani GC. Diurnal expression of Dgat2 induced by time-restricted feeding maintains cardiac health in the Drosophila model of circadian disruption. Aging Cell 2024:e14169. [PMID: 38616316 DOI: 10.1111/acel.14169] [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: 10/02/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024] Open
Abstract
Circadian disruption is associated with an increased risk of cardiometabolic disorders and cardiac diseases. Time-restricted feeding/eating (TRF/TRE), restricting food intake within a consistent window of the day, has shown improvements in heart function from flies and mice to humans. However, whether and how TRF still conveys cardiac benefits in the context of circadian disruption remains unclear. Here, we demonstrate that TRF sustains cardiac performance, myofibrillar organization, and regulates cardiac lipid accumulation in Drosophila when the circadian rhythm is disrupted by constant light. TRF induces oscillations in the expression of genes associated with triglyceride metabolism. In particular, TRF induces diurnal expression of diacylglycerol O-acyltransferase 2 (Dgat2), peaking during the feeding period. Heart-specific manipulation of Dgat2 modulates cardiac function and lipid droplet accumulation. Strikingly, heart-specific overexpression of human Dgat2 at ZT 0-10 significantly improves cardiac performance in flies exposed to constant light. We have demonstrated that TRF effectively attenuates cardiac decline induced by circadian disruption. Moreover, our data suggests that diurnal expression of Dgat2 induced by TRF is beneficial for heart health under circadian disruption. Overall, our findings have underscored the relevance of TRF in preserving heart health under circadian disruptions and provided potential targets, such as Dgat2, and strategies for therapeutic interventions in mitigating cardiac aging, metabolic disorders, and cardiac diseases in humans.
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Affiliation(s)
- Yiming Guo
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah Abou Daya
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hiep Dinh Le
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Girish C Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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12
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Wu K, Huang S, Zhao Y, Umar A, Chen H, Yu Z, Huang J. Hepatocyte nuclear factor 4 located in different developmental stages in Schistosoma japonicum and involved in important metabolic pathways. Biomed J 2024:100726. [PMID: 38621646 DOI: 10.1016/j.bj.2024.100726] [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: 08/22/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Nuclear receptors (NRs) are vital for regulating gene expression un organisms. Hepatocyte nuclear factor 4 (HNF4), a class of NRs, participates in blood feeding and intestinal maintenance in schistosomes. However, there is limited research on the molecular and functional characterization of HNF4 in Schistosoma japonicum (S. japonicum). METHODS Highly specific polyclonal antibodies were generated to analyze the expression and tissue localization of S. japonicum HNF4 (SjHNF4). The potential biological functions of SjHNF4 were characterized by transcriptome and pull-down analysis. Subsequently, enrichment analysis was performed to identify the specific signaling pathways linked to SjHNF4. RESULTS The SjHNF4 protein was expressed heterologously and purified successfully. High purity and high potency polyclonal antibodies were further prepared. The expression of SjHNF4 was higher in female compared to male worms at both transcriptional and protein levels. Female worms expressed SjHNF4 in their perithecium, reproductive system, and certain parts of the intestinal tissues. SjHNF4 was also detected in the perithecium of male worms, as well as in the head, body of cercaria, and eggs. Furthermore, our findings highlighted the potential role of SjHNF4 in blood feeding and its interaction with crucial pathways such as glucose metabolism, lipid metabolism, and nucleotide metabolism. CONCLUSIONS This study shed light on the location of SjHNF4 in different life stages of S. japonicum, particularly associated with the female schistosomes. A strong correlation was observed between SjHNF4 and essential metabolic pathways. These findings laid a solid groundwork for the research on the relationship between NRs and schistosomes.
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Affiliation(s)
- Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Shuaiqin Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Yiming Zhao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Abdulrahim Umar
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013.
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13
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Kim W, Kim M, Kim B. Unraveling the enigma: housekeeping gene Ugt1a7c as a universal biomarker for microglia. Front Psychiatry 2024; 15:1364201. [PMID: 38666091 PMCID: PMC11043603 DOI: 10.3389/fpsyt.2024.1364201] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Background Microglia, brain resident macrophages, play multiple roles in maintaining homeostasis, including immunity, surveillance, and protecting the central nervous system through their distinct activation processes. Identifying all types of microglia-driven populations is crucial due to the presence of various phenotypes that differ based on developmental stages or activation states. During embryonic development, the E8.5 yolk sac contains erythromyeloid progenitors that go through different growth phases, eventually resulting in the formation of microglia. In addition, microglia are present in neurological diseases as a diverse population. So far, no individual biomarker for microglia has been discovered that can accurately identify and monitor their development and attributes. Summary Here, we highlight the newly defined biomarker of mouse microglia, UGT1A7C, which exhibits superior stability in expression during microglia development and activation compared to other known microglia biomarkers. The UGT1A7C sensing chemical probe labels all microglia in the 3xTG AD mouse model. The expression of Ugt1a7c is stable during development, with only a 4-fold variation, while other microglia biomarkers, such as Csf1r and Cx3cr1, exhibit at least a 10-fold difference. The UGT1A7C expression remains constant throughout its lifespan. In addition, the expression and activity of UGT1A7C are the same in response to different types of inflammatory activators' treatment in vitro. Conclusion We propose employing UGT1A7C as the representative biomarker for microglia, irrespective of their developmental state, age, or activation status. Using UGT1A7C can reduce the requirement for using multiple biomarkers, enhance the precision of microglia analysis, and even be utilized as a standard for gene/protein expression.
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Affiliation(s)
| | | | - Beomsue Kim
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
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14
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Ren J, Ji X, Zhang J, Yu Z, Wang X, Xiong L, Yang N, Tang L, Li Z, Fan Z. Discovery of Trisubstituted N-Phenylpyrazole Containing Diamides with Improved Insecticidal Activity. J Agric Food Chem 2024; 72:8072-8080. [PMID: 38547359 DOI: 10.1021/acs.jafc.3c08759] [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] [Indexed: 04/11/2024]
Abstract
To increase the structural diversity of insecticides and meet the needs of effective integrated insect management, the structure of chlorantraniliprole was modified based on a previously established three-dimensional quantitative structure-activity relationship (3D-QSAR) model. The pyridinyl moiety in the structure of chlorantraniliprole was replaced with a 4-fluorophenyl group. Further modifications of this 4-fluorophenyl group by introducing a halogen atom at position 2 and an electron-withdrawing group (e.g., iodine, cyano, and trifluoromethyl) at position 5 led to 34 compounds with good insecticidal efficacy against Mythimna separata, Plutella xylostella, and Spodoptera frugiperda. Among them, compound IV f against M. separata showed potency comparable to that of chlorantraniliprole. IV p against P. xylostella displayed a 4.5 times higher potency than chlorantraniliprole. In addition, IV d and chlorantraniliprole exhibited comparable potencies against S. frugiperda. Transcriptome analysis showed that the molecular target of compound IV f is the ryanodine receptor. Molecular docking was further performed to verify the mode of action and insecticidal activity against resistant P. xylostella.
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Affiliation(s)
- Jinzhou Ren
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xia Ji
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jin Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhenwu Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xinyuan Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lixia Xiong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Na Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Tang L, Ye Y, Ji J, Wang JS, Huang Z, Sun J, Sheng L, Sun X. PI3K/Akt/FoxO Pathway Mediates Antagonistic Toxicity in HepG2 Cells Coexposed to Deoxynivalenol and Enniatins. J Agric Food Chem 2024; 72:8214-8224. [PMID: 38557103 DOI: 10.1021/acs.jafc.4c01888] [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] [Indexed: 04/04/2024]
Abstract
The emerging mycotoxins enniatins (ENNs) and the traditional mycotoxin deoxynivalenol (DON) often co-contaminate various grain raw materials and foods. While the liver is their common target organ, the mechanism of their combined effect remains unclear. In this study, the combined cytotoxic effects of four ENNs (ENA, ENA1, ENB, and ENB1) with DON and their mechanisms were investigated using the HepG2 cell line. Additionally, a population exposure risk assessment of these mycotoxins was performed by using in vitro experiments and computer simulations. The results showed that only ENA at 1/4 IC50 and ENB1 at 1/8 IC50 coexposed with DON showed an additive effect, while ENB showed the strongest antagonism at IC50 (CI = 3.890). Co-incubation of ENNs regulated the signaling molecule levels which were disrupted by DON. Transcriptome analysis showed that ENB (IC50) up-regulated the PI3K/Akt/FoxO signaling pathway and inhibited the expression of apoptotic genes (Bax, P53, Caspase 3, etc.) via phosphorylation of FoxO, thereby reducing the cytotoxic effects caused by DON. Both types of mycotoxins posed serious health risks, and the cumulative risk of coexposure was particularly important for emerging mycotoxins.
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Affiliation(s)
- Luyao Tang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
| | - Jia-Sheng Wang
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602, United States
| | - Zhicong Huang
- Food and Drug Administration, Zhongshan City West District Street, Zhongshan, Guangdong 528401, PR China
| | - Jiadi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
| | - Xiulan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, PR China
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Wang Q, Wang Z, Guan J, Song J. Transcriptome Analysis Reveals the Important Role of Vitamin B 12 in the Response of Natronorubrum daqingense to Salt Stress. Int J Mol Sci 2024; 25:4168. [PMID: 38673755 PMCID: PMC11050368 DOI: 10.3390/ijms25084168] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Natronorubrum daqingense JX313T is an extremely halophilic archaea that can grow in a NaCl-saturated environment. The excellent salt tolerance of N. daqingense makes it a high-potential candidate for researching the salt stress mechanisms of halophilic microorganisms from Natronorubrum. In this study, transcriptome analysis revealed that three genes related to the biosynthesis of vitamin B12 were upregulated in response to salt stress. For the wild-type (WT) strain JX313T, the low-salt adaptive mutant LND5, and the vitamin B12 synthesis-deficient strain ΔcobC, the exogenous addition of 10 mg/L of vitamin B12 could maximize their cell survival and biomass in both optimal and salt stress environments. Knockout of cobC resulted in changes in the growth boundary of the strain, as well as a significant decrease in cell survival and biomass, and the inability to synthesize vitamin B12. According to the HPLC analysis, when the external NaCl concentration (w/v) increased from 17.5% (optimal) to 22.5% (5% salt stress), the intracellular accumulation of vitamin B12 in WT increased significantly from (11.54 ± 0.44) mg/L to (15.23 ± 0.20) mg/L. In summary, N. daqingense is capable of absorbing or synthesizing vitamin B12 in response to salt stress, suggesting that vitamin B12 serves as a specific compatible solute effector for N. daqingense during salt stress.
