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Identification of overlay differentially expressed genes in both rats and goats with blast lung injury through comparative transcriptomics

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Chinese Journal of Traumatology 2024年第1期27卷 34-41页

作者： Hong Wang Jun-Hong Gao Xiao-Lin Fan Qing Lu Liang Li Ning Ma Qi Wang Yu-Hao Zhang Xi'an Key Laboratory of Toxicology and Biological Effects Research Center for Toxicological and Biological EffectsInstitute for Hygiene of Ordnance IndustryXi'an710065China

Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BL

关键词： Blast lung injury transcriptomic Target genes Differentially expressed genes

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Physiological and Transcriptome Analysis Illuminates the Molecular Mechanisms of the Drought Resistance Improved by Alginate Oligosaccharides in Triticum aestivum L.

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Phyton-International Journal of Experimental Botany 2024年第2期93卷 185-212页

作者： Yunhong Zhang Yonghui Yang Jiawei Mao Institute of Plant Nutrition Agricultural Resource and Environmental ScienceHenan Academy of Agricultural SciencesZhengzhou450002China Henan Key Laboratory of Agricultural Eco-Environment Henan Academy of Agricultural SciencesZhengzhou450002China

Alginate oligosaccharides(AOS)enhance drought resistance in wheat(Triticum aestivum L.),but the definite mechanisms remain largely unknown.The physiological and transcriptome responses of wheat seedlings treated with AOS were analyzed under drought stress simulated with polyethylene glycol-6000.The results showed that AOS promoted the growth of wheat seedlings and reduced oxidative damage by improving peroxidase and superoxide dismutase activities under drought stress.A total of 10,064 and 15,208 differentially expressed unigenes(DEGs)obtained from the AOS treatment and control samples at 24 and 72 h after dehydration,respectively,were mainly enriched in the biosynthesis of secondary metabolites(phenylpropanoid biosynthesis,flavonoid biosynthesis),carbohydrate metabolism(starch and sucrose metabolism,carbon fixation in photosynthetic organisms),lipid metabolism(fatty acid elongation,biosynthesis of unsaturated fatty acids,alpha-linolenic acid metabolism,cutin,suberine and wax biosynthesis),and signaling transduction pathways.The up-regulated genes were related to,for example,chlorophyll a-b binding protein,amylosynthease,phosphotransferase,peroxidase,phenylalanine ammonia lyase,flavone synthase,glutathione synthetase.Signaling molecules(including MAPK,plant hormones,H_(2)O_(2) and calcium)and transcription factors(mainly including NAC,MYB,MYB-related,WRKY,bZIP family members)were involved in the AOS-induced wheat drought resistance.The results obtained in this study help underpin the mechanisms of wheat drought resistance improved by AOS,and provides a theoretical basis for the application of AOS as an environmentally sustainable biological method to improve drought resistance in agriculture.

关键词： Alginate oligosaccharides Triticum aestivum L. drought resistance transcriptomic physiological analysis

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Response of Salmonella enterica serovar Typhimurium to alginate oligosaccharides fermented with fecal inoculum:integrated transcriptomic and metabolomic analyses

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Marine Life Science & Technology 2023年第2期5卷 242-256页

作者： Jiaying Cheng Mengshi Xiao Xinmiao Ren Francesco Secundo Ying Yu Shihao Nan Weimiao Chen Changliang Zhu Qing Kong Youtao Huang Xiaodan Fu Haijin Mou College of Food Science and Engineering Ocean University of ChinaQingdao 266003China Istituto di Scienze e Tecnologie Chimiche“Giulio Natta” Consiglio Nazionale delle Ricerche20131 MilanItaly State Key Laboratory of Food Science and Technology China-Canada Joint Laboratory of Food Science and Technology(Nanchang)Key Laboratory of Bioactive Polysaccharides of Jiangxi ProvinceNanchang UniversityNanchang 330047China School of Medicine and Pharmacy Ocean University of ChinaQingdao 266003China

