Article
Agriculture, Dairy & Animal Science
Liqin Liao, Ziqi Yao, Jie Kong, Xinheng Zhang, Hongxin Li, Weiguo Chen, Qingmei Xie
Summary: In early embryonic development, precise and strict control of gene expression is crucial for the proper development of cells and organs. Through the construction of a small RNA library and bioinformatic analysis, this study identified and analyzed the expression of 2,459 miRNAs in chick embryos at different stages. Pathway analysis revealed the important role of miRNAs in regulating gene expression and coordinating various developmental processes.
Article
Cell Biology
Hai-Quan Wang, Yang Liu, Dong Li, Jing-Yu Liu, Yue Jiang, Yuanlin He, Ji-Dong Zhou, Zhi-Long Wang, Xin-Yi Tang, Yang Zhang, Xin Zhen, Zhi-Wen Cao, Xiao-Qiang Sheng, Chao-Fan Yang, Qiu-Ling Yue, Li-Jun Ding, Ya-Li Hu, Zhi-Bin Hu, Chao-Jun Li, Gui-Jun Yan, Hai-Xiang Sun
Summary: Embryo implantation requires a temporospatial dialogue between the mother and the embryo. Through RNA sequencing and embryo sequencing, researchers found that luminal epithelial cells in the uterus differentiate into adhesive epithelial cells and supporting epithelial cells under the influence of progesterone. Embryonic signals activate these cells, enhancing embryo attachment and development. This differentiation process is also present in humans and mice. It was also discovered that defects in the development and function of human endometrial epithelial cells can lead to thin endometrium and recurrent implantation failure.
DEVELOPMENTAL CELL
(2023)
Article
Agriculture, Dairy & Animal Science
Daqing Wang, Yanyan Yang, Yongli Song, Shaoyin Fu, Xiaolong He, Biao Wang, Liwei Wang, Xin Chen, Xihe Li, Yongbin Liu, Guifang Cao
Summary: The addition of ghrelin to the in vitro maturation system of sheep oocytes was found to shorten the maturation time and hinder early embryonic development. The RNA-seq analysis revealed alterations in cell cycle signaling pathways and the inhibition of P53. Overall, these findings provide new insights into the effects of exogenous ghrelin on sheep oocyte maturation and early embryonic development in vitro.
Article
Environmental Sciences
Fang Su, Shilin Liu, Lili Xing, Da Huo, Hongsheng Yang, Lina Sun
Summary: In this study, RNA sequencing was performed on six key stages of Apostichopus japonicus development, and a total of 32,353 genes were identified. WGCNA analysis revealed that genes in the blue, yellow, and darkslateblue modules were highly correlated with the gastrula, auricularia, and blastula stages, respectively. Further analysis showed that these genes were mainly associated with signal transduction, cellular immunity, and extracellular matrix functions. The results of this study provide a comprehensive understanding of the molecular characteristics of sea cucumber embryonic development and theoretical guidance for larva rearing in sea cucumber culture.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Engineering, Environmental
Mohamed Mohsen, Lina Sun, Chenggang Lin, Da Huo, Hongsheng Yang
Summary: The study found that MFs can alter gene expression, with the number of affected genes increasing as the transfer process progresses. The top genes regulated by MF transfer are mainly related to metabolic processes and signal transduction pathways, with upregulated genes following low MF transfer and downregulated genes following high MF transfer. Functional enrichment analysis revealed the pathways in which differentially expressed genes were enriched under different MF transfer scenarios.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Zhujun Li, Tianxiang Gao, Zhiqiang Han
Summary: This study analyzed the transcriptome of Argyrosomus japonicus gill tissue to identify DEGs under salinity changes. The DEGs were significantly enriched in transportation, metabolism, and stress response, and in some signaling pathways. Multiple genes were found to be involved, suggesting a complex process of salinity adaptation in A. japonicus.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Entomology
Guan-Feng Xu, Cheng-Cheng Gong, Hao Lyu, Hui-Min Deng, Si-Chun Zheng
Summary: This study investigated the gene expression control of Bombyx mori embryonic development stages using RNA sequencing, identifying key genes related to DNA replication, transcription, and various developmental pathways. The findings indicate distinct gene expression patterns in early and late embryos, with a focus on organogenesis. These results enhance our understanding of the molecular mechanisms underlying embryonic development and B. mori regulation.
