Review
Genetics & Heredity
Kangmei Zhao, Seung Yon Rhee
Summary: Pathway enrichment analysis is crucial for interpreting omics datasets and generating hypotheses. This article discusses