Article
Nutrition & Dietetics
Ali Mahmoudi, Stephen L. Atkin, Nikita G. Nikiforov, Amirhossein Sahebkar
Summary: This study investigated the effect of curcumin on critical genes and pathways related to diabetes. The results showed that curcumin targeted several important genes involved in diabetes and may have potential as a therapeutic agent for diabetes.
Article
Nutrition & Dietetics
Ali Mahmoudi, Alexandra E. Butler, Muhammed Majeed, Maciej Banach, Amirhossein Sahebkar
Summary: Curcumin may improve or inhibit the progression of NAFLD by modulating genes and proteins associated with the disease, specifically targeting stress and lipid metabolism pathways.
Article
Agronomy
Jing Guo, Xiuli Song, Shiqi Sun, Baihui Shao, Bo Tao, Lili Zhang
Summary: This study focused on selecting potato varieties with tolerance and sensitivity to bentazone, determining key genes involved in tolerance, and providing a theoretical basis for selecting stress-resistant resources in the future. The research found that tolerant potato plants showed a significantly higher photosynthetic rate and experienced faster degradation of bentazone compared to sensitive plants, with specific genes such as PPO, AOMT3, RBCS-C, and CHS2 identified as contributing to bentazone tolerance.
Article
Biotechnology & Applied Microbiology
Swetha Kumar, Venkata Gayatri Dhara, Linda D. Orzolek, Haiping Hao, Abbie J. More, Eduardo Catchon Lau, Michael J. Betenbaugh
Summary: The study found that plant-based hydrolysates, such as cottonseed hydrolysate, can positively impact CHO cell growth and productivity by upregulating transcription and translation, and affecting pathways related to the cell cycle and metabolism.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Cell & Tissue Engineering
Mei Hanying, Yueling Zhao, Na Suo
Summary: The study identified specific modules and hub microRNAs related to osteosarcoma through WGCNA analysis, some of which have been reported to play a role in the pathological process of OS patients, providing insights for the identification and research of new biomarkers and treatment strategies.
JOURNAL OF BIOMATERIALS AND TISSUE ENGINEERING
(2021)
Article
Oncology
Diego A. Pedroza, Matthew Ramirez, Venkatesh Rajamanickam, Ramadevi Subramani, Victoria Margolis, Tugba Gurbuz, Adriana Estrada, Rajkumar Lakshmanaswamy
Summary: Our study reveals that therapeutic targeting of PGRMC1 in aggressive breast cancers leads to the activation of miRNAs targeting overexpressed genes and deactivation of miRNAs with oncogenic potential.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biology
Ambritha Balasundaram, C. George Priya Doss
Summary: This study identified differentially expressed genes in non-small cell lung cancer (NSCLC) and constructed a circRNA-miRNA-mRNA regulatory network to explore the potential mechanism of NSCLC.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Multidisciplinary Sciences
Peng Liu, Jessica Ewald, Zhiqiang Pang, Elena Legrand, Yeon Seon Jeon, Jonathan Sangiovanni, Orcun Hacariz, Guangyan Zhou, Jessica A. Head, Niladri Basu, Jianguo Xia
Summary: ExpressAnalyst is a web-based platform that efficiently processes and analyzes RNA-sequencing data from any eukaryotic species, providing statistical and functional analysis. It includes modules for processing and annotating FASTQ files, as well as analyzing count tables or gene lists. By integrating ultra-fast read mapping algorithms with high-resolution ortholog databases, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights within 24 h.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Hung Nguyen, Duc Tran, Jonathan M. Galazka, Sylvain Costes, Afshin Beheshti, Juli Petereit, Sorin Draghici, Tin Nguyen
Summary: CPA is a web-based platform designed to help researchers conduct pathway analysis using various methods to gain a better understanding of complex biological systems. Users can perform meta-analysis, combine methods and multiple datasets for analysis, and interactively explore impacted pathways.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Claudia Gutierrez-Garcia, Shiek S. S. J. Ahmed, Sathishkumar Ramalingam, Dhivya Selvaraj, Aashish Srivastava, Sujay Paul, Ashutosh Sharma
Summary: This study utilized high-throughput sequencing technology to analyze the miRNA profile of Murraya koenigii and identified miRNAs associated with secondary metabolite biosynthesis. The results showed that these miRNAs targeted key enzymes in the terpenoid backbone and flavonoid biosynthesis pathways. The sequencing results were validated by qPCR. This is the first report of the miRNA profile of Murraya koenigii, providing valuable information for studying the involvement of miRNAs in secondary metabolism.