Article
Endocrinology & Metabolism
Dandan Song, Huan He, Rajitha Indukuri, Zhiqiang Huang, Lina Stepanauskaite, Indranil Sinha, Lars-Arne Haldosen, Chunyan Zhao, Cecilia Williams
Summary: This study investigates the differences between estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ) in regulating cell proliferation and migration. The results show that ERα and ERβ have opposite effects on cell proliferation and different impacts on migration. Furthermore, they regulate distinct sets of target genes, providing valuable insights into the mechanisms of these two different ER isoforms.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wenxiao Du, Xuedong Wang, Lin Wang, Mingyong Wang, Chao Liu
Summary: Avermectin concentration has lethal effects on the development of zebrafish heart, causing malformation abnormalities, changes in heart rate, and reduction in hatching rate and body length. Transcriptome analysis revealed alterations in signal pathways related to cardiac circulation and myocardial fiber development. Avermectin primarily targets the heart and affects its development and function through the modulation of cardiac-related gene expression.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY
(2023)
Article
Biology
Thomas L. Williams, Maria T. Colzani, Robyn G. C. Macrae, Emma L. Robinson, Stuart Bloor, Edward J. D. Greenwood, Jun Ru Zhan, Gregory Strachan, Rhoda E. Kuc, Duuamene Nyimanu, Janet J. Maguire, Paul J. Lehner, Sanjay Sinha, Anthony P. Davenport
Summary: Patients with cardiovascular comorbidities are more vulnerable to severe infection with SARS-CoV-2, which can directly harm cardiovascular tissue. Researchers have developed a screening platform using human embryonic stem cell-derived cardiomyocytes to identify new inhibitors of SARS-CoV-2 infection, with benztropine and DX600 found as potential inhibitors. This discovery of new medicines is crucial for protecting the heart in SARS-CoV-2 patients and those who cannot be vaccinated.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shehu Sidi, Osvaldo Bogado Pascottini, Daniel Angel-Velez, Nima Azari-Dolatabad, Krishna Chaitanya Pavani, Gretania Residiwati, Tim Meese, Filip Van Nieuwerburgh, Elias Kambai Bawa, Ambrose Alikidon Voh, Joseph Olusegun Ayo, Ann Van Soom
Summary: Lycopene supplementation in atmospheric oxygen conditions during in vitro maturation of bovine oocytes has antioxidant effects, reducing oxidative stress and improving embryo development and quality. Transcriptomic analysis revealed differentially expressed genes associated with cellular function, metabolism, DNA repair, and anti-apoptosis, indicating the modulation of key pathways by lycopene.
Article
Genetics & Heredity
Jared A. Tangeman, Agustin Luz-Madrigal, Sutharzan Sreeskandarajan, Erika Grajales-Esquivel, Lin Liu, Chun Liang, Panagiotis A. Tsonis, Katia Del Rio-Tsonis
Summary: This study explored the mechanisms of embryonic RPE reprogramming through RNA-seq analysis, revealing that FGF2 and the MAPK cascade are crucial drivers. Key processes involved cell cycle progression, injury response, migration, and ECM regulation, highlighting the important roles of ECM and EMT dynamics in the reprogramming process.
Article
Cell Biology
Baohua Tan, Sheng Wang, Shanshan Wang, Jiekang Zeng, Linjun Hong, Zicong Li, Jie Yang, Gengyuan Cai, Enqin Zheng, Zhenfang Wu, Ting Gu
Summary: This study provided a comprehensive genome-wide view of H3K27me3 during porcine embryonic muscle development, revealing its continuous increase and negative correlation with gene expression. It also showed that H3K27me3 could enrich in the promoter to negatively regulate gene expression and impact muscle cell differentiation in pigs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhanmin Sun, Sanjie Jiang, Dan Wang, Linxia Li, Boxin Liu, Qifan Ran, Lizhen Hu, Junbo Xiong, Yixiong Tang, Xiaofeng Gu, Yanmin Wu, Zhe Liang
Summary: Using single-cell RNA sequencing, we obtained the transcriptome profiles of seven major cell types in the root tips of Lotus japonicus, a legume model species. Our findings revealed regulatory programs associated with phytohormones and nodulation for specific cell types, and identified conserved and diverged features for these cell types.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Fisheries
Yaqun Zhang, Na Yao, Chuantao Zhang, Xiangshan Sun, Jingxian Huang, Bingran Zhao, Hengde Li
Summary: This study identified differentially expressed mRNAs and lncRNAs in the hepatopancreas of Penaeus japonicas in response to white spot syndrome virus (WSSV) infection. Functional enrichment analysis revealed that these differentially expressed genes were related to immune response and viral infectivity. Some lncRNAs were induced by WSSV infection and may be involved in regulating immune processes.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Chaochao Hu, Sijia Yuan, Wan Sun, Wan Chen, Wei Liu, Peng Li, Qing Chang
Summary: Wild boars, native to the temperate region of Eurasia, have experienced recent population expansion that has attracted attention. Understanding genetic diversity and population structure is essential for conservation and management of wild populations. Geographical features can influence species dispersal patterns and genetic structures.
Article
Ecology
Peng Li, John J. Wiens
Summary: This study provides a comprehensive comparison of the types of traits that can drive diversification in lizard and snake families. It shows that the rate of range expansion is the most important variable for explaining diversification rates and richness patterns in squamates.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biotechnology & Applied Microbiology
Qi Xiao, Youfu Lin, Hong Li, Yu Chen, Wei Wei, Peng Li, Lian Chen
Summary: This study performed a high-throughput transcriptome analysis of Pomacea canaliculata to investigate its responses to cold acclimation and cold stress. The results revealed the involvement of lncRNAs and mRNAs in the cold acclimation and stress response of P. canaliculata. The findings provide new insights into the molecular mechanisms underlying cold adaptation in this invasive snail species.
Article
Ecology
Haixia Wu, Shuo Gao, Longjie Xia, Peng Li
Summary: Comparative genomic analyses of reptiles reveal higher evolutionary rates and positively selected genes in body-size-related genes in snakes compared to lizards. Key genes regulating body size evolution in squamates were identified. Ecological factors had varying degrees of impact on body size and evolutionary rate of body-size-related genes in reptiles.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Longjie Xia, Fengna Cai, Shasha Chen, Yao Cai, Kaiya Zhou, Jie Yan, Peng Li
Summary: In this study, the genetic diversity, genetic structure, and historical population dynamics of Gekko japonicus populations in China were assessed using mitochondrial DNA sequences. The results showed low genetic diversity in Chinese populations of G. japonicus, which can be attributed to founder and bottleneck events. These findings provide important insights into the population genetics and origin of G. japonicus.
Article
Multidisciplinary Sciences
Yunxia Yang, Fangcao Jin, Wanyi Liu, Guangming Huo, Feng Zhou, Jie Yan, Kaiya Zhou, Peng Li
Summary: Eriocheir sinensis larvae undergo 11 stages, with the most notable change being the folding of the reduced abdomen under the thorax during the transformation from megalopa to juvenile crab. The molecular mechanisms behind this brachyurization process are still unknown. To shed light on this, researchers constructed transcriptome, digital gene expression (DGE), and proteome libraries for Chinese mitten crab larvae in two developmental stages (megalopa and first stage of juvenile crab) and performed RNA sequencing and iTRAQ analysis. They found that 1106 genes and 871 proteins showed differential expression between the two stages. Several important pathways, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and disease pathways, were identified. Muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway were also found to play important roles in brachyurization. Additionally, certain components, such as actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin, were upregulated in the megalopa stage compared to the first stage of juvenile crab.
Article
Agriculture, Dairy & Animal Science
Xin-Ru Jiang, Ying-Yu Dai, Yu-Rong Wang, Kun Guo, Yu Du, Jian-Fang Gao, Long-Hui Lin, Peng Li, Hong Li, Xiang Ji, Yan-Fu Qu
Summary: This study compared the gut microbiota of wild-caught Japanese geckos and captive conspecifics fed with mealworms and fruit flies, revealing that the mealworm-fed geckos had higher richness and diversity of gut microbial community compared to wild geckos. The diversity of gut microbiota was sex dependent. The study also found that G. japonicus had a gut microbiota composition more similar to the common leopard gecko and that a higher diversity of gut microbiota was associated with higher chitin content in the diet.
Article
Biotechnology & Applied Microbiology
Shasha Chen, Xianfeng Jiang, Longjie Xia, Zhiyi Chen, Kaiya Zhou, Jie Yan, Peng Li
Summary: In this study, all members of the Hox genes were identified and analyzed in E. sinensis using genome-wide analysis. The mRNA expression levels of Scr and Antp genes fluctuated significantly during the differentiation of reduced abdomen and emphasized claws. Evolutionary analysis revealed positively selected sites in Ubx. These findings contribute to a better understanding of the function of Hox genes in E. sinensis and provide molecular evolutionary information for further investigation on their roles in the brachyurization of crabs.
Article
Ecology
Jun-Qiong Chen, Lu-Wen Zhang, Ru-Meng Zhao, Hai-Xia Wu, Long-Hui Lin, Peng Li, Hong Li, Yan-Fu Qu, Xiang Ji
Summary: This study compared gut microbes in two lizard species of the genus Phrynocephalus and found that gut microbiota plays an important role in helping lizards adapt to cold environments. The role of gut microbiota was more evident in P. erythrurus, which inhabits colder habitats throughout the year.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Juan Lu, Shixing Yang, Chunmei Wang, Hao Wang, Ga Gong, Yuan Xi, Jiamin Pan, Xiaochun Wang, Jian Zeng, Ju Zhang, Peng Li, Quan Shen, Tongling Shan, Wen Zhang
Summary: This study investigated the viral communities in the gut of highland-dwelling Phrynocephalus lizards using viral metagenomic analysis. Bacteriophages, especially of the Caudovirales order, dominated the viral communities of different lizard species. The virome of Phrynocephalus erythrurus had a unique structure with a high abundance of the Parvoviridae family. The study also identified vertebrate-infecting viruses and antibiotic resistance genes. These findings contribute to the understanding of gut viromes in highland lizards and have implications for the protection of threatened species and interspecific differences in commensal viral transmission.
MICROBIOLOGY SPECTRUM
(2022)
Article
Fisheries
Wei Xie, Bin Sun, Peng Li, Jie Yan, Wan Chen, Kaiya Zhou
TURKISH JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Diana Medina-Felix, Francisco Vargas-Albores, Estefania Garibay-Valdez, Luis Rafael Martinez-Cordova, Marcel Martinez-Porchas
Summary: In this research, the effects of Nocardia infection on fish gastrointestinal microbiota were analyzed. It was found that the infection led to decreased survival rate, severe damage to the stomach microbiota, and a significant increase in Proteobacteria. A negative correlation network between Proteobacteria and other important phyla was observed. Therefore, Nocardia sp. is an emerging pathogen capable of inducing dysbiosis and causing significant mortalities.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Lele Wu, Wen Sun, Jiale Zhou, Yaolin Li, Jun Li, Zongcheng Song, Changbin Song, Shihong Xu, Xinlu Yue, Xian Li
Summary: The study finds that red light induces dichromatic skin pigmentation in turbot juveniles, with some individuals displaying black coloration and others displaying lighter skin. The upregulated gene expressions related to melanin synthesis and the involvement of the nervous system in spectral environment-driven color regulation are both crucial factors.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)