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Affiliation(s)
| | | | | | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China; (Q.W.); (Z.W.); (J.G.)
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17
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Chakravarthi VP, Dilower I, Ghosh S, Borosha S, Mohamadi R, Dahiya V, Vo K, Lee EB, Ratri A, Kumar V, Marsh CA, Fields PE, Rumi MAK. ERβ Regulation of Indian Hedgehog Expression in the First Wave of Ovarian Follicles. Cells 2024; 13:644. [PMID: 38607081 PMCID: PMC11011683 DOI: 10.3390/cells13070644] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Increased activation of ovarian primordial follicles in Erβ knockout (ErβKO) rats becomes evident as early as postnatal day 8.5. To identify the ERβ-regulated genes that may control ovarian primordial follicle activation, we analyzed the transcriptome profiles of ErβKO rat ovaries collected on postnatal days 4.5, 6.5, and 8.5. Compared to wildtype ovaries, ErβKO ovaries displayed dramatic downregulation of Indian hedgehog (Ihh) expression. IHH-regulated genes, including Hhip, Gli1, and Ptch1, were also downregulated in ErβKO ovaries. This was associated with a downregulation of steroidogenic enzymes Cyp11a1, Cyp19a1, and Hsd17b1. The expression of Ihh remained very low in ErβKO ovaries despite the high levels of Gdf9 and Bmp15, which are known upregulators of Ihh expression in the granulosa cells of activated ovarian follicles. Strikingly, the downregulation of the Ihh gene in ErβKO ovaries began to disappear on postnatal day 16.5 and recovered on postnatal day 21.5. In rat ovaries, the first wave of primordial follicles is rapidly activated after their formation, whereas the second wave of primordial follicles remains dormant in the ovarian cortex and slowly starts activating after postnatal day 12.5. We localized the expression of Ihh mRNA in postnatal day 8.5 wildtype rat ovaries but not in the age-matched ErβKO ovaries. In postnatal day 21.5 ErβKO rat ovaries, we detected Ihh mRNA mainly in the activated follicles in the ovaries' peripheral regions. Our findings indicate that the expression of Ihh in the granulosa cells of the activated first wave of ovarian follicles depends on ERβ.
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Affiliation(s)
- V. Praveen Chakravarthi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Iman Dilower
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Subhra Ghosh
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Shaon Borosha
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Ryan Mohamadi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Vinesh Dahiya
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Kevin Vo
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Eun B. Lee
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Anamika Ratri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Vishnu Kumar
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - Courtney A. Marsh
- Obstetrics and Gynecology, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA;
| | - Patrick E. Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
| | - M. A. Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center (KUMC), Kansas City, KS 66160, USA; (V.P.C.); (I.D.); (S.G.); (S.B.); (R.M.); (V.D.); (K.V.); (E.B.L.); (A.R.); (V.K.); (P.E.F.)
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18
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Seki T, Ohshima S, Komatsu S, Yamada S, Kashiwagi H, Goto Y, Tsuda B, Kanno A, Yasuda A, Kuno H, Tsuji NM, Shiina T, Kametani Y. Coccomyxa subellipsoidea KJ Components Enhance the Expression of Metallothioneins and Th17 Cytokines during Human T Cell Activation. Microorganisms 2024; 12:741. [PMID: 38674685 PMCID: PMC11051862 DOI: 10.3390/microorganisms12040741] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Coccomyxa subellipsoidea KJ (C-KJ) is a green alga with unique immunoregulatory characteristics. Here, we investigated the mechanism underlying the modification of T cell function by C-KJ components. The water-soluble extract of C-KJ was fractionated into protein (P) and sugar (S) fractions acidic (AS), basic (BS), and neutral (NS). These fractions were used for the treatment of peripheral blood mononuclear cells stimulated with toxic shock syndrome toxin-1. Transcriptome analysis revealed that both P and AS enhanced the expression of the genes encoding metallothionein (MT) family proteins, inflammatory factors, and T helper (Th) 17 cytokine and suppressed that of those encoding Th2 cytokines in stimulated T cells. The kinetics of MT1 and MT2A gene expression showed a transient increase in MT1 and maintenance of MT2A mRNA after T cell stimulation in the presence of AS. The kinetics of Th17-related cytokine secretion in the early period were comparable to those of MT2A mRNA. Furthermore, our findings revealed that static, a STAT-3 inhibitor, significantly suppressed MT2A gene expression. These findings suggest that the expression of MTs is involved in the immune regulatory function of C-KJ components, which is partially regulated by Th17 responses, and may help develop innovative immunoregulatory drugs or functional foods.
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Affiliation(s)
- Toshiro Seki
- Department of Internal Medicine, Division of Nephrology, Endocrinology and Metabolism, Tokai University School of Medicine, Isehara 259-1193, Japan; (T.S.); (A.Y.)
| | - Shino Ohshima
- Department of Molecular Life Science, Division of Basic Medical Science, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.O.); (T.S.)
| | - Satoko Komatsu
- DENSO CORPORATION, Kariya 448-0029, Japan; (S.K.); (H.K.)
| | - Soga Yamada
- Department of Molecular Life Science, Division of Basic Medical Science, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.O.); (T.S.)
| | - Hirofumi Kashiwagi
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Yumiko Goto
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Banri Tsuda
- Department of Palliative Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Akiko Kanno
- DENSO CORPORATION, Kariya 448-0029, Japan; (S.K.); (H.K.)
| | - Atsushi Yasuda
- Department of Internal Medicine, Division of Nephrology, Endocrinology and Metabolism, Tokai University School of Medicine, Isehara 259-1193, Japan; (T.S.); (A.Y.)
| | - Hitoshi Kuno
- DENSO CORPORATION, Kariya 448-0029, Japan; (S.K.); (H.K.)
| | - Noriko M Tsuji
- Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
- Department of Food Science, Jumonji University, Niiza 352-8510, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.O.); (T.S.)
- Institute of Advanced Biosciences, Tokai University, Hiratsuka 259-1207, Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Division of Basic Medical Science, Tokai University School of Medicine, Isehara 259-1193, Japan; (S.O.); (T.S.)
- Institute of Advanced Biosciences, Tokai University, Hiratsuka 259-1207, Japan
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19
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Hao EY, Liu XL, Chang LY, Xue H, Su BF, Chen YF, Wang DH, Shi L, Chen H. Melatonin alleviates endoplasmic reticulum stress to improve ovarian function by regulating the mTOR pathway in aged laying hens. Poult Sci 2024; 103:103703. [PMID: 38631228 PMCID: PMC11040121 DOI: 10.1016/j.psj.2024.103703] [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: 01/21/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Granular cell apoptosis is a key factor leading to follicular atresia and decreased laying rate in aged laying hens. Endoplasmic reticulum stress (ERS) induced cell apoptosis is a new type of apoptosis pathway. Previous studies have shown that the ERS pathway is involved in the regulation of follicular development and atresia, and can be regulated by mTOR. Melatonin (MEL) can protect the normal development of follicles, but the precise mechanism by which MEL regulates follicular development is not yet clear. So, we investigated the potential relationship between MEL and ERS and mTOR signaling pathway in vivo through intraperitoneal injection of MEL in aged laying hens. The results show that the laying rate, ovarian follicle number, plasma MEL, E2, LH, FSH concentrations, as well as the mRNA expression of mTOR signaling-associated genes TSC1, TSC2, mTOR, 4E-BP1, and S6K in old later-period chicken control (Old-CN) group was significantly decreased (P < 0.01). In contrast, the ERS-related of plasma and granular cell layer mRNA expression of Grp78, CHOP, and Caspase-3 was significantly increased (P < 0.01). While both of the effects were reversed by MEL. Then, aging granulosa cells were treated with MEL in vitro, followed by RNA seq analysis, and it was found that 259 and 322 genes were upregulated and downregulated. After performing GO enrichment analysis, it was found that DEGs significantly contribute to the biological processes including cell growth and apoptosis. Using pathway enrichment analysis, we found significant overrepresentation of cellular processes related to mTOR signaling and endoplasmic reticulum (ER) stress, involving genes such as GRB10, SGK1, PRKCA, RPS6KA2, RAF1, PIK3R3, FOXO1, DERL3, HMOX1, TLR7, VAMP7 and INSIG2. The obtained results of RT-PCR showed consistency with the RNA-Seq data. In summary, the underlined results revealed that MEL has significantly contributed to follicular development via activating the mTOR signaling pathway-related genes and alleviating ERS-related genes in laying hens. The current study provides a theoretical background for enhancing the egg-laying capability of hens and also providing a basis for elucidating the molecular mechanism of follicular selection.
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Affiliation(s)
- Er-Ying Hao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xue-Lu Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Li-Yun Chang
- Tangshan Normal University, Tangshan, Hebei 063002, China
| | - Han Xue
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Bo-Fei Su
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yi-Fan Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - De-He Wang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lei Shi
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Hui Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei 071001, China.