Alginate oligosaccharides(AOS),extracted from marine brown algae,are a common functional feed additive;however,it remains unclear whether they modulate the gut microbiota and microbial metabolites.The response of Salmonella enterica serovar Typhimurium,a common poultry pathogen,to AOS fermented with chicken fecal inocula was investigated using metabolomic and transcriptomic analyses.Single-strain cultivation tests showed that AOS did not directly inhibit the growth of S.Typhimurium.However,when AOS were fermented by chicken fecal microbiota,the supernatant of fermented AOS(F-AOS)exhibited remarkable antibacterial activity against S.Typhimurium,decreasing the abundance ratio of S.Typhimurium in the fecal microbiota from 18.94 to 2.94%.transcriptomic analyses showed that the 855 diferentially expressed genes induced by F-AOS were mainly enriched in porphyrin and chlorophyll metabolism,oxidative phosphorylation,and Salmonella infection-related pathways.RT-qPCR confrmed that F-AOS downregulated key genes involved in fagellar assembly and the type III secretory system of S.Typhimurium,indicating metabolites in F-AOS can infuence the growth and metabolism of S.Typhimurium.Metabolomic analyses showed that 205 microbial metabolites were signifcantly altered in F-AOS.Among them,the increase in indolelactic acid and 3-indolepropionic acid levels were further confrmed using HPLC.This study provides a new perspective for the application of AOS as a feed additive against pathogenic intestinal bacteria.

关键词： Alginate oligosaccharides Gut microbiota Metabolite Salmonella enterica serovar Typhimurium Metabolomics transcriptomic

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Integrated Data Reveal the Flavonoid Biosynthesis Metabolic Pathway in Semen Ziziphi Spinosae Using transcriptomic and Metabolomic

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Phyton-International Journal of Experimental Botany 2023年第2期92卷 369-382页

作者： Wei Tian Lingdi Liu Zhongxing Song Zhishu Tang Chunxiu Wen Tao Jiang Institute of Cash Crops Hebei Academy of Agricultural and Forestry SciencesShijiazhuang050051China State Key Laboratory of Research&Development of Characteristic Qin Medicine Resources(Cultivation) Shaanxi University of Chinese MedicineXianyang712046China

The extract from Semen Ziziphi Spinosae(SZS)contains many secondary metabolites(flavonoids,alkaloids,and terpenoids),widely reported for their high medicinal value.In order to know the number and type of flavonoids and the regulating mechanism of flavonoid biosynthesis during the growth and development of SZS,we identified and analyzed the flavonoid metabolites and genes in SZS using metabolomic and transcriptomic.A total of 13,232 differentially expressed genes and 83 flavonoid metabolites were identified at three different growth and development stages(T1,T2,and T3)of SZS.The main flavonoid metabolic components of SZS were catechin,L-epicatechin,(–)-epigallocatechin,(+)-gallocatechin,spinosin and its derivatives.A total of 53 unigenes encoding 15 enzymes were identified as candidate genes involved in flavonoid biosynthesis in SZS.Among,PAL,C4H,4CL,CHS,CHI,FLS,FNS,ANS,ANR,LAR,and UFGT genes were all downregulated in T3 than in T1.The expression levels of these genes influence the accumulation of flavonoids in SZS.Our results should provide valuable information for flavonoid metabolites and candidate genes involved in flavonoid biosynthesis on SZS .

关键词： Spinosin secondary metabolites transcriptomic metabolomic gene expression

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transcriptomic analysis in Anemone flaccida rhizomes reveals ancillary pathway for triterpene saponins biosynthesis and differential responsiveness to phytohormones

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Chinese Journal of Natural Medicines 2019年第2期17卷 131-144页

作者： MO Guo-Yan HUANG Fang FANG Yin HAN Lin-Tao Kayla K.Pennerman BU Li-Jing DU Xiao-Wei Joan W.Bennett YIN Guo-Hua China Key Laboratory of TCM Resource and Prescription Ministry of EducationHubei University of Chinese Medicine Department of Plant Biology and Pathology RutgersThe State University of New Jersey Department of Biology University of New Mexico Department of Pharmacy Heilongjiang University of Chinese Medicine

