Article
Environmental Sciences
Yuhang Ren, Yuan Tian, Xuebin Mao, Haishen Wen, Xin Qi, Jinku Li, Jifang Li, Yun Li
Summary: This study investigated the gene expression profiles and alternative splicing events in the spotted sea bass fish under hypoxia stress. The results revealed the activation of the HIF signal network system and the suppression of the cell cycle process in response to hypoxia. Additionally, key biological pathways and alternative splicing events associated with hypoxia were identified. These findings contribute to a better understanding of the molecular mechanisms of hypoxia response in spotted sea bass and other fish species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Cardiac & Cardiovascular Systems
Alba Alvarez-Franco, Raquel Rouco, Rafael J. Ramirez, Guadalupe Guerrero-Serna, Maria Tiana, Sara Cogliati, Kuljeet Kaur, Mohammed Saeed, Ricardo Magni, Jose Antonio Enriquez, Fatima Sanchez-Cabo, Jose Jalife, Miguel Manzanares
Summary: Transcriptomic and proteomic analysis of AF progression in a large animal model shows significant changes occurring at early stages, including previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.
CARDIOVASCULAR RESEARCH
(2021)
Article
Fisheries
Zhi Hu, Jie Feng, Hao Song, Cong Zhou, Zheng-Lin Yu, Mei-Jie Yang, Pu Shi, Yong-Jun Guo, Yong-Ren Li, Tao Zhang
Summary: This study elucidated the molecular defense mechanisms of hard clams against the synergistic effects of heat and hypoxia. The results showed that protein folding and microtubule-related genes were upregulated under stress conditions, and protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis were common stress-induced pathways.
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Chaoqiong Ding, Xiang Yan, Mengying Xu, Ran Zhou, Yuancun Zhao, Dan Zhang, Zongyao Huang, Zhenzhong Pan, Peng Xiao, Huifang Li, Lu Chen, Yuan Wang
Summary: This study reports the full-length transcriptome of mouse neural stem cells (NSCs) at different developmental stages, providing an important resource for studying NSC fate determination, neural development, and disease in the neuroscience community.
Article
Biotechnology & Applied Microbiology
Pabodha Hettige, Uzma Tahir, Kiisa C. Nishikawa, Matthew J. Gage
Summary: This study examines the tissue-specific responses to mdm mutation through differential gene expression analysis. The results demonstrate that mdm mutation leads to significant changes in mitochondrial respiration and metabolism-related genes. These findings provide insights into the complex molecular cascade associated with mdm mutation.
Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Laura Puente-Santamaria, Lucia Sanchez-Gonzalez, Ricardo Ramos-Ruiz, Luis del Peso
Summary: This study focuses on the transcriptional response to hypoxia and generates widely applicable classifiers that can accurately identify hypoxic samples and regions, and can be applied to a variety of gene expression datasets and formats.
BMC BIOINFORMATICS
(2022)
Article
Fisheries
Wenjun Shi, Pan Wang, Runhao Hu, Xihe Wan, Hui Shen, Hui Li, Libao Wang, Yi Qiao, Ge Jiang, Jie Cheng, Zeyu Yang
Summary: This study investigated the molecular mechanisms underlying the adaptation of the ridgetail white prawn to hypoxia and reoxygenation through transcriptomic analysis. It identified key genes and pathways related to hypoxia and reoxygenation, shedding light on the biological responses of the prawn during these processes.
AQUACULTURE INTERNATIONAL
(2021)
Article
Dermatology
Zijun Wu, Qin Yang, Kai Xu, Juanjuan Wu, Bin Yang
Summary: This study aims to explore the key genes and molecular mechanisms of IL-27-induced keratinocyte proliferation. The findings suggest that IL-27 promotes keratinocyte proliferation by enhancing glycolysis, mitochondrial function, and mitochondrial fusion, which may contribute to understanding the role of IL-27 in the pathogenesis of psoriasis.