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20
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Wang D, Chen M, Peng J, Zheng H, Lu Y, Wu G, Wu J, Li J, Chen J, Yan F, Rao S. Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection. Int J Mol Sci 2024; 25:4012. [PMID: 38612822 PMCID: PMC11012278 DOI: 10.3390/ijms25074012] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
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21
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Cao L, Wang G, Ye X, Li F, Wang S, Li H, Wang P, Wang J. Physiological, Metabolic, and Transcriptomic Analyses Reveal Mechanisms of Proliferation and Somatic Embryogenesis of Litchi ( Litchi chinensis Sonn.) Embryogenic Callus Promoted by D-Arginine Treatment. Int J Mol Sci 2024; 25:3965. [PMID: 38612774 PMCID: PMC11012067 DOI: 10.3390/ijms25073965] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
D-arginine (D-Arg) can promote embryogenic callus (EC) proliferation and increase the rate of somatic embryo induction of litchi (Litchi chinensis Sonn.), yet the mechanism underlying the processes is incompletely understood. To investigate the mechanism, physiological responses of polyamines (PAs) [putrescine (Put), spermidine (Spd), and spermine (Spm)] were investigated for D-Arg-treated litchi EC and enzyme activity related to polyamine metabolism, plant endogenous hormones, and polyamine- and embryogenic-related genes were explored. Results showed that the exogenous addition of D-Arg reduces the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) in EC, reduces the production of H2O2, promotes EC proliferation, and increases the (Spd + Spm)/Put ratio to promote somatic embryo induction. Exogenous D-Arg application promoted somatic embryogenesis (SE) by increasing indole-3-acetyl glycine (IAA-Gly), kinetin-9-glucoside (K9G), and dihydrozeatin-7-glucoside (DHZ7G) levels and decreasing trans-zeatin riboside (tZR), N-[(-)-jasmonoyl]-(L)-valine (JA-Val), jasmonic acid (JA), and jasmonoyl-L-isoleucine (Ja-ILE) levels on 18 d, as well as promoting cell division and differentiation. The application of exogenous D-Arg regulated EC proliferation and somatic embryo induction by altering gene expression levels of the WRKY family, AP2/ERF family, C3H family, and C2H2 family. These results indicate that exogenous D-Arg could regulate the proliferation of EC and the SE induction of litchi by changing the biosynthesis of PAs through the alteration of gene expression pattern and endogenous hormone metabolism.
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Affiliation(s)
- Ludan Cao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China;
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Guo Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Fang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Shujun Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Huanling Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Jiabao Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (G.W.); (F.L.); (S.W.); (H.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
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22
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Chen Z, Zhu Y, Chen S, Li Z, Fu G, Wang Y. Immune patterns of cuproptosis in ischemic heart failure: A transcriptome analysis. J Cell Mol Med 2024; 28:e18187. [PMID: 38509725 PMCID: PMC10955177 DOI: 10.1111/jcmm.18187] [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: 07/04/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
Cuproptosis is a recently discovered programmed cell death pattern that affects the tricarboxylic acid (TCA) cycle by disrupting the lipoylation of pyruvate dehydrogenase (PDH) complex components. However, the role of cuproptosis in the progression of ischemic heart failure (IHF) has not been investigated. In this study, we investigated the expression of 10 cuproptosis-related genes in samples from both healthy individuals and those with IHF. Utilizing these differential gene expressions, we developed a risk prediction model that effectively distinguished healthy and IHF samples. Furthermore, we conducted a comprehensive evaluation of the association between cuproptosis and the immune microenvironment in IHF, encompassing infiltrated immunocytes, immune reaction gene-sets and human leukocyte antigen (HLA) genes. Moreover, we identified two different cuproptosis-mediated expression patterns in IHF and explored the immune characteristics associated with each pattern. In conclusion, this study elucidates the significant influence of cuproptosis on the immune microenvironment in ischemic heart failure (IHF), providing valuable insights for future mechanistic research exploring the association between cuproptosis and IHF.
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Affiliation(s)
- Zhebin Chen
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
| | - Yunhui Zhu
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
| | - Songzan Chen
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
| | - Zhengwei Li
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
| | - Guosheng Fu
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
| | - Yao Wang
- Department of Cardiology, Sir Run Run Shaw HospitalSchool of Medicine, Zhejiang UniversityHangzhouPeople's Republic of China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang ProvinceHangzhouPeople's Republic of China
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23
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Zhang G, Liu P, Liang R, Ying F, Liu D, Su M, Chen L, Zhang Q, Liu Y, Liu S, Zhao G, Li Q. Transcriptome analysis reveals the genes involved in spermatogenesis in white feather broilers. Poult Sci 2024; 103:103468. [PMID: 38359768 PMCID: PMC10875292 DOI: 10.1016/j.psj.2024.103468] [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: 09/05/2023] [Revised: 12/23/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Semen volume is an important economic trait of broilers and one of the important indices for continuous breeding. The objective of this study was to identify genes related to semen volume through transcriptome analysis of the testis tissue of white feather broilers. The testis samples with the highest semen volume (H group, n = 5) and lowest semen volume (L group, n = 5) were selected from 400-day-old roosters for transcriptome analysis by RNA sequencing. During the screening of differentially expressed genes (DEGs) between the H and L groups, a total of 386 DEGs were identified, among which 348 were upregulated and 38 were downregulated. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune response, leukocyte differentiation, cell adhesion molecules and collagen binding played vital roles in spermatogenesis. The results showed that 4 genes related to spermatogenesis, namely, COL1A1, CD74, ARPC1B and APOA1, were significantly expressed in Group H, which was consistent with the phenotype results. Our findings may provide a basis for further research on the genetic mechanism of semen volume in white feather broilers.
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Affiliation(s)
- Gaomeng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Peihao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ruiping Liang
- Beijing Changping District Center for Animal Disease Prevention and Control, Beijing, P. R. China
| | - Fan Ying
- MiLe Xinguang Agricultural and Animal Industrials Corporation, Mile, P. R. China
| | - Dawei Liu
- MiLe Xinguang Agricultural and Animal Industrials Corporation, Mile, P. R. China
| | - Meng Su
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yuhong Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Sha Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
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24
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Qu K, Yin Z, Gao C, Song G, Guo Z, Yin G, Tang J, Yuan Y, Dong C, Jiang Y, Niu J, Li Q. Mutagenesis-Derived Resistance to Black Point in Wheat. Plant Dis 2024; 108:899-907. [PMID: 37822099 DOI: 10.1094/pdis-07-23-1369-re] [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] [Indexed: 10/13/2023]
Abstract
Black point, a severe global wheat disease, necessitates deploying resistant cultivars for effective control. However, susceptibility remains prevalent among most wheat cultivars. Identifying new sources of resistance and understanding their mechanisms are crucial for breeding resistant cultivars. This study pinpointed black point resistance in an ethyl methane sulfonate (EMS)-mutagenized wheat population of Wanyuanbai 1 (WYB) and analyzed resistant mutants using RNA-Seq. The findings revealed the following: (i) wyb-18, among 10,008 EMS-mutagenized lines, exhibited robust resistance with significantly lower black point incidence under artificial Bipolaris sorokiniana inoculation in 2020 and 2021 (average incidence of 5.2% over 2 years), markedly reduced compared with WYB (50.9%). (ii) wyb-18 kernels displayed black point symptoms at 12 days after inoculation (dai), 3 days later than WYB. At 15 dai, wyb-18 kernels had isolated black spots, unlike WYB kernels, where the entire embryo turned black. (iii) wyb-18 showed heightened antioxidant enzyme activity, including peroxidase, catalase, and superoxide dismutase. (iv) Analysis of 543 differentially expressed genes between wyb-18 and WYB at 9 dai identified enrichment in the MAPK signaling pathway through KEGG analysis. Ten genes in this pathway exhibited upregulated expression, while one was downregulated in wyb-18. Among these genes, PR1, WRKY11, SAPK5, and TraesCS1A02G326800 (chitin recognition protein) consistently showed upregulation in wyb-18, making them potential candidates for black point resistance. These results offer valuable germplasm resources for breeding and novel insights into the mechanisms of black point resistance.
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Affiliation(s)
- Kefei Qu
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhao Yin
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Chuang Gao
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Gaili Song
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenfeng Guo
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Guihong Yin
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianwei Tang
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuhao Yuan
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Chunhao Dong
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yumei Jiang
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Jishan Niu
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiaoyun Li
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
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25
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Joo S, Lee SY, Lee SY, Hwang Y, Kim M, Jeong JW, Jang SI, Fang S. Triamcinolone acetonide alleviates benign biliary stricture by ameliorating biliary fibrosis and inflammation. BMB Rep 2024; 57:200-205. [PMID: 38523372 PMCID: PMC11058357] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/29/2023] [Accepted: 01/25/2024] [Indexed: 03/26/2024] Open
Abstract
We conducted a comprehensive series of molecular biological studies aimed at unraveling the intricate mechanisms underlying the anti-fibrotic effects of triamcinolone acetonide (TA) when used in conjunction with fully covered self-expandable metal stents (FCSEMS) for the management of benign biliary strictures (BBS). To decipher the molecular mechanisms responsible for the anti-fibrotic effects of corticosteroids on gallbladder mucosa, we conducted a comprehensive analysis. This analysis included various methodologies such as immunohistochemistry, ELISA, real-time PCR, and transcriptome analysis, enabling us to examine alterations in factors related to fibrosis and inflammation at both the protein and RNA levels. Overall, our findings revealed a dose-dependent decrease in fibrosisrelated signaling with higher TA concentrations. The 15 mg of steroid treatment (1X) exhibited anti-fibrosis and anti-inflammatory effects after 4 weeks, whereas the 30 mg of steroid treatment (2X) rapidly reduced fibrosis and inflammation within 2 weeks in BBS. Transcriptomic analysis results consistently demonstrated significant downregulation of fibrosis- and inflammation-related pathways and genes in steroid-treated fibroblasts. Use of corticosteroids, specifically TA, together with FCSEMS was effective for the treatment of BBS, ameliorating fibrosis and inflammation. Our molecular biological analysis supports the potential development of steroid-eluted FCSEMS as a therapeutic option for BBS in humans resulting from various surgical procedures. [BMB Reports 2024; 57(4): 200-205].
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Affiliation(s)
- Seyeon Joo
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - See Young Lee
- Division of Gastroenterology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Su Yeon Lee
- Division of Gastroenterology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jae Woong Jeong
- Department of Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sung Ill Jang
- Division of Gastroenterology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
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Wang R, Li Y, Xu S, Huang Q, Tu M, Zhu Y, Cen H, Dong J, Jiang L, Yao X. Genome-wide association study reveals the genetic basis for petal-size formation in rapeseed (Brassica napus) and CRISPR-Cas9-mediated mutagenesis of BnFHY3 for petal-size reduction. Plant J 2024; 118:373-387. [PMID: 38159103 DOI: 10.1111/tpj.16609] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Petals in rapeseed (Brassica napus) serve multiple functions, including protection of reproductive organs, nutrient acquisition, and attraction of pollinators. However, they also cluster densely at the top, forming a thick layer that absorbs and reflects a considerable amount of photosynthetically active radiation. Breeding genotypes with large, small, or even petal-less varieties, requires knowledge of primary genes for allelic selection and manipulation. However, our current understanding of petal-size regulation is limited, and the lack of markers and pre-breeding materials hinders targeted petal-size breeding. Here, we conducted a genome-wide association study on petal size using 295 diverse accessions. We identified 20 significant single nucleotide polymorphisms and 236 genes associated with petal-size variation. Through a cross-analysis of genomic and transcriptomic data, we focused on 14 specific genes, from which molecular markers for diverging petal-size features can be developed. Leveraging CRISPR-Cas9 technology, we successfully generated a quadruple mutant of Far-Red Elongated Hypocotyl 3 (q-bnfhy3), which exhibited smaller petals compared to the wild type. Our study provides insights into the genetic basis of petal-size regulation in rapeseed and offers abundant potential molecular markers for breeding. The q-bnfhy3 mutant unveiled a novel role of FHY3 orthologues in regulating petal size in addition to previously reported functions.