Anemone flaccida Fr. Schmidt is a perennial medicinal herb that contains pentacyclic triterpenoid saponins as the major bioactive constituents. In China, the rhizomes are used as treatments for a variety of ailments including arthritis. However, yields of the saponins are low, and little is known about the plant's genetic background or phytohormonal responsiveness. Using one-quarter of the 454 pyrosequencing information from the Roche GS FLX Titanium platform, we performed a transcriptomic analysis to identify 157 genes putatively encoding 26 enzymes involved in the synthesis of the bioactive compounds. It was revealed that there are two biosynthetic pathways of triterpene saponins in A. flaccida. One pathway depends on β-amyrin synthase and is similar to that found in other plants. The second, subsidiary("backburner") pathway is catalyzed by camelliol C synthase and yields β-amyrin as minor byproduct. Both pathways used cytochrome P450-dependent monooxygenases(CYPs) and family 1 uridine diphosphate glycosyltransferases(UGTs) to modify the triterpenoid backbone. The expression of CYPs and UGTs were quite different in roots treated with the phytohormones methyl jasmonate, salicylic acid and indole-3-acetic acid. This study provides the first large-scale transcriptional dataset for the biosynthetic pathways of triterpene saponins and their phytohormonal responsiveness in the genus Anemone.

关键词： Anemone flaccida Fr.Schmidt Triterpenoid saponins Biosynthetic pathways transcriptomic analysis Phytohormonal responsiveness

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transcriptomic Responses of Acinetobacter harbinensis HITLi 7~T at Low Temperatures

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Biomedical and Environmental Sciences 2019年第5期32卷 371-375页

作者： MA Yin Peng ZHANG Shu Mei MENG Li Qiang LI Wei Guang Institute of Microbiology Heilongjiang Academy of SciencesHarbin 150010HeilongjiangChina School of Environment Harbin Institute of TechnologyHarbin 150090HeilongjiangChina State Key Laboratory of Urban Water Resource and Environment Harbin 150090HeilongjiangChina

Acinetobacter harbinensis HITLi 7^T, a novel species in the genus Acinetobacter, was isolated from Songhua River in Harbin, China. It is a psychrotolerant heterotrophic nitrification bacterium that grows in temperatures from 2 ℃ to 35 ℃ with an optimal growth temperature of 8 ℃- 20 ℃[1]. The strain plays an important role in ammonium removal from source water and water sanitation improvement in cold areas. Biologically enhanced activated carbon (BEAC) filters immobilized with HITLi 7^T are used to treat source water in winter, exhibiting stronger ammonium removal capability and higher microbial stability during BEAC treatment at low temperatures[2]. However, the low temperature adaptation mechanism of HITLi 7^T has not been clearly elucidated yet.

关键词： transcriptomic Responses Acinetobacter

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transcriptomic profiling of sorghum leaves and roots responsive to drought stress at the seedling stage

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Journal of Integrative Agriculture 2019年第9期18卷 1980-1995页

作者： ZHANG Deng-feng ZENG Ting-ru LIU Xu-yang GAO Chen-xi LI Yong-xiang LI Chun-hui SONG Yan-chun SHI Yun-su WANG Tian-yu LI Yu Institute of Crop Sciences Chinese Academy of Agricultural Sciences

Drought stress affects the growth and productivity of crop plants including sorghum.To study the molecular basis of drought tolerance in sorghum,we conducted the transcriptomic profiling of sorghum leaves and roots under drought stress using RNA-Seq method.A total of 510,559,and 3 687 differentially expressed genes(DEGs)in leaves,3 368,5 093,and 4 635 DEGs in roots responding to mild drought,severe drought,and re-watering treatments were identified,respectively.Among them,190 common DEGs in leaves and 1 644 common DEGs in roots were responsive to mild drought,severe drought,and re-watering environment.Gene Ontology(GO)enrichment analysis revealed that the GO categories related to drought tolerance include terms related to response to stimulus especially response to water deprivation,abscisic acid stimulus,and reactive oxygen species.The major transcription factor genes responsive to drought stress include heat stress transcription factor(HSF),ethylene-responsive transcription factor(ERF),Petunia NAM,Arabidopsis ATAF1/2 and CUC2(NAC),WRKY transcription factor(WRKY),homeodomain leucine zipper transcription factor(HD-ZIP),basic helix-loop-helix transcription factor(bHLH),and V-myb myeloblastosis viral oncogene homolog transcription facotr(MYB).Functional protein genes for heat shock protein(HSPs),late-embryogenesis-abundant protein(LEAs),chaperones,aquaporins,and expansins might play important roles in sorghum drought tolerance.Moreover,the genomic regions enriched with HSP,expansin,and aquaporin genes responsive to drought stress could be used as powerful targets for improvement of drought tolerance in sorghum and other cereals.Overall,our results provide a genome-wide analysis of DEGs in sorghum leaves and roots under mild drought,severe drought,and re-watering environments.This study contributes to a better understanding of the molecular basis of drought tolerance of sorghum and can be useful for crop improvement.