CLINICAL COSMETIC AND INVESTIGATIONAL DERMATOLOGY
(2023)
Article
Cardiac & Cardiovascular Systems
Yu Jin Chung, Pawel Swietach, M. Kate Curtis, Vicky Ball, Peter A. Robbins, Samira Lakhal-Littleton
Summary: Iron-deficiency anemia leads to metabolic remodeling in the heart towards a glycolytic, lactic acid-producing phenotype, characteristic of hypoxia. This results in negative impacts on biological pathways such as oxidative phosphorylation and cardiac contraction.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Muchun Niu, Wenjian Cao, Yongcheng Wang, Qiangyuan Zhu, Jiayi Luo, Baiping Wang, Hui Zheng, David A. Weitz, Chenghang Zong
Summary: The profiling of individual synapses reveals molecular heterogeneity, which is crucial for signal transmission and shows considerable morphological and electrophysiological heterogeneity. However, there is currently a lack of high-throughput methods to analyze the molecular heterogeneity among individual synapses.
NATURE BIOTECHNOLOGY
(2023)
Article
Fisheries
Deodatta S. Gajbhiye, Itay Oz, Yaara Y. Columbus-Shenkar, Matan Golan
Summary: The study provides a detailed staging system for hatchery-reared sunshine bass larvae, identifying a biphasic pattern of larval growth and demonstrating that age and standard length are good predictors of larval stage.
Article
Gastroenterology & Hepatology
Lihong Mao, Chaoqun Li, Xiaoyu Wang, Mingyu Sun, Yifan Li, Zihan Yu, Binxin Cui, Gaoyue Guo, Wanting Yang, Yangyang Hui, Xiaofei Fan, Jie Zhang, Kui Jiang, Chao Sun
Summary: This study found that in decompensated cirrhosis, low subcutaneous adipose tissue index (SATI) and concurrent total adipose tissue index (TATI) were associated with an increased risk of frailty.
JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY
(2023)
Article
Allergy
Qiuyan Liang, Jinrong Fu, Xiang Wang, Lijuan Liu, Wenfeng Xiao, Yajing Gao, Lan Yang, Hongmiao Yu, Xueru Xie, Zikun Tu, Saihua Huang, Xiao Han, Liling Qian, Yufeng Zhou
Summary: This study identified 372 differentially expressed circRNAs in peripheral blood mononuclear cells (PBMCs) of children with asthma. Among them, a circRNA called circS100A11 was highly expressed in monocytes and significantly upregulated in children with asthma. Further experiments demonstrated that circS100A11 promoted M2a macrophage activation by enhancing translation of its host gene, S100A11, and exacerbated lung inflammation in a mouse model of asthma. The study also found that circS100A11 competitively bound to CAPRIN1 to promote S100A11 translation, thereby enhancing M2a macrophage activation.
Article
Fisheries
Min Cao, Qi Li, Xiantong Liu, Qiang Fu, Chao Li
Summary: Sebastes schlegelii is a fish species with high economic value, but the outbreak of diseases in its aquaculture industry has caused significant economic losses. Study of the fish immune system, particularly the immunoglobulin genes, can provide insights into the immune response to pathogens and contribute to the development of prevention and control methods. This study successfully identified and cloned the immunoglobulin heavy chain genes (sIgM, mIgM, sIgT, and mIgT) of S. schlegelii, revealing their high conservation during evolution.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Fisheries
Xiaoyan Zhang, Haohui Yu, Ningning Wang, Chao Li
Summary: Evidence suggests that lncRNAs are involved in various immune responses in vertebrates. In the snakehead fish, immune-related lncRNAs play crucial roles in regulating immune responses against Nocardia seriolae infection. This study analyzed the transcription landscapes of lncRNAs and mRNAs in snakehead, revealing potential functions of lncRNAs in modulating mRNA expression levels and regulating downstream immune signaling pathways.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Fisheries
Xin Cai, Chengbin Gao, Alan J. Lymbery, Nicola J. Armstrong, Le Ma, Chao Li
Summary: Recently, the Gram-negative pathogenic bacterium Vibrio anguillarum has become a major obstacle to the turbot aquaculture industry due to its global distribution, wide host range, and potential devastating impacts. This study conducted comprehensive analyses of whole-transcriptome sequencing in turbot liver infected by V. anguillarum and found differential expression of circRNAs, miRNAs, and mRNAs. Interaction pairs between miRNA-circRNA and miRNA-mRNA were predicted and circRNA-related ceRNA regulatory networks were constructed. The study identified novel target genes for disease prevention and control in turbot.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Fisheries
Yiping Liu, Min Cao, Xu Yan, Xin Cai, Yuqing Li, Chao Li, Ting Xue
Summary: Cell-to-cell communication through gap junction channels is essential for coordinating cellular functions in multicellular tissues. This study identified 48 members of the gap junction protein family in Sebastes schlegelii, classifying them into connexin and pannexin types. The connexins were further divided into five subfamilies. The study also revealed the protein structure and interactions of GJs, and showed that GJ proteins were highly expressed in intestinal tissues and regulated after bacterial infection. The findings provide valuable insights for further understanding the function of GJ proteins in S. schlegelii.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Pediatrics
Mei Mei, Dan Dai, Zhuoyao Guo, Congcong Zhang, Jing Liu, Yuanyuan Qi, Xiaochuan Wang, Libo Wang, Liling Qian
Summary: This study retrospectively analyzed the clinical characteristics and underlying causes of 551 hospitalized children with recurrent pneumonia from January 2016 to January 2021 at the Children's Hospital of Fudan University. The majority (87.7%) of the children had underlying causes, with recurrent aspiration, primary immunodeficiency, and congenital heart diseases being the most common. Genetic defects were identified in about a quarter of the patients. Primary immunodeficiency, primary ciliary dyskinesia, bronchiolitis obliterans, and the age of >3 years at diagnosis were risk factors for severe outcomes. Aspiration and an abnormal family history were risk factors for rehospitalization.
PEDIATRIC PULMONOLOGY
(2023)
Article
Computer Science, Information Systems
Jian Cheng, Quanyuan Feng, Chao Li, Wenxiu Yang
Summary: In this paper, a new run-time monitoring technique is proposed to detect hardware Trojans (HT) on working field-programmable gate array (FPGA), which can enhance the hardware security of IoT devices. The technique places multiple temperature sensors on FPGA and collects their values at each time interval. A predictive model is constructed to estimate the real-time distribution of sensor frequency. If the difference between the predicted value and the real one exceeds a dynamically updated threshold, an HT activation is reported. The experiment results demonstrate that the technique achieves high detection accuracy (>= 98%), low false negative ratio (<= 1.5%), and zero false positive ratio under various FPGA HT benchmarks.
Article
Biochemistry & Molecular Biology
Donglei Sun, Xin Qi, Haishen Wen, Chao Li, Jianlong Li, Jiwei Chen, Zexin Tao, Mingxin Zhu, Xiaoyan Zhang, Yun Li
Summary: A new yellow-mutant northern snakehead with market-favoured yellow skin was discovered in China. It was confirmed to be an albino with a non-sense mutation in slc45a2 gene as the causation for the yellow skin. Comparative transcriptomic analysis revealed the potential involvement of fibroblasts in pigmentation in fish.
Article
Biochemistry & Molecular Biology
Min Cao, Ting Xue, Huijun Huo, Xiaoyan Zhang, Ning Ning Wang, Xu Yan, Chao Li
Summary: Spatial transcriptomes were used to study the transcriptomic landscape in the posterior intestine of Sebastes schlegelii following Edwardsiella piscicida infection. A molecular regionalization of the posterior intestine was observed in the healthy condition. After bacterial infection, immune-related genes were predominantly found in the mucosa layer. The expression of regeneration-related genes suggested the constant proliferation of new cells in response to pathogen invasion, while increasing microbiota communities indicated their role in maintaining intestinal integrity and shaping the mucosal immune system.
Article
Pediatrics
Lingyu Lai, Yong Lu, Zhimin Xi, Fang Liu, Liling Qian, Libo Wang, Quming Zhao
Summary: This article reports two cases of bronchial Dieulafoy's disease in children, causing recurrent massive hemoptysis. The disease was diagnosed through imaging examinations and bronchial arteriography, and was successfully treated with bronchial artery embolization, with no recurrence of hemoptysis.
TRANSLATIONAL PEDIATRICS
(2023)
Article
Construction & Building Technology
Youmei Zhou, Hao Lei, Xiyu Zhang, Shan Wang, Yingying Xu, Chao Li, Jie Zhang
Summary: This research explores how to incorporate social attributes and social interaction into scenario simulation in the digital twin city research and development, which is a problem to be addressed in the refinement and planning of future digital platforms and management in terms of decision-making. The findings have important implications for inspiring the application of computational decision-making support in urban governance and enhancing comprehensive and sustainable urban regeneration.
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)