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Affiliation(s)
- Ruisen Wang
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
| | - Yafei Li
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Shiqi Xu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Qi Huang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Haiyan Cen
- College of Food Science and Bioengineering, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Xiangtan Yao
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
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Zhang Z, Chen T, Yin X, Wang W, Li W, Chen X, Ma J, Long Y. Honokiol inhibits Botryosphaeria dothidea, the causal pathogen of kiwifruit soft rot, by targeting membrane lipid biosynthesis. Pest Manag Sci 2024; 80:1779-1794. [PMID: 38031205 DOI: 10.1002/ps.7910] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/23/2023] [Accepted: 11/30/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Kiwifruit soft rot is mainly caused by Botryosphaeria dothidea, representing a considerable threat to kiwifruit industry. This investigation assessed the inhibitory consequences and mechanisms of honokiol against B. dothidea, evaluating the inhibitory effects and underlying mechanism. RESULTS A strain of B.dothidea (XFCT-2) was isolated from infected soft rot kiwifruit. The findings indicate that honokiol hindered the mycelial growth, conidial germination, and pathogenicity of B. dothidea in a dose-dependent manner, both in vitro and in vivo. Furthermore, ultrastructural examinations showed that honokiol impaired the integrity of B. dothidea, leading to an elevation in cell membrane permeability, engendering a multitude of intracellular substance extravasations and hampering energy metabolism. Transcriptome analysis exhibited that honokiol-regulated genes were related to membrane lipid biosynthesis, comprising ACC1, FAS2, Arp2, gk, Cesle, and Etnk1. These findings indicate that honokiol impedes B. dothidea by obstructing lipid biosynthesis within the cell membrane and compromising its integrity, halting the growth of the mycelia, which could potentially cause cellular demise. CONCLUSION This investigation illustrates how honokiol functions as an eco-friendly approach to prevent the occurrence of soft rot in kiwifruits. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Zhuzhu Zhang
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Teaching Experiment Farm, Guizhou University, Guiyang, China
| | - Tingting Chen
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Teaching Experiment Farm, Guizhou University, Guiyang, China
| | - Xianhui Yin
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
| | - Weizhen Wang
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
| | - Wenzhi Li
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
| | - Xuetang Chen
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiling Ma
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
| | - Youhua Long
- Research Center for Engineering Technology of Kiwifruit, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Teaching Experiment Farm, Guizhou University, Guiyang, China
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28
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Renukdas NN, Kelly AM, Zinta G, Sinha AK. Hepatic transcriptome profiling of largemouth bass (Micropterus salmoides Lacépède) injected with Flavobacterium covae or lipopolysaccharide. J Fish Dis 2024:e13948. [PMID: 38558407 DOI: 10.1111/jfd.13948] [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] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Flavobacterium covae (columnaris) is the most detrimental bacterial disease affecting the largemouth bass (Micropterus salmoides Lacépède) aquaculture industry. In the current study, fish received an intraperitoneal injection of either 1× PBS (100 μL), LPS in PBS (100 μL, 10 μg/mL), or F. covae (100 μL, 2.85 × 1011 CFU/mL) to simulate immunological challenges. After 24 h post-injection, liver tissue from the control and treated groups were then collected for transcriptome analysis. Results of the Gene Ontology (GO) and KEGG pathway analyses for the F. covae and LPS-injected groups found differentially expressed genes (DEGs) enriched primarily in toll-like receptors (TLRs), cytokine-cytokine receptors, complement and coagulation cascades, and the PPAR signalling pathways. This suggests that the liver immune system is enhanced by these five combined pathways. Additionally, the DEGs TLR5, MYD88, and IL-1 were significantly upregulated in F. covae and LPS-injected fish compared to the controls, whereas IL-8 was downregulated. The upregulation of TLR5 was unexpected as F. covae lacks flagellin, the protein that binds to TLR5. Additionally, it is unknown whether the TLR5 is upregulated by LPS. Further research into the upregulation of TLR5 is warranted. These results provide insight into immune responses and associated pathways contributing to the immune system in the liver during columnaris infection and induced response to LPS in largemouth bass.
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Affiliation(s)
- Nilima N Renukdas
- Aquaculture Laboratory, Arkansas Department of Agriculture, Little Rock, Arkansas, USA
- Department of Aquaculture and Fisheries, University of Arkansas at Pine Bluff, Pine Bluff, Arkansas, USA
| | - Anita M Kelly
- Department of Aquaculture and Fisheries, University of Arkansas at Pine Bluff, Pine Bluff, Arkansas, USA
- Alabama Fish Farming Center, Auburn University, Greensboro, Alabama, USA
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Amit Kumar Sinha
- Department of Aquaculture and Fisheries, University of Arkansas at Pine Bluff, Pine Bluff, Arkansas, USA
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29
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Zhen X, Liu C, Guo Y, Yu Z, Han Y, Zhang B, Liang Y. Leaf Senescence Regulation Mechanism Based on Comparative Transcriptome Analysis in Foxtail Millet. Int J Mol Sci 2024; 25:3905. [PMID: 38612713 PMCID: PMC11011800 DOI: 10.3390/ijms25073905] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Leaf senescence, a pivotal process in plants, directly influences both crop yield and nutritional quality. Foxtail millet (Setaria italica) is a C4 model crop renowned for its exceptional nutritional value and stress tolerance characteristics. However, there is a lack of research on the identification of senescence-associated genes (SAGs) and the underlying molecular regulatory mechanisms governing this process. In this study, a dark-induced senescence (DIS) experimental system was applied to investigate the extensive physiological and transcriptomic changes in two foxtail millet varieties with different degrees of leaf senescence. The physiological and biochemical indices revealed that the light senescence (LS) variety exhibited a delayed senescence phenotype, whereas the severe senescence (SS) variety exhibited an accelerated senescence phenotype. The most evident differences in gene expression profiles between these two varieties during DIS included photosynthesis, chlorophyll, and lipid metabolism. Comparative transcriptome analysis further revealed a significant up-regulation of genes related to polysaccharide and calcium ion binding, nitrogen utilization, defense response, and malate metabolism in LS. In contrast, the expression of genes associated with redox homeostasis, carbohydrate metabolism, lipid homeostasis, and hormone signaling was significantly altered in SS. Through WGCNA and RT-qPCR analyses, we identified three SAGs that exhibit potential negative regulation towards dark-induced leaf senescence in foxtail millet. This study establishes the foundation for a further comprehensive examination of the regulatory network governing leaf senescence and provides potential genetic resources for manipulating senescence in foxtail millet.
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Affiliation(s)
| | | | | | | | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (X.Z.); (C.L.); (Y.G.); (Z.Y.); (B.Z.)
| | | | - Yinpei Liang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (X.Z.); (C.L.); (Y.G.); (Z.Y.); (B.Z.)
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30
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Toh YH, Lin GH. Roles of DJ41_1407 and DJ41_1408 in Acinetobacter baumannii ATCC19606 Virulence and Antibiotic Response. Int J Mol Sci 2024; 25:3862. [PMID: 38612672 PMCID: PMC11011904 DOI: 10.3390/ijms25073862] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Acinetobacter baumannii is a major cause of nosocomial infections, and its highly adaptive nature and broad range of antibiotic resistance enable it to persist in hospital environments. A. baumannii often employs two-component systems (TCSs) to regulate adaptive responses and virulence-related traits. This study describes a previously uncharacterized TCS in the A. baumannii ATCC19606 strain, consisting of a transcriptional sensor, DJ41_1407, and its regulator, DJ41_1408, located adjacent to GacA of the GacSA TCS. Markerless mutagenesis was performed to construct DJ41_1407 and DJ41_1408 single and double mutants. DJ41_1408 was found to upregulate 49 genes and downregulate 43 genes, most of which were associated with carbon metabolism and other metabolic pathways, such as benzoate degradation. MEME analysis revealed a putative binding box for DJ41_1408, 5'TGTAAATRATTAYCAWTWAT3'. Colony size, motility, biofilm-forming ability, virulence, and antibiotic resistance of DJ41_1407 and DJ41_1408 single and double mutant strains were assessed against wild type. DJ41_1407 was found to enhance motility, while DJ41_1408 was found to upregulate biofilm-forming ability, and may also modulate antibiotic response. Both DJ41_1407 and DJ41_1408 suppressed virulence, based on results from a G. mellonella infection assay. These results showcase a novel A. baumannii TCS involved in metabolism, with effects on motility, biofilm-forming ability, virulence, and antibiotic response.
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Affiliation(s)
- Yee-Huan Toh
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, Hualien 970374, Taiwan;
| | - Guang-Huey Lin
- Department of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien 970374, Taiwan
- International College, Tzu Chi University, Hualien 970374, Taiwan
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31
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Divekar G, Colmant AMG, Furlong MJ, Etebari K. Transcriptome Analysis Reveals a Diverse Range of Novel Viruses in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2024; 16:516. [PMID: 38675859 PMCID: PMC11054854 DOI: 10.3390/v16040516] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
In Australia, Soldier flies (Inopus spp.) are economically significant pests of sugarcane that currently lack a viable management strategy. Despite various research efforts, the mechanisms underlying the damage caused by soldier fly larvae remain poorly understood. Our study aims to explore whether this damage is associated with the transmission of plant viruses during larval feeding. We also explore the larval transcriptome to identify any entomopathogenic viruses with the potential to be used as biocontrol agents in future pest management programs. Seven novel virus sequences are identified and characterised using de novo assembly of RNA-Seq data obtained from salivary glands of larvae. The novel virus sequences belong to different virus families and are tentatively named SF-associated anphevirus (SFaAV), SF-associated orthomyxo-like virus (SFaOV), SF-associated narna-like virus (SFaNV), SF-associated partiti-like virus (SFaPV), SF-associated toti-like virus (SFaTV-1 and SFaTV-2) and SF-associated densovirus (SFaDV). These newly identified viruses are more likely insect-associated viruses, as phylogenetic analyses show that they cluster with other insect-specific viruses. Small RNA analysis indicates prominent peaks at both 21 nt and 26-29 nt, suggesting the activation of host siRNA and piwiRNA pathways. Our study helps to improve understanding of the virome of soldier flies and could identify insect viruses for deployment in novel pest management strategies.