关键词： sorghum(Sorghum bicolor L.) transcriptomic profiling drought leaves roots

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transcriptomic signatures decode Th17 cell pathogenicity

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Cellular & Molecular Immunology 2016年第5期13卷 557-559页

作者： PA Reyfman ET Bartom BD Singer Northwestern University Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine Chicago IL 60611 USA Northwestern University Feinberg School of Medicine Department of Biochemistry and Molecular Genetics Chicago IL 60611 USA

Systems immunology is a growing field that attempts to integrate high-throughput experiments with sophisticated computational analysis and modeling approaches. In the field of systems immunology, single-cell transcrip- tomic profiling （RNA-seq） is an experimental technique that has proven effective for delineating molecular heterogeneity within immune cell subtypes.

关键词： transcriptomic signatures decode

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transcriptomic analysis reveals the transcription factors involved in regulating the expression of EPSPS gene,which confers glyphosate resistance of goosegrass (Eleusine indica)

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Journal of Integrative Agriculture 2021年第8期20卷 2180-2194页

作者： ZHANG Chun YU Chao-jie ZHANG Tai-jie GUO Wen-lei TIAN Xing-shan Guangdong Provincial Key Laboratory of High Technology for Plant Protection Institute of Plant ProtectionGuangdong Academy of Agricultural SciencesGuangzhou 510640P.R.China

Glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase(EPSPS)and overexpression of the EPSPS gene is one of the molecular mechanisms conferring glyphosate resistance in weeds.A regulatory sequence of EPSPS gene was isolated previously,and an alteration in its 5´-untranslated region(UTR)pyrimidine(Py)-rich stretch element is involved in the regulation of EPSPS expression in glyphosate-resistant(GR)Eleusine indica.However,the transcription factors involved in this regulatory sequence remain to be elucidated.In this study,we investigated the regulatory network of EPSPS overexpression associated genes in a GR E.indica population by RNA-seq.The differentially expressed transcript analyses revealed that glyphosate treatment caused an increase in the expression of 2752 unigenes and a decrease in the expression of 4025 unigenes in the GR E.indica,compared to the glyphosatesusceptible(GS)E.indica.Among them,1373 unigenes were identified to be co-expressed with the EPSPS gene in GR E.indica.GO and KEGG pathway analyses showed that the up-regulated unigenes were mainly enriched in chloroplasts and associated with the shikimate biosynthesis pathway,chlorophy II and peroxisome metabolism processes.Notably,the expression of a Shikimate kinase which catalyzed the conversion of Shikimate to Shikimate 3-phosphate(S3P,a substrate of EPSPS),was also up-regulated.Eight transcription factors were identified as likely to be involved in the regulation of the EPSPS expression,and three of them(ARF2,ARF8 and BPC6)showed more binding sites because of a(CT)n insertion of the 5´-UTR Py-rich stretch element in GR.However,the yeast one-hybrid assay illustrated that ARF8 and BPC6 could bind to the 5´-UTR Py-rich stretch element of wild type EPSPS,but could not bind to the mutated form.Our data suggests that the transcriptional regulation of EPSPS expression is complex and was significantly altered in GR E.indica.These discoveries provide new references for further study of the EPSPS overexpression mechanism that endows glyp

关键词： transcriptomic EPSPS 5´-UTR Py-rich stretch element transcription factor glyphosate resistance

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Reply to Zwaenepoel et al.: Meeting the Challenges of Detecting Polyploidy Events from transcriptomic Data

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Molecular Plant 2019年第2期12卷 137-140页

作者： Haifeng Wang Chunce Guo Hong Ma Ji Qi State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi Key Lab of Sugarcane Biology College of Agriculture Guangxi University Nanning Guangxi China Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization Forestry College Jiangxi Agricultural University Nanchang China Department of Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University University Park PA USA State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China

Dear Editor,transcriptomic data have been widely employed to infer whole genome duplications (WGDs, or paleopolyploidy)(Jiao et al., 2011;Barker et al., 2016;Huang et al., 2016), through the use of large numbers of re... 详细信息

关键词： Challenges Detecting Polyploidy Events transcriptomic Data

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