Article
Multidisciplinary Sciences
Alex J. La Reau, Noah B. Strom, Ellen Filvaroff, Konstantinos Mavrommatis, Tonya L. Ward, Dan Knights
Summary: The microbiome plays a role in human diseases, but identifying key microbes and their functions requires large studies. 16S sequencing is commonly used for large studies, but has poor resolution. Shallow shotgun sequencing provides a more specific and reproducible alternative to 16S sequencing for large-scale microbiome studies, at a lower cost than deep shotgun sequencing.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Xiaoxi Dong, Kovidh Vegesna, Cory Brouwer, Weijun Luo
Summary: SBGNview is a comprehensive R package that addresses the limitations in pathway analysis and data visualization by adopting the standard SBGN format. It greatly extends pathway coverage and data format, and provides essential infrastructure for manipulating and processing SBGN data.
Article
Neurosciences
Rongrong Han, Peng Zhang, Hongfang Li, Yun Chen, Yongnan Hao, Qiang Guo, Aimei Zhang, Daojing Li
Summary: This study used transcriptome sequencing technology to analyze the global transcriptome expression profile of patients with and without hemorrhagic transformation (HT) after acute ischemic stroke. The results showed differential expression of various RNA types, suggesting a potential correlation with HT and providing valuable information for new biomarkers or therapeutic targets.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemical Research Methods
Jessica Carballido, Rocio Cecchini
Summary: This article presents a different analysis method for marker gene research, starting from the biological significance of known gene groups and evaluating the proportion of differentially expressed genes. The research findings show that the percentage of differentially expressed genes is generally low in gene sets annotated in KEGG. However, the use of differentially expressed genes consistently improves the results of statistical and machine learning models in the training and prediction process.
CURRENT BIOINFORMATICS
(2022)
Article
Immunology
Raushan Kumar Chaudhary, L. Ananthesh, Prakash Patil, Uday Venkat Mateti, Sanjit Sah, Aroop Mohanty, Rama S. Rath, Bijaya Kumar Padhi, Sumira Malik, Kadhim Hussein Jassim, Moustafa A. Al-Shammari, Yasir Waheed, Prakasini Satapathy, Joshuan J. Barboza, Alfonso J. Rodriguez-Morales, Ranjit Sah
Summary: This study identified key genes and pathways associated with H5N1 infection in humans through protein-protein interaction and functional enrichment analysis. These hub genes and pathways play important roles in the diagnosis, prognosis, and treatment of H5N1 infection.
Article
Fisheries
Tian Jiang, Jun Long Sun, Yue Gu, Fu Cheng, Ye Song Liang, Yi Fan Liu, Kai Xi Zhang, Fei Biao Song, Li Zhou, Zhong Wei Wang, Jian Fang Gui, Jian Luo
Summary: This study investigates the physiological, biochemical, and transcript indicators of metabolism and apoptosis in golden pompano under hypoxic conditions. The results reveal metabolic changes and cell apoptosis activation, providing new insights into the metabolic responses to hypoxia in teleosts.