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Affiliation(s)
- Gayatri Divekar
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
| | - Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), 13005 Marseille, France
| | - Michael J. Furlong
- School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Kayvan Etebari
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
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32
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Li F, Ye H, Wang Y, Zhou J, Zhang G, Liu X, Lu X, Wang F, Chen Q, Chen G, Xiao Y, Tang W, Deng H. Transcriptomic Profiling of Two Rice Thermo-Sensitive Genic Male Sterile Lines with Contrasting Seed Storability after Artificial Accelerated Aging Treatment. Plants (Basel) 2024; 13:945. [PMID: 38611475 PMCID: PMC11013862 DOI: 10.3390/plants13070945] [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] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Seed storability has a significant impact on seed vitality and is a crucial genetic factor in maintaining seed value during storage. In this study, RNA sequencing was used to analyze the seed transcriptomes of two rice thermo-sensitive genic male sterile (TGMS) lines, S1146S (storage-tolerant) and SD26S (storage-susceptible), with 0 and 7 days of artificial accelerated aging treatment. In total, 2658 and 1523 differentially expressed genes (DEGs) were identified in S1146S and SD26S, respectively. Among these DEGs, 729 (G1) exhibited similar regulation patterns in both lines, while 1924 DEGs (G2) were specific to S1146S, 789 DEGs (G3) were specific to SD26S, and 5 DEGs (G4) were specific to contrary differential expression levels. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that "translation", "ribosome", "oxidative phosphorylation", "ATP-dependent activity", "intracellular protein transport", and "regulation of DNA-templated transcription" were significantly enriched during seed aging. Several genes, like Os01g0971400, Os01g0937200, Os03g0276500, Os05g0328632, and Os07g0214300, associated with seed storability were identified in G4. Core genes Os03g0100100 (OsPMEI12), Os03g0320900 (V2), Os02g0494000, Os02g0152800, and Os03g0710500 (OsBiP2) were identified in protein-protein interaction (PPI) networks. Seed vitality genes, MKKK62 (Os01g0699600), OsFbx352 (Os10g0127900), FSE6 (Os05g0540000), and RAmy3E (Os08g0473600), related to seed storability were identified. Overall, these results provide novel perspectives for studying the molecular response and related genes of different-storability rice TGMS lines under artificial aging conditions. They also provide new ideas for studying the storability of hybrid rice.
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Affiliation(s)
- Fan Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Hongbing Ye
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yingfeng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Jieqiang Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Qiuhong Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Guihua Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
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Wang H, Han T, Bai A, Xu H, Wang J, Hou X, Li Y. Potential Regulatory Networks and Heterosis for Flavonoid and Terpenoid Contents in Pak Choi: Metabolomic and Transcriptome Analyses. Int J Mol Sci 2024; 25:3587. [PMID: 38612398 PMCID: PMC11011442 DOI: 10.3390/ijms25073587] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Pak choi exhibits a diverse color range and serves as a rich source of flavonoids and terpenoids. However, the mechanisms underlying the heterosis and coordinated regulation of these compounds-particularly isorhamnetin-remain unclear. This study involved three hybrid combinations and the detection of 528 metabolites from all combinations, including 26 flavonoids and 88 terpenoids, through untargeted metabolomics. Analysis of differential metabolites indicated that the heterosis for the flavonoid and terpenoid contents was parent-dependent, and positive heterosis was observed for isorhamnetin in the two hybrid combinations (SZQ, 002 and HMG, ZMG). Moreover, there was a high transcription level of flavone 3'-O-methyltransferase, which is involved in isorhamnetin biosynthesis. The third group was considered the ideal hybrid combination for investigating the heterosis of flavonoid and terpenoid contents. Transcriptome analysis identified a total of 12,652 DEGs (TPM > 1) in various groups that were used for comparison, and DEGs encoding enzymes involved in various categories, including "carotenoid bio-synthesis" and "anthocyanin biosynthesis", were enriched in the hybrid combination (SZQ, 002). Moreover, the category of anthocyanin biosynthesis also was enriched in the hybrid combination (HMG, ZMG). The flavonoid pathway demonstrated more differential metabolites than the terpenoid pathway did. The WGCNA demonstrated notable positive correlations between the dark-green modules and many flavonoids and terpenoids. Moreover, there were 23 ERF genes in the co-expression network (r ≥ 0.90 and p < 0.05). Thus, ERF genes may play a significant role in regulating flavonoid and terpenoid biosynthesis. These findings enhance our understanding of the heterosis and coordinated regulation of flavonoid and terpenoid biosynthesis in pak choi, offering insights for genomics-based breeding improvements.
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Affiliation(s)
- Haibin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
| | - Tiantian Han
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
| | - Aimei Bai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
| | - Huanhuan Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
- Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (T.H.); (A.B.); (H.X.); (J.W.); (X.H.)
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Ku W, Su Y, Peng X, Wang R, Li H, Xiao L. Comparative Transcriptome Analysis Reveals Inhibitory Roles of Strigolactone in Axillary Bud Outgrowth in Ratoon Rice. Plants (Basel) 2024; 13:899. [PMID: 38592943 PMCID: PMC10975295 DOI: 10.3390/plants13060899] [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] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Axillary bud outgrowth, a key factor in ratoon rice yield formation, is regulated by several phytohormone signals. The regulatory mechanism of key genes underlying ratoon buds in response to phytohormones in ratoon rice has been less reported. In this study, GR24 (a strigolactone analogue) was used to analyze the ratooning characteristics in rice cultivar Huanghuazhan (HHZ). Results show that the elongation of the axillary buds in the first seasonal rice was significantly inhibited and the ratoon rate was reduced at most by up to 40% with GR24 treatment. Compared with the control, a significant reduction in the content of auxin and cytokinin in the second bud from the upper spike could be detected after GR24 treatment, especially 3 days after treatment. Transcriptome analysis suggested that there were at least 742 and 2877 differentially expressed genes (DEGs) within 6 h of GR24 treatment and 12 h of GR24 treatment, respectively. Further bioinformatics analysis revealed that GR24 treatment had a significant effect on the homeostasis and signal transduction of cytokinin and auxin. It is noteworthy that the gene expression levels of OsCKX1, OsCKX2, OsGH3.6, and OsGH3.8, which are involved in cytokinin or auxin metabolism, were enhanced by the 12 h GR24 treatment. Taken overall, this study showed the gene regulatory network of auxin and cytokinin homeostasis to be regulated by strigolactone in the axillary bud outgrowth of ratoon rice, which highlights the importance of these biological pathways in the regulation of axillary bud outgrowth in ratoon rice and would provide theoretical support for the molecular breeding of ratoon rice.
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Affiliation(s)
- Wenzhen Ku
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Yi Su
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
| | - Xiaoyun Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
| | - Haiou Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (W.K.); (Y.S.); (X.P.); (R.W.)
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Wang B, van der Kloet F, Kes MBMJ, Luirink J, Hamoen LW. Improving gene set enrichment analysis (GSEA) by using regulation directionality. Microbiol Spectr 2024; 12:e0345623. [PMID: 38294221 PMCID: PMC10913524 DOI: 10.1128/spectrum.03456-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.IMPORTANCEMeasuring the activity of all genes in cells is a common way to elucidate the function and regulation of genes. These transcriptome analyses produce large amounts of data since genomes contain thousands of genes. The analysis of these large data sets is challenging. Therefore, we developed a new software tool called GINtool that can facilitate the analysis of transcriptome data by using prior knowledge of gene sets controlled by the same regulator, the so-called regulons. An important novelty of GINtool is that it can take into account the directionality of gene regulation in these analyses, i.e., whether a gene is activated or repressed, which is crucial to assess whether a regulon or functional category is affected. GINtool also includes new graphical methods to facilitate the visual inspection of regulation events in transcriptome data sets. These and additional analysis methods included in GINtool make it a powerful software tool to analyze transcriptome data.
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Affiliation(s)
- Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Frans van der Kloet
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Mariah B. M. J. Kes
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joen Luirink
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Ren X, Li K, Fang X, Zhu Z, Chen Q, Li C, Hua H. Oral mucosal changes in tight junction proteins in patients with oral lichen planus. Oral Dis 2024. [PMID: 38439057 DOI: 10.1111/odi.14912] [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: 11/18/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
OBJECTIVE This study aimed to investigate the expression of tight junction, its distribution pattern in oral lichen planus samples and its potential association with the severity of oral lichen planus. MATERIALS AND METHODS Cross-sectional study designs were conducted. Transcriptome sequencing was conducted using oral mucosal tissues from 22 patients with oral lichen planus and 11 healthy controls. Immunohistochemistry and quantitative reverse transcription PCR were performed to verify the expression of claudin-1, claudin-4, occludin and zonula occludens-1 in oral mucosal tissues from another 30 patients with oral lichen planus and 26 healthy controls. The relationship between tight junction protein expression and oral lichen planus severity was explored using correlation analysis. RESULTS 5603 and 2475 differentially expressed genes were upregulated and downregulated respectively, in oral lichen planus tissues. KEGG analysis showed that tight junctions including CLDN1, CLDN4, OCLN and TJP1 were downregulated in oral lichen planus. Claudin-1, claudin-4, occludin and zonula occludens-1 expression was verified to be significantly lower in oral lichen planus. Furthermore, correlation analyses showed that decreased occludin expression was positively related to oral lichen planus severity. CONCLUSION Decreased expression of TJ barrier proteins may be associated with the development of oral lichen planus.
