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expression profiles of antimicrobial peptides (AMPs) and their regulation by Relish

Chinese Journal of Oceanology and Limnology 2012年第4期30卷 611-619页

作者：王冬冬李富花李诗豪温荣相建海 Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of Sciences Graduate University of Chinese Academy of Sciences

Antimicrobial peptides （AMPs）, as key immune effectors, play important roles in the innate immune system of invertebrates. Different types of AMPs, including Penaeidin, Crustin, ALF （anti- lipopolysaccharide factor） have been identified in different penaeid shrimp; however, systematic analyses on the function of different AMPs in shrimp responsive to different types of bacteria are very limited. In this study, we analyzed the expression profiles of AMPs in the Chinese shrimps, Fenneropenaeus chinensis, simultaneously by real-time RT-PCR （reverse transcription-polymerase chain reaction） when shrimp were challenged with Micrococcus lysodeikticus （Gram-positive, G＋） or Hbrio anguillarium （Gram-negative, G-）. Different AMPs showed different expression profiles when shrimp were injected with one type of bacterium, and one AMP also showed different expression profiles when shrimp were challenged with different bacteria. Furthermore, the expression of these AMPs showed temporal expression profiles, suggesting that different AMPs function coordinately in bacteria-infected shrimp. An RNA interference approach was used to study the function of the Relish transcription factor in regulating the transcription of different AMPs. The current study showed that Relish could regulate the transcription of different AMPs in shrimp. Differential expression profiles of AMPs in shrimp injected with different types of bacteria indicated that a complicated antimicrobial response network existed in shrimp. These data contribute to our understanding of immunity in shrimp and may provide a strategy for the control of disease in shrimp.

关键词： antimicrobial peptides (AMPs) expression profiles bacteria Relish RNA interference

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Bioinformatics Analysis on lncRNA and mRNA expression profiles for Novel Biological Features of Valvular Heart Disease with Atrial Fibrillation

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Journal of Electronic Science and Technology 2021年第1期19卷 53-69页

作者： Wei Zeng Ni-Ni Rao Ke Liu the School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 610054 the Guangdong Institute of Electronic Information Engineering University of Electronic Science and Technology of ChinaDongguan 523107 the Department of Sichuan Academy of Medical Science Sichuan Provincial People’s HospitalChengdu 610072

The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)expression profiles constructed by using bioinformatics methods and tools for biological features of *** change and t-test were used to identify differentially expressed(DE)lncRNAs and *** enrichment analysis of DE mRNAs was *** subgroups formed by lncRNAs and nearby mRNAs were screened,and a transcriptional regulation network among lncRNAs,mRNAs,and transcription factors(TFs)was *** interactions between mRNAs related to lncRNAs and drugs were *** 620 AF-VHDrelated DE lncRNAs and 452 DE mRNAs were *** 3 lncRNA subgroups were *** 665 regulations mediated by lncRNAs and TFs were *** 9 mRNAs related to lncRNAs had 1 or more potential drug interactions,totaling 37 *** these,9 drugs targeting 3 genes are already known to be able to control or trigger atrial fibrillation(AF)or other cardiac *** found biological features of AF-VHD provide foundations for further biological experiments to better understand the roles of lncRNAs in development from the valvular heart disease(VHD)to AF-VHD.

关键词： expression profiles long non-coding RNA(lncRNA) messenger RNA(mRNA) valvular heart disease(VHD) valvular heart disease with atrial fibrillation(AF-VHD).

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Identification and expression profiles analysis of odorant-binding proteins in soybean aphid,Aphis glycines(Hemiptera:Aphididae)

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Insect Science 2020年第5期27卷 1019-1030页

作者： Ling Wang Ying-Dong Bi Ming Liu Wei Li Miao Liu Shu-Feng Di Shuai Yang Chao Fan Lei Bai Yong-Cai Lai Institute of Crop Cultivation and Tillage Heilongjiang Academy of Agricultural SciencesHarbinChina Heilongjiang Academy of Agricultural Sciences Postdoctoral Program HarbinChina Virus-free Seedling Research Institute Heilongjiang Academy of Agricultural SciencesHarbinChina College of Agriculture Northeast Agricultural UniversityHarbinChina