Article
Agriculture, Multidisciplinary
Lin-zhen Zhang, Li He, Ning Wang, Jia-hua An, Gen Zhang, Jin Chai, Yu-jie Wu, Chang-jiu Dai, Xiao-han Li, Ting Lian, Ming-zhou Li, Long Jin
Summary: This study identified a natural antisense transcript, APMAP-AS, which is associated with lipid synthesis and positively regulates adipogenic differentiation. APMAP-AS forms an RNA-RNA duplex with APMAP, increasing its stability and promoting lipid metabolism while inhibiting the expression of inflammatory factors.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Genetics & Heredity
Zhiming Wang, Jin Chai, Yuhao Wang, Yiren Gu, Keren Long, Mingzhou Li, Long Jin
Summary: Animal fat deposition has a significant impact on meat flavor and texture. In this study, we investigated the regulatory role of lncPLAAT3-AS in promoting preadipocyte proliferation and adipocyte differentiation. Our findings suggest that lncPLAAT3-AS upregulates PLAAT3 expression through a sponge-like mechanism involving miR-503-5p binding.
Article
Agriculture, Dairy & Animal Science
Hulong Lei, Qian Du, Naisheng Lu, Xueyuan Jiang, Mingzhou Li, Dong Xia, Keren Long
Summary: This study compared the effects of copper sulfate and copper glycinate on fecal microbiota and metabolites in pigs, and found that copper glycinate had more positive effects on gut health.
Article
Biochemistry & Molecular Biology
Xiaokai Li, Zhining Zhong, Ruowei Zhang, Jiaman Zhang, Yu Zhang, Sha Zeng, Qinjiao Du, Haoming Wang, Songling Zhang, Lu Lu, Mingzhou Li, Keren Long
Summary: In this study, a muscular dystrophy mouse model was created by Ptrf knockout, and single-nucleus RNA sequencing was used to investigate the transcriptional changes in skeletal muscle. The study revealed significant alterations in the transcriptome of different types of muscle fibers and mononuclear cells in response to muscular dystrophy, providing valuable insights into the molecular mechanisms of muscular dystrophy.
Article
Multidisciplinary Sciences
Long Jin, Danyang Wang, Jiaman Zhang, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang, Mingzhou Li
Summary: Using a pig model, the study investigates how chromatin architecture in adipose tissue is regulated in relation to obesity. Analysis of the data reveals similarities and differences in chromatin architecture between humans and pigs, providing valuable insights into the regulation of obesity-related genes.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yujie Wang, Xun Wang, Yi Luo, Jiaman Zhang, Yu Lin, Jie Wu, Bo Zeng, Lei Liu, Peiqi Yan, Jiyuan Liang, Hongrui Guo, Long Jin, Qianzi Tang, Keren Long, Mingzhou Li
Summary: This study generated a de novo pigeon genome assembly and conducted a high resolution spatio-temporal transcriptomic analysis of the crop epithelium in pigeons. The study identified "lactation"-related genes involved in lipid and protein metabolism and revealed extensive reorganization of promoter-enhancer interactions linked to the expression of these genes. The spatial localization of gene expression in specific epithelial layers was correlated with phenotypic changes in the crop.
Article
Biology
Qin Zou, Rong Yuan, Yu Zhang, Yifei Wang, Ting Zheng, Rui Shi, Mei Zhang, Yujing Li, Kaixin Fei, Ran Feng, Binyun Pan, Xinyue Zhang, Zhengyin Gong, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Summary: Studying cellular specialization in different anatomical regions of pig skin can enhance our understanding of skin information and provide insights for human skin research.