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Affiliation(s)
- Xiaomeng Ren
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
| | - Kaiyi Li
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China
| | - Xin Fang
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Department of Oral Medicine, Yunnan Key Laboratory of Stomatology, Kunming Medical University School and Hospital of Stomatology, Kunming, China
| | - Zhengda Zhu
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Department of Oral Medicine, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Qianming Chen
- Department of Oral Medicine, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Chunlei Li
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
| | - Hong Hua
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
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Wang B, Yang J, Zhao X, Feng X, Xu S, Li P, Li L, Chen Y. Antifungal activity of the botanical compound rhein against Phytophthora capsici and the underlying mechanisms. Pest Manag Sci 2024; 80:1228-1239. [PMID: 37897133 DOI: 10.1002/ps.7852] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/18/2023] [Accepted: 10/28/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Phytophthora capsici is an extremely destructive phytopathogenic oomycete that causes huge economic losses. However, due to the drug resistance risk and environmental threat of chemical fungicides, it is necessary to develop environmentally friendly biocontrol alternatives. Rhein is a major medicinal ingredient of traditional Chinese herbs, and it is widely used in the medical field. However, its inhibitory effect against phytopathogens is unknown. Herein, the antifungal spectrum of rhein and its possible action mechanism against P. capsici were investigated. RESULTS Rhein possessed broad-spectrum antifungal activity against phytopathogens, particularly P. capsici, Phytophthora infestans, Helminthosporium maydis, and Rhizoctonia solani. Rhein inhibited the mycelial growth as well as the spore germination of P. capsici with mean 50% effective concentration (EC50 ) values of 4.68 μg mL-1 and 6.57 μg mL-1 against 117 P. capsici isolates, respectively. Rhein effectively suppressed the occurrence and spread of Phytophthora blight and significantly destroyed the cell membrane permeability and integrity of P. capsici, corroded its cell wall integrity, and damaged its morphology and ultrastructure. Moreover, rhein caused a considerable reduction in the phospholipid and cellulose contents. Genome-wide transcriptional profiling of P. capsici in response to rhein indicated significant reduction in the expression levels of genes participating in glycerolipid metabolism and starch and sucrose metabolism. Additionally, rhein strengthened the disease defense system of pepper by enhancing related enzyme activities. CONCLUSION This study demonstrated that rhein could effectively inhibit P. capsici using multiple mechanisms of action. Rhein has the potential to be an efficient alternative to control diseases caused by P. capsici. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Jingjing Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Xingzeng Zhao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Xu Feng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Pirui Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Linwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Yu Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
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Hani T, Fujita K, Kudo T, Taya Y, Sato K, Soeno Y. Tissue-Targeted Transcriptomics Reveals SEMA3D Control of Hypoglossal Nerve Projection to Mouse Tongue Primordia. Acta Histochem Cytochem 2024; 57:35-46. [PMID: 38463205 PMCID: PMC10918430 DOI: 10.1267/ahc.23-00073] [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: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 03/12/2024] Open
Abstract
The mouse hypoglossal nerve originates in the occipital motor nuclei at embryonic day (E)10.5 and projects a long distance, reaching the vicinity of the tongue primordia, the lateral lingual swellings, at E11.5. However, the details of how the hypoglossal nerve correctly projects to the primordia are poorly understood. To investigate the molecular basis of hypoglossal nerve elongation, we used a novel transcriptomic approach using the ROKU method. The ROKU algorithm identified 3825 genes specific for lateral lingual swellings at E11.5, of which 34 genes were predicted to be involved in axon guidance. Ingenuity Pathway Analysis-assisted enrichment revealed activation of the semaphorin signaling pathway during tongue development, and quantitative PCR showed that the expressions of Sema3d and Nrp1 in this pathway peaked at E11.5. Immunohistochemistry detected NRP1 in the hypoglossal nerve and SEMA3D as tiny granules in the extracellular space beneath the epithelium of the tongue primordia and in lateral and anterior regions of the mandibular arch. Fewer SEMA3D granules were localized around hypoglossal nerve axons and in the space where they elongated. In developing tongue primordia, tissue-specific regulation of SEMA3D might control the route of hypoglossal nerve projection via its repulsive effect on NRP1.
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Affiliation(s)
- Taisuke Hani
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
| | - Kazuya Fujita
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
| | - Tomoo Kudo
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
| | - Yuji Taya
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
| | - Kaori Sato
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
| | - Yuuichi Soeno
- Department of Pathology, The Nippon Dental University, School of Life Dentistry at Tokyo, 1-9-20, Fujimi, Chiyoda-ku, 102-8159 Tokyo, Japan
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Wang J, Lu Y, Zhang X, Hu W, Lin L, Deng Q, Xia H, Liang D, Lv X. Effects of Potassium-Containing Fertilizers on Sugar and Organic Acid Metabolism in Grape Fruits. Int J Mol Sci 2024; 25:2828. [PMID: 38474075 DOI: 10.3390/ijms25052828] [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: 01/28/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
To identify suitable potassium fertilizers for grape (Vitis vinifera L.) production and study their mechanism of action, the effects of four potassium-containing fertilizers (complex fertilizer, potassium nitrate, potassium sulfate, and potassium dihydrogen phosphate) on sugar and organic acid metabolism in grape fruits were investigated. Potassium-containing fertilizers increased the activity of sugar and organic acid metabolism-related enzymes at all stages of grape fruit development. During the later stages of fruit development, potassium-containing fertilizers increased the total soluble solid content and the sugar content of the different sugar fractions and decreased the titratable acid content and organic acid content of the different organic acid fractions. At the ripening stage of grape fruit, compared with the control, complex fertilizer, potassium nitrate, potassium sulfate, and potassium dihydrogen phosphate increased the total soluble solid content by 1.5, 1.2, 3.5, and 3.4 percentage points, decreased the titratable acid content by 0.09, 0.06, 0.18, and 0.17 percentage points, respectively, and also increased the total potassium content in grape fruits to a certain degree. Transcriptome analysis of the differentially expressed genes (DEGs) in the berries showed that applying potassium-containing fertilizers enriched the genes in pathways involved in fruit quality, namely, carbon metabolism, carbon fixation in photosynthetic organisms, glycolysis and gluconeogenesis, and fructose and mannose metabolism. Potassium-containing fertilizers affected the expression levels of genes regulating sugar metabolism and potassium ion uptake and transport. Overall, potassium-containing fertilizers can promote sugar accumulation and reduce acid accumulation in grape fruits, and potassium sulfate and potassium dihydrogen phosphate had the best effects among the fertilizers tested.
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Affiliation(s)
- Jin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuemei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Hu
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Lijin Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hui Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Dong Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiulan Lv
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
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Wei P, Zhou J, Xiong S, Yi F, Xu K, Liu M, Xi H, Zhou Z, Qiu Z, Liu H, Zeng J, Liu Y, Qiu P, Zhou J, Liu S, Long Z, Li J, Xiong L. Chestnut-Inspired Hollow Hydroxyapatite 3D Printing Scaffolds Accelerate Bone Regeneration by Recruiting Calcium Ions and Regulating Inflammation. ACS Appl Mater Interfaces 2024; 16:9768-9786. [PMID: 38349802 DOI: 10.1021/acsami.3c17087] [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] [Indexed: 02/15/2024]
Abstract
This study aims to overcome the drawbacks associated with hydroxyapatite (HAP) dense structures after sintering, which often result in undesirable features such as large grain size, reduced porosity, high crystallinity, and low specific surface area. These characteristics hinder osseointegration and limit the clinical applicability of the material. To address these issues, a new method involving the preparation of hollow hydroxyapatite (hHAP) microspheres has been proposed. These microspheres exhibit distinctive traits including weak crystallization, high specific surface area, and increased porosity. The weak crystallization aligns more closely with early mineralization products found in the human body and animals. Moreover, the microspheres' high specific surface area and porosity offer advantages for protein loading and facilitating osteoblast attachment. This innovative approach not only mitigates the limitations of conventional HAP structures but also holds the potential for improving the effectiveness of hydroxyapatite in biomedical applications, particularly in enhancing osseointegration. Three-dimensional printed hHAP/chitosan (CS) scaffolds with different hHAP concentration gradients were manufactured, and the physical and biological properties of each group were systematically evaluated. In vitro and in vivo experiments show that the hHAP/CS scaffold has excellent performance in bone remodeling. Furthermore, in-scaffold components, hHAP and CS were cocultured with bone marrow mesenchymal stem cells to explore the regulatory role of hHAP and CS in the process of bone healing and to reveal the cell-level specific regulatory network activated by hHAP. Enrichment analysis showed that hHAP can promote bone regeneration and reconstruction by recruiting calcium ions and regulating inflammatory reactions.
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Affiliation(s)
- Peng Wei
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Jingyu Zhou
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Shilang Xiong
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
- Department of Orthopedics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Feng Yi
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Kejun Xu
- Jiangxi Jiayou Shuguang Orthopedic Hospital, Nanchang 330009, Jiangxi, China
| | - Min Liu
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Hanrui Xi
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Zhigang Zhou
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Zhiqiang Qiu
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Hantian Liu
- Queen Mary School, Nanchang University, Nanchang 330036, China
| | - Jianhua Zeng
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yayun Liu
- Department of Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Peng Qiu
- Department of Orthopedics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Jianguo Zhou
- Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Shiwei Liu
- Ganzhou People's Hospital, Ganzhou, Jiangxi 341000, China
| | - Zhisheng Long
- Department of Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Jingtang Li
- Department of Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi, China
| | - Long Xiong
- Department of Orthopedics, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi, China
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Liu B, Wang N, Yang R, Wang X, Luo P, Chen Y, Wang F, Li M, Weng J, Zhang D, Yong H, Han J, Zhou Z, Zhang X, Hao Z, Li X. ZmADF5, a Maize Actin-Depolymerizing Factor Conferring Enhanced Drought Tolerance in Maize. Plants (Basel) 2024; 13:619. [PMID: 38475468 DOI: 10.3390/plants13050619] [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] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 03/14/2024]
Abstract
Drought stress is seriously affecting the growth and production of crops, especially when agricultural irrigation still remains quantitatively restricted in some arid and semi-arid areas. The identification of drought-tolerant genes is important for improving the adaptability of maize under stress. Here, we found that a new member of the actin-depolymerizing factor (ADF) family; the ZmADF5 gene was tightly linked with a consensus drought-tolerant quantitative trait locus, and the significantly associated signals were detected through genome wide association analysis. ZmADF5 expression could be induced by osmotic stress and the application of exogenous abscisic acid. Its overexpression in Arabidopsis and maize helped plants to keep a higher survival rate after water-deficit stress, which reduced the stomatal aperture and the water-loss rate, as well as improved clearance of reactive oxygen species. Moreover, seventeen differentially expressed genes were identified as regulated by both drought stress and ZmADF5, four of which were involved in the ABA-dependent drought stress response. ZmADF5-overexpressing plants were also identified as sensitive to ABA during the seed germination and seedling stages. These results suggested that ZmADF5 played an important role in the response to drought stress.
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Affiliation(s)
- Bojuan Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
| | - Ruisi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaonan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ping Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingshun Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianfeng Weng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Degui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongjun Yong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jienan Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiqiang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Texcoco 06600, Mexico
| | - Zhuanfang Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinhai Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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He Y, Li C, Yang M, Wang C, Guo H, Liu J, Liu H. Transcriptome Analysis Reveals the Mechanisms of Accumulation and Conversion of Folate Derivatives during Germination of Quinoa ( Chenopodium quinoa Willd.) Seeds. J Agric Food Chem 2024; 72:3800-3813. [PMID: 38327020 DOI: 10.1021/acs.jafc.3c08209] [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] [Indexed: 02/09/2024]
Abstract
Folate was enriched during quinoa germination, while molecular mechanisms were not well understood. In this study, three quinoa varieties were selected for germination, and changes in substrate content and enzyme activity of the folate biosynthesis pathway were monitored. 5-Methyltetrahydrofolate (5-CH3-THF) and 5-formyltetrahydrofolate (5-CHO-THF) were significantly enriched in quinoa sprouts. Among the selected varieties, QL-2 exhibited the lowest content of the oxidation product MeFox and the highest total folate content. Based on transcriptome analysis, the p-ABA branch was found to be crucial for folate accumulation, while the pterin branch served as a key control point for the one carbon pool by folate pathway, which limited further folate biosynthesis. In the one carbon pool by folate pathway, genes CqMTHFR and CqAMT significantly contributed to the enrichment of 5-CH3-THF and 5-CHO-THF. Findings gained here would facilitate the potential application of quinoa sprouts as an alternative strategy for folate supplementation.
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Affiliation(s)
- Yanan He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Cui Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Miao Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Haiyun Guo
- Hebei Tongfu Group Co., Ltd., Shijiazhuang 050000, China
| | - Jun Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Haijie Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Ye W, Fan J, Wu W, Chen Z, Huang Q, Qian L. Effects of fecal microbiota transplantation on metabolic health of DBA mice. Front Microbiol 2024; 15:1352555. [PMID: 38444807 PMCID: PMC10912182 DOI: 10.3389/fmicb.2024.1352555] [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: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Numerous studies have demonstrated that C57BL/6 mice exhibit superior growth rates and overall growth performance compared to DBA mice. To investigate whether this discrepancy in growth performance is linked to the composition of gut microorganisms, we conducted fecal microbiome transplantation (FMT) experiments. Methods Specifically, we transplanted fecal fluids from adult C57BL/6 mice, high-fat C57BL/6 mice, and Wistar rats into weaned DBA mice (0.2mL/d), and subsequently analyzed their gut contents and gene expression through 16S rRNA sequencing and transcriptome sequencing. During the test period, C57BL/6 mice and Wistar rats were provided with a normal diet, and high-fat C57BL/6 mice were provided with a high-fat diet. Results The results of our study revealed that mice receiving FMT from all three donor groups exhibited significantly higher daily weight gain and serum triglyceride (TG) levels compared to mice of CK group. 16S rRNA sequensing unveiled substantial differences in the abundance and function of the gut microbiota between the FMT groups and the CK group. Transcriptome analysis revealed a total of 988 differential genes, consisting of 759 up-regulated genes and 187 down-regulated genes, between the three experimental groups and the CK group. Functional Gene Ontology (GO) annotation suggested that these genes were primarily linked to lipid metabolism, coagulation, and immunity. Pearson correlation analysis was performed on the differential genes and clusters, and it revealed significant correlations, mainly related to processes such as fatty acid metabolism, fat digestion and absorption, and cholesterol metabolism. Discussion In summary, FMT from dominant strains improved the growth performance of DBA mice, including body weight gain, institutional growth, and immune performance. This change may be due to the increase of probiotic content in the intestinal tract by FMT and subsequent alteration of intestinal gene expression. However, the effects of cross-species fecal transplantation on the intestinal flora and gene expression of recipient mice were not significant.
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Affiliation(s)
- Wenxin Ye
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jinghui Fan
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Wenzi Wu
- Hainan Institute of Zhejiang University, Sanya, China
| | - Zhuo Chen
- Hainan Institute of Zhejiang University, Sanya, China
| | - Qixin Huang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lichun Qian
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
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Zhu PK, Zeng MY, Lin YH, Tang Y, He TY, Zheng YS, Chen LY. Variability in Leaf Color Induced by Chlorophyll Deficiency: Transcriptional Changes in Bamboo Leaves. Curr Issues Mol Biol 2024; 46:1503-1515. [PMID: 38392215 PMCID: PMC10888276 DOI: 10.3390/cimb46020097] [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: 01/04/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The diversity of leaf characteristics, particularly leaf color, underscores a pivotal area of inquiry within plant science. The synthesis and functionality of chlorophyll, crucial for photosynthesis, largely dictate leaf coloration, with varying concentrations imparting different shades of green. Complex gene interactions regulate the synthesis and degradation of chlorophyll, and disruptions in these pathways can result in abnormal chlorophyll production, thereby affecting leaf pigmentation. This study focuses on Bambusa multiplex f. silverstripe, a natural variant distinguished by a spectrum of leaf colors, such as green, white, and green-white, attributed to genetic variations influencing gene expression. By examining the physiological and molecular mechanisms underlying chlorophyll anomalies and genetic factors in Silverstripe, this research sheds light on the intricate gene interactions and regulatory networks that contribute to leaf color diversity. The investigation includes the measurement of photosynthetic pigments and nutrient concentrations across different leaf color types, alongside transcriptomic analyses for identifying differentially expressed genes. The role of key genes in pathways such as ALA biosynthesis, chlorophyll synthesis, photosynthesis, and sugar metabolism is explored, offering critical insights for advancing research and plant breeding practices.
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Affiliation(s)
- Peng-Kai Zhu
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei-Yin Zeng
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu-Han Lin
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Tang
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tian-You He
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu-Shan Zheng
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ling-Yan Chen
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yu K, Liang P, Yu H, Liu H, Guo J, Yan X, Li Z, Li G, Wang Y, Wang C. Integrating Transcriptome and Chemical Analyses to Provide Insights into Biosynthesis of Terpenoids and Flavonoids in the Medicinal Industrial Crop Andrographis paniculate and Its Antiviral Medicinal Parts. Molecules 2024; 29:852. [PMID: 38398604 PMCID: PMC10893308 DOI: 10.3390/molecules29040852] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Andrographis paniculata is a medicinal plant traditionally used to produce diterpene lactones and flavonoids, which possess various biological activities. Widely distributed in China, India, and other Southeast Asia countries, A. paniculata has become an important economic crop, significantly treating SARS-CoV-2, and is being cultivated on a large scale in southern China. The biosynthesis of active ingredients in A. paniculata are regulated and controlled by genes, but their specific roles are still not fully understood. To further explore the growth regulation factors and utilization of its medicinal parts of this industrial crop, chemical and transcriptome analyses were conducted on the roots, stems, and leaves of A. paniculata to identify the biosynthesis pathways and related candidate genes of the active ingredients. The chemical analysis revealed that the main components of A. paniculata were diterpene lactones and flavonoids, which displayed potential ability to treat SARS-CoV-2 through molecular docking. Moreover, the transcriptome sequencing annotated a total of 40,850 unigenes, including 7962 differentially expressed genes. Among these, 120 genes were involved in diterpene lactone biosynthesis and 60 genes were involved in flavonoid biosynthesis. The expression of diterpene lactone-related genes was the highest in leaves and the lowest in roots, consistent with our content determination results. It is speculated that these highly expressed genes in leaves may be involved in the biosynthesis pathway of diterpenes. Furthermore, two class Ⅰ terpene synthases in A. paniculata transcriptome were also annotated, providing reference for the downstream pathway of the diterpene lactone biosynthesis. With their excellent market value, our experiments will promote the study of the biosynthetic genes for active ingredients in A. paniculata and provide insights for subsequent in vitro biosynthesis.
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Affiliation(s)
- Kuo Yu
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Pengjie Liang
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Heshui Yu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Hui Liu
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Jialiang Guo
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Xiaohui Yan
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Guoqiang Li
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Ying Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Chunhua Wang
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
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Fu L, Tan D, Sun X, Ding Z, Zhang J. Extensive post-transcriptional regulation revealed by integrative transcriptome and proteome analyses in salicylic acid-induced flowering in duckweed ( Lemna gibba). Front Plant Sci 2024; 15:1331949. [PMID: 38390296 PMCID: PMC10883067 DOI: 10.3389/fpls.2024.1331949] [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] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Duckweed is an aquatic model plant with tremendous potential in industrial and agricultural applications. Duckweed rarely flowers which significantly hinders the resource collection and heterosis utilization. Salicylic acid (SA) can significantly induce duckweed to flower; however, the underlying regulatory mechanisms remain largely unknown. In this work, transcriptome and proteome were conducted in parallel to examine the expression change of genes and proteins in Lemna gibba under SA treatment. A high-quality reference transcriptome was generated using Iso-Seq strategy, yielding 42,281 full-length transcripts. A total of 422, 423, and 417 differentially expressed genes (DEGs), as well as 213, 51, and 92 differentially expressed proteins (DEPs), were identified at flower induction, flower initiation, and flowering stages by ssRNA-seq and iTRAQ methods. Most DEGs and DEPs were only regulated at either the transcriptomic or proteomic level. Additionally, DEPs exhibited low expression correlations with the corresponding mRNAs, suggesting that post-transcriptional regulation plays a pivotal role in SA-induced flowering in L. gibba. Specifically, the genes related to photosynthesis, stress, and hormone metabolism were mainly regulated at the mRNA level, those associated with mitochondrial electron transport / ATP synthesis, nucleotide synthesis, and secondary metabolism were regulated at the protein level, while those related to redox metabolism were regulated at the mRNA and/or protein levels. The post-transcriptional regulation of genes relevant to hormone synthesis, transcription factors, and flowering was also extensively analyzed and discussed. This is the first study of integrative transcriptomic and proteomic analyses in duckweed, providing novel insights of post-transcriptional regulation in SA-induced flowering of L. gibba.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Kang JN, Hur M, Kim CK, Yang SH, Lee SM. Enhancing transcriptome analysis in medicinal plants: multiple unigene sets in Astragalus membranaceus. Front Plant Sci 2024; 15:1301526. [PMID: 38384760 PMCID: PMC10879423 DOI: 10.3389/fpls.2024.1301526] [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: 09/26/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Astragalus membranaceus is a medicinal plant mainly used in East Asia and contains abundant secondary metabolites. Despite the importance of this plant, the available genomic and genetic information is still limited. De novo transcriptome construction is recognized as an essential method for transcriptome research when reference genome information is incomplete. In this study, we constructed three individual transcriptome sets (unigene sets) for detailed analysis of the phenylpropanoid biosynthesis pathway, a major metabolite of A. membranaceus. Set-1 was a circular consensus sequence (CCS) generated using PacBio sequencing (PacBio-seq). Set-2 consisted of hybridized assembled unigenes with Illumina sequencing (Illumina-seq) reads and PacBio CCS using rnaSPAdes. Set-3 unigenes were assembled from Illumina-seq reads using the Trinity software. Construction of multiple unigene sets provides several advantages for transcriptome analysis. First, it provides an appropriate expression filtering threshold for assembly-based unigenes: a threshold transcripts per million (TPM) ≥ 5 removed more than 88% of assembly-based unigenes, which were mostly short and low-expressing unigenes. Second, assembly-based unigenes compensated for the incomplete length of PacBio CCSs: the ends of the 5`/3` untranslated regions of phenylpropanoid-related unigenes derived from set-1 were incomplete, which suggests that PacBio CCSs are unlikely to be full-length transcripts. Third, more isoform unigenes could be obtained from multiple unigene sets; isoform unigenes missing in Set-1 were detected in set-2 and set-3. Finally, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that phenylpropanoid biosynthesis and carbohydrate metabolism were highly activated in A. membranaceus roots. Various sequencing technologies and assemblers have been developed for de novo transcriptome analysis. However, no technique is perfect for de novo transcriptome analysis, suggesting the need to construct multiple unigene sets. This method enables efficient transcript filtering and detection of longer and more diverse transcripts.
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Affiliation(s)
- Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Mok Hur
- Department of Herbal Crop Resources, National Institute of Horticultural & Herbal Science, Eumseong-gun, Chungcheongbuk-do, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - So-Hee Yang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju-si, Jeollabuk-do, Republic of Korea
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Tian Q, Xie X, Lai R, Cheng C, Zhang Z, Chen Y, XuHan X, Lin Y, Lai Z. Functional and Transcriptome Analysis Reveal Specific Roles of Dimocarpus longan DlRan3A and DlRan3B in Root Hair Development, Reproductive Growth, and Stress Tolerance. Plants (Basel) 2024; 13:480. [PMID: 38498444 PMCID: PMC10891736 DOI: 10.3390/plants13040480] [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] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Ran GTPases play essential roles in plant growth and development. Our previous studies revealed the nuclear localization of DlRan3A and DlRan3B proteins and proposed their functional redundancy and distinction in Dimocarpus longan somatic embryogenesis, hormone, and abiotic stress responses. To further explore the possible roles of DlRan3A and DlRan3B, gene expression analysis by qPCR showed that their transcripts were both more abundant in the early embryo and pulp in longan. Heterologous expression of DlRan3A driven by its own previously cloned promoter led to stunted growth, increased root hair density, abnormal fruits, bigger seeds, and enhanced abiotic stress tolerance. Conversely, constitutive promoter CaMV 35S (35S)-driven expression of DlRan3A, 35S, or DlRan3B promoter-controlled expression of DlRan3B did not induce the alterations in growth phenotype, while they rendered different hypersensitivities to abiotic stresses. Based on the transcriptome profiling of longan Ran overexpression in tobacco plants, we propose new mechanisms of the Ran-mediated regulation of genes associated with cell wall biosynthesis and expansion. Also, the transgenic plants expressing DlRan3A or DlRan3B genes controlled by 35S or by their own promoter all exhibited altered mRNA levels of stress-related and transcription factor genes. Moreover, DlRan3A overexpressors were more tolerant to salinity, osmotic, and heat stresses, accompanied by upregulation of oxidation-related genes, possibly involving the Ran-RBOH-CIPK network. Analysis of a subset of selected genes from the Ran transcriptome identified possible cold stress-related roles of brassinosteroid (BR)-responsive genes. The marked presence of genes related to cell wall biosynthesis and expansion, hormone, and defense responses highlighted their close regulatory association with Ran.
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Affiliation(s)
- Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Xiying Xie
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
- School of Media and Design, Nantong Institute of Technology, Nantong 226019, China
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.T.); (X.X.); (R.L.); (C.C.); (Z.Z.); (Y.C.); (X.X.); (Y.L.)
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Liao JH, Chen S, Liu D, Zhang JJ, Liu YF. [Identification and expression of genome of uridine diphosphate glycosyltransferase (UGT) gene family from Chrysanthemum indicum]. Zhongguo Zhong Yao Za Zhi 2024; 49:702-716. [PMID: 38621874 DOI: 10.19540/j.cnki.cjcmm.20231115.102] [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] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Uridine diphosphate glycosyltransferase(UGT) is involved in the glycosylation of a variety of secondary metabolites in plants and plays an important role in plant growth and development and regulation of secondary metabolism. Based on the genome of a diploid Chrysanthemum indicum, the UGT gene family from Ch. indicum was identified by bioinformatics methods, and the physical and chemical properties, subcellular localization prediction, conserved motif, phylogeny, chromosome location, gene structure, and gene replication events of UGT protein were analyzed. Transcriptome and real-time fluorescence quantitative polymerase chain reaction(PCR) were used to analyze the expression pattern of the UGT gene in flowers and leaves of Ch. indicum. Quasi-targeted metabolomics was used to analyze the differential metabolites in flowers and leaves. The results showed that a total of 279 UGT genes were identified in the Ch. indicum genome. Phylogenetic analysis showed that these UGT genes were divided into 8 subfamilies. Members of the same subfamily were distributed in clusters on the chromosomes. Tandem duplications were the main driver of the expansion of the UGT gene family from Ch. indicum. Structural domain analysis showed that 262 UGT genes had complete plant secondary metabolism signal sequences(PSPG box). The analysis of cis-acting elements indicated that light-responsive elements were the most ubiquitous elements in the promoter regions of UGT gene family members. Quasi-targeted metabolome analysis of floral and leaf tissue revealed that most of the flavonoid metabolites, including luteolin-7-O-glucoside and kaempferol-7-O-glucoside, had higher accumulation in flowers. Comparative transcriptome analysis of flower and leaf tissue showed that there were 72 differentially expressed UGT genes, of which 29 genes were up-regulated in flowers, and 43 genes were up-regulated in leaves. Correlation network and phylogenetic analysis showed that CindChr9G00614970.1, CindChr2G00092510.1, and CindChr2G00092490.1 may be involved in the synthesis of 7-O-flavonoid glycosides in Ch. indicum, and real-time fluorescence quantitative PCR analysis further confirmed the reliability of transcriptome data. The results of this study are helpful to understand the function of the UGT gene family from Ch. indicum and provide data reference and theoretical basis for further study on the molecular regulation mechanism of flavonoid glycosides synthesis in Ch. indicum.
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Affiliation(s)
- Jia-Hao Liao
- School of Pharmacy, Hubei University of Chinese Medicine Wuhan 430065, China
| | - Shi Chen
- School of Pharmacy, Hubei University of Chinese Medicine Wuhan 430065, China
| | - Di Liu
- School of Pharmacy, Hubei University of Chinese Medicine Wuhan 430065, China
| | - Jing-Jing Zhang
- School of Pharmacy, Hubei University of Chinese Medicine Wuhan 430065, China
| | - Yi-Fei Liu
- School of Pharmacy, Hubei University of Chinese Medicine Wuhan 430065, China
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Cruz-Miranda GM, Olarte-Carrillo I, Bárcenas-López DA, Martínez-Tovar A, Ramírez-Bello J, Ramos-Peñafiel CO, García-Laguna AI, Cerón-Maldonado R, May-Hau D, Jiménez-Morales S. Transcriptome Analysis in Mexican Adults with Acute Lymphoblastic Leukemia. Int J Mol Sci 2024; 25:1750. [PMID: 38339034 PMCID: PMC10855968 DOI: 10.3390/ijms25031750] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) represents around 25% of adult acute leukemias. Despite the increasing improvement in the survival rate of ALL patients during the last decade, the heterogeneous clinical and molecular features of this malignancy still represent a major challenge for treatment and achieving better outcomes. To identify aberrantly expressed genes in bone marrow (BM) samples from adults with ALL, transcriptomic analysis was performed using Affymetrix Human Transcriptome Array 2.0 (HTA 2.0). Differentially expressed genes (DEGs) (±2-fold change, p-value < 0.05, and FDR < 0.05) were detected using the Transcriptome Analysis Console. Gene Ontology (GO), Database for Annotation, Visualization, and Integrated Discovery (DAVID), and Ingenuity Pathway Analysis (IPA) were employed to identify gene function and define the enriched pathways of DEGs. The protein-protein interactions (PPIs) of DEGs were constructed. A total of 871 genes were differentially expressed, and DNTT, MYB, EBF1, SOX4, and ERG were the top five up-regulated genes. Meanwhile, the top five down-regulated genes were PTGS2, PPBP, ADGRE3, LUCAT1, and VCAN. An association between ERG, CDK6, and SOX4 expression levels and the probability of relapse and death was observed. Regulation of the immune system, immune response, cellular response to stimulus, as well as apoptosis signaling, inflammation mediated by chemokines and cytokines, and T cell activation were among the most altered biological processes and pathways, respectively. Transcriptome analysis of ALL in adults reveals a group of genes consistently associated with hematological malignancies and underscores their relevance in the development of ALL in adults.
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Affiliation(s)
- Gabriela Marisol Cruz-Miranda
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Irma Olarte-Carrillo
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Adolfo Martínez-Tovar
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Julian Ramírez-Bello
- Subdirección de Investigación Clínica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
| | | | - Anel Irais García-Laguna
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Rafael Cerón-Maldonado
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Didier May-Hau
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
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