The soybean aphid,Aphis glycines,is an extreme specialist and an important invasive pest that relies on olfaction for behaviors such as feeding,mating,and ***-binding proteins(OBPs)play a vital role in olfaction by binding to volatile compounds and by regulating insect sensing of the *** this work we used rapid amplification of complementary DNA ends technology to identify and characterize 10 genes encoding *** OBPs(AglyOBPs)belonging to 3 subfamilies,including 4 classic OBPs,5 Plus-C OBPs,and one Minus-C *** real-time polymerase chain reaction demonstrated variable specific expression patterns for the 10 genes based on developmental stage and aphid tssue *** levels of 7 AglyOBPs(2,3,4,5,7,9,and 10)were highest in the 4th instar,indicating that the 4th nymphal instar is an important developmental period during which soybean aphids regulate feeding and search for host ***-specific expression results demonstrated that AglyOBP2,7,and 9 exhibited significantly higher expression levels in ***,ligand-binding analysis of5 OBPs demonstrated binding of AglyOBP2 and AglyOBP3 to a broad spectrum of volatiles released by green leaf plants,with bias toward 6-to 8-carbon chain volatiles and strong binding of AglyOBP7 to *** together,our findings build a foundation of knowledge for use in the study of molecular olfaction mechanisms and prov ide insights to guide future soybean aphid research.

关键词： Aphis glycines expression profiles fluorescence binding assay odorant-binding proteins

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Molecular characterization and expression profiles of nicotinic acetylcholine receptors in the rice striped stem borer, Chilo suppressalis （Lepidoptera： Crambidae）

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Insect Science 2017年第3期24卷 371-384页

作者： Gang Xu Shun-Fan Wu Zi-Wen Teng Hong-Wei Yao Qi Fang Jia Huang Gong-Yin Ye State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture Institute of Insect SciencesZhejiang University Hangzhou China State & Local Joint Engineering Research Center of Green Pesticide Invention and Application College of Plant Protection Nanjing Agricultural University Nanjing China

Nicotinic acetylcholine receptors （nAChRs） are members of the cys-loop ligand- gated ion channel （cysLGIC） superfamily, mediating fast synaptic cholinergic transmission in the central nervous system in insects. Insect nAChRs are the molecular targets of economically important insecticides, such as neonicotinoids and spinosad. Identification and characterization of the nAChR gene family in the rice striped stem borer, Chilo suppressa[is, could provide beneficial information about this important receptor gene family and contribute to the investigation of the molecular modes of insecticide action and resistance for current and future chemical control strategies. We searched our C. suppressalis transcriptome database using Bombyx mori nAChR sequences in local BLAST searches and obtained the putative nAChR subunit complementary DNAs （cDNAs） via reverse transcription polymerase chain reaction （RT-PCR） and rapid amplification of cDNA ends methods. Similar to B. mori, C. suppressalis possesses 12 nAChR subunits, including nine c^-type and three/%type subunits. Quantitative RT-PCR analysis revealed the expression profiles of the nAChR subunits in various tissues, including the brain, subesophageal ganglion, thoracic ganglion, abdominal ganglion, hemocytes, fat body, foregut, midgut, hindgut and Malpighian tubules. Developmental expression analyses showed clear differential expression of nAChR subunits throughout the C. suppressalis life cycle. The identification of nAChR subunits in this study will provide a foundation for investigating the diverse roles played by nAChRs in C. suppressalis and for exploring specific target sites for chemicals that control agricultural pests while sparing beneficial species

关键词： Chilo suppressalis expression profiles nAChRs

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CircRNA expression profiles in decidual tissue of patients with early recurrent miscarriage

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Genes & Diseases 2020年第3期7卷 414-423页

作者： Chunli Li Xuemei Chen Xueqing Liu Xiaoli Liu Junlin He Yubin Ding Chao Tong Chuan Peng Yingxiong Wang Rufei Gao Laboratory of Reproductive Biology School of Public Health and ManagementChongqing Medical UniversityChongqing400016China Department of Clinical Laboratory Chongqing Health Center for Women and ChildrenChongqing401174China Joint International Research Laboratory of Reproduction&Development Chongqing Medical UniversityChongqing400016China Department of Family Planning Chongqing Health Center for Women and ChildrenChongqing401174PR China Department of Obstetrics The First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China Laboratory of Maternal and Fetal Medicine The First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China

Circular RNAs(circRNAs)are a novel class of endogenous noncoding RNAs that play important roles in gene expression *** study aimed to evaluate the potential role of circRNAs in decidual tissue of patients with early recurrent miscarriage(RM).We constructed circRNA expression profiles in decidual tissue using microarray data.A total of 123 differentially expressed circRNAs,including 78 upregulated and 45 downregulated circRNAs were detected in the early RM group compared with the control group(P<0.05).Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis also revealed the enrichment of specific *** verified circRNA-targeted miRNA-mRNA network was constructed,most of the circRNAs harbored miRNA binding *** network involved 3 circRNAs,27 microRNAs and 82 ***_circRNA_103092-miR-224-PRLR network was selected to verify by *** results showed that circRNAs are aberrantly expressed in the decidual tissue in early RM patients and play potential roles in the development of early *** gives new insights into the mechanism of recurrent miscarriage.

关键词： Circular RNAs Decidual tissue Early recurrent miscarriage expression profiles Microarray

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expression profiles of mi RNAs in Gossypium raimondii

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2015年第4期16卷 296-303页

作者： Jun MA Teng-long GUO Qing-lian WANG Kun-bo WANG Run-run SUN Bao-hong ZHANG Department of Biology East Carolina University Heze Academy of Agricultural Sciences Henan Collaborative Innovation Center of Modern Biological Breeding Henan Institute of Science and Technology Cotton Research Institute Chinese Academy of Agricultural Sciences

miRNAs are a class of conserved, small, endogenous, and non-protein-coding RNA molecules with 20- 24 nucleotides （nt） in length that function as post-transcriptional modulators of gene expression in eukaryotic cells. Functional studies have demonstrated that plant miRNAs are involved in the regulation of a wide range of plant de- velopmental processes. To date, however, no research has been carried out to study the expression profiles of miRNAs in Gossypium raimondii, a model cotton species. We selected 16 miRNAs to profile their tissue-specific expression patterns in G. raimondii four different tissues, and these miRNAs are reported to play important roles in plant growth and development. Our results showed that the expression levels of these miRNAs varied significantly from one to another in a tissue-dependent manner. Eight miRNAs, including miR-159, miR-162, miR-164, miR-172, miR-390, miR-395, miR-397, and miR-398, exhibited exclusively high expression levels in flower buds, suggesting that these miRNAs may play significant roles in floral development. The expression level of miR-164 was relatively high in shoots beside flower buds, implying that the function of miR-164 is not only limited to floral development but it may also play an important role in shoot development. Certain miRNAs such as miR-166 and miR-160 were extremely highly expressed in all of the four tissues tested compared with other miRNAs investigated, suggesting that they may play regulatory roles at multiple development stages. This study will contribute to future studies on the functional charac- terization of rniRNAs in cotton.

关键词： Cotton miRNA expression profiles Quantitative real-time PCR (qRT-PCR) Gossypium raimondii

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Functional Annotation of Metastasis-associated MicroRNAs of Melanoma： A Meta-analysis of expression profiles

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Chinese Medical Journal 2016年第20期129卷 2484-2490页

作者： Jing-Yi Li Li-Li Zheng Ting-Ting Wang Min Hu Department of Stomatology Chinese People's Liberation Army General HospitalBeijing 100853China Department of Endocrinology and Metabolism The First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan 450000China

Background：Melanoma is a type of cancer that develops from the pigment-containing *** now,its pathological mechanisms remain largely *** aim of this study was to identify metastasis-related microRNA （miRNAs） and gain an understanding of the biological functions in the metastasis of ***：We searched the PubMed and Gene expression Omnibus database to collect miRNA expression profiling datasets about melanoma,with key words of＂melanoma＂,＂miRNA＂,＂microarray＂,and ＂gene expression profiling＂.Only the original experimental works published before June 2016 for analyzing the metastasis of melanoma were retained,other nonhuman studies,reviews,and meta-analyses were *** performed a meta-analysis to explore the differentially expressed miRNA between metastatic and nonmetastatic ***,we predicted target genes of the miRNAs to study their biological roles for these ***：We identified a total of 63 significantly differentially expressed miRNAs by meta-analysis of the melanoma expression profiling *** regulatory network constructed by using these miRNAs and the predicted targets identified several key genes involved in the metastasis of *** annotation of these genes indicated that they are mainly enriched in some biological pathways such as mitogen-activated protein kinase signaling pathway,cell junction,and focal ***：By collecting the miRNA expression datasets from different platforms,multiple biological markers were identified for the metastasis of *** study provided novel insights into the molecular mechanisms underlying this disease,thereby aiding the diagnosis and treatment of the disease.

关键词： expression profiles Melanoma Metastasis MicroRNA

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Genome-wide characterization of mapk gene family in black rockfish Sebastes schlegelii and their expression patterns against Edwardsiella piscicida infection

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Journal of Oceanology and Limnology 2023年第6期41卷 2348-2362页

作者： Xiaoyan ZHANG Yuan TIAN Haohui YU Min CAO Chao LI School of Marine Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Key Laboratory of Mariculture(Ocean University of China) Ministry of EducationOcean University of ChinaQingdao 266003China