Article
Geriatrics & Gerontology
Linyuan Shen, Tianci Liao, Qiuyang Chen, Yuhang Lei, Linghui Wang, Hao Gu, Yanhao Qiu, Ting Zheng, Yiting Yang, Chenggang Wei, Lei Chen, Ye Zhao, Lili Niu, Shunhua Zhang, Yan Zhu, Mingzhou Li, Jinyong Wang, Xuewei Li, Mailin Gan, Li Zhu
Summary: This study explores the role of tRNA-derived small RNAs (tsRNAs), specifically 5'tiRNA-Gly, in skeletal muscle regeneration. It is found that 5'tiRNA-Gly is significantly up-regulated after muscle injury and promotes inflammation through the TGF-beta signaling pathway. These findings provide a new potential target for skeletal muscle regeneration treatment.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Physiology
Jinwei Zhang, Yang Shen, Guitao Yang, Jing Sun, Chuang Tang, Hao Liang, Jideng Ma, Xiaoqian Wu, Haoran Cao, Meng Wu, Yuchun Ding, Mingzhou Li, Zuohua Liu, Liangpeng Ge
Summary: This study analyzed the impact of commensal microbiota on the host's mucosal immunity. It found that the absence of commensal microbiota led to smaller Peyer's patches in the gastrointestinal tract, particularly regarding B and T cells. Gene expression analysis revealed that commensal microbiota plays an important role in the development of mucosal immunity in the intestine. Overall, this study revealed the regulatory mechanisms of commensal microbiota in the host's Peyer's patches and emphasized the importance of early microbial colonization for mucosal immunity development.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Weiqiang Liu, Pingfen Zhu, Meng Li, Zihao Li, Yang Yu, Gaoming Liu, Juan Du, Xiao Wang, Jing Yang, Ran Tian, Inge Seim, Alaattin Kaya, Mingzhou Li, Ming Li, Vadim N. Gladyshev, Xuming Zhou
Summary: The variation in lifespan among mammals is significant, and the study aims to uncover the evolutionary forces and molecular features related to longevity. Comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species revealed that only a few genes have common expression patterns with longevity. However, pathways related to translation fidelity and methionine restriction showed correlation with lifespan. The study suggests that lifespan regulation through gene expression is driven by polygenic and indirect natural selection.
Article
Biochemistry & Molecular Biology
Jingyi Bai, Yu Lin, Jiaman Zhang, Ziyu Chen, Yujie Wang, Mingzhou Li, Jing Li
Summary: The study used ATAC-seq and rRNA-depleted RNA-seq to analyze the chromatin accessibility and transcriptional features in multiple tissues of newborn pigs and during porcine liver development. The researchers obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage, and found that tissue-specific accessible promoters were associated with active transcription and tissue-specific functions. Additionally, they observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. This study expands our understanding of epigenetic regulation in mammalian tissues and organ development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jing Yang, Xingxing Zhu, Rui Wang, Mingzhou Li, Qianzi Tang
Summary: In this study, we comprehensively evaluated the performance of 24 popular state-of-the-art methods for complete end-to-end Hi-C data analysis using manually curated or experimentally validated benchmark datasets. Our results indicate that HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances in different aspects, providing a reference for researchers to choose suitable Hi-C analysis tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Yan Li, Rui Liu, Mingzhou Li
Summary: The storage of lipids as energy in adipose tissue is conserved, but there are substantial differences in the physiological activities of adipose tissues among species. This study characterized the transcriptional and lipidomic profiles of subcutaneous and visceral adipose tissues across 15 vertebrate species, spanning more than 300 million years of evolution. The data revealed greater variation in AT transcriptome and lipidome among species than within the same species, providing a resource for future studies on functional differences among adipose tissues in vertebrate species.
Article
Biochemistry & Molecular Biology
Jing Li, Teng Yuan, Anjing Zhang, Peidong Yang, Li He, Keren Long, Chuang Tang, Li Chen, Mingzhou Li, Lu Lu
Summary: Macrophages are essential for immunity and play important roles in tissue homeostasis and metabolism. There is currently no standardized method for isolating and differentiating porcine macrophages. This study identified distinct M1 and M2 macrophage subsets in pigs and compared their gene expression profiles. The results showed that porcine macrophages have similar gene signatures to human and mouse macrophages. The study also demonstrated the potential prognostic value of macrophage signatures in differentiating pathogen infections.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)