Mitogen-activated protein kinases(MAPKs)play pivotal roles in response to environmental stresses and bacterial *** with those in the higher vertebrates,studies of mapk gene family are still limited in ***,characterization,classification,and expression profiling of totally 15 mapk genes in black rockfish(Sebastes schlegelii)were *** relationships show that these mapk genes could be divided into extracellular signal-regulated kinase(ERK),c-Jun N-terminal kinase(JNK),and p38 *** addition,gene structures,syntenic analysis,and selective pressure analysis are performed to confirm their *** of selective pressure analysis indicate that mapk1,mapk3,mapk7,mapk10,mapk11,and mapk12 underwent significantly-positive selections,while the others genes such as mapk4,mapk6,mapk15,mapk8a,mapk8b,mapk9,mapk13,mapk14a,and mapk14b were under purifying ***,results of qRT-PCR indicate that mapk genes in 8 healthy tissues displayed different expression *** expression patterns of several mapk genes including mapk12,mapk13,mapk14a,mapk14b,and mapk15 were significantly changed in mucosal tissues after Edwardsiella piscicida *** study demonstrates that mapk genes in black rockfish play vital prevention roles against bacterial infection,which not only helps us understand the structure and function of mapk genes in black rockfish,but also provides a reference to understand the role of mapk genes in teleost immune responses.

关键词： Sebastes schlegelii mitogen activated protein kinases(mapk) Edwardsiella piscicida expression profiles

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Dynamic expression of MicroRNA-127 During Porcine Prenatal and Postnatal Skeletal Muscle Development

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Journal of Integrative Agriculture 2014年第6期13卷 1331-1339页

作者： YANG Ya-lan LI Yan LIANG Ru-yi ZHOU Rong AO Hong MU Yu-lian YANG Shu-lin LI Kui TANG Zhong-lin Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation Ministry of Agriculture/Institute of Animal ScienceChinese Academy of Agricultural Sciences Department of Animal Genetics Breeding and ReproductionCollege of Animal Science and TechnologyNanjing Agricultural University

MicroRNAs （miRNAs）, evolutionarily conserved non-coding RNAs in length 21-24 bp, play a critical role in skeletal muscle development. In this study, to explore the function of mircoRNA-127 in porcine skeletal muscle development, eight tissue samples from adult pigs and longissimus muscle samples at 26 developmental stages were collected from Tongcheng and Landrace pigs. The spatial-temporal expression proifles of miRNA-127 were carried out using step-loop quantitative real-time PCR （stem-loop RT-PCR）. To explore the molecular functions of miRNA-127, we predicted its target genes and performed functional annotation using bioinformatics methods. Results suggested that miRNA-127 was abundantly expressed in heart, ovary, uterus and spleen tissues and was weakly expressed in liver, lung, kidney and small intestine in both Tongcheng and Landrace pigs. And miRNA-127 showed signiifcant expression differences in heart, ovary, spleen and uterus tissues between these two breeds. miRNA-127 basically kept at a relatively stable high level in middle and later embryonic stages and a low expression level in early embryonic stages and postnatal stages, but the expression levels of miRNA-127 were higher in Tongcheng pigs than in Landrace at most developmental stages. miRNA-127 potentially regulated 240 candidate genes. Results of Gene Ontology and KEGG pathway analysis indicated that these genes could be involved in many molecular functions and mechanisms, such as regulation of the force of heart contraction, regulation of transcription, regulation of T cell differentiation, MAPK signaling pathway and GnRH signaling pathway. Many signiifcantly enriched GO terms and KEGG pathways were related to skeletal muscle development. This study will be helpful to understand the biological function for miRNA-127 and identify candidate gene associated with meat production traits in pigs.

关键词： porcine microRNA-127 expression profiles skeletal muscle development target prediction

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Genome-wide identification and prediction of long noncoding RNAs in half-smooth tongue sole Cynoglossus semilaevis

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Journal of Oceanology and Limnology 2020年第1期38卷 226-235页

作者： JIANG Xiaoli JING Xiaohong LÜ Yan SHAN Changmin LI Jiahua YU Yan WU Yuyong SUN Yeying College of Pharmacy Binzhou Medical UniversityYantai 264003China College of Life Science Yantai UniversityYantai 264005China

At present,the function and profile of long noncoding RNAs(lncRNAs)in half-smooth tongue soles Cynoglossus semilaevis remain poorly ***,we identified lncRNAs in the species using large-scale deep sequencing approaches.A total of 96726222 clean reads and 2497 lncRNAs were obtained from the compound *** total,1694 known lncRNAs and 803 novel lncRNAs were *** of the novel lncRNAs distributed mainly in a range of 200-3000 nt and contained 2-6 *** novel lncRNAs were selected for expression analysis by quantitative reverse transcription-polymerase chain reaction,of which lnc_770 and lnc_150 were expressed mainly in the *** study provides a valuable resource for lncRNA studies of half-smooth tongue sole and improves our understanding of the function of non-coding RNA in fish.

关键词： Cynoglossus semilaevis long noncoding RNAs(lncRNAs) expression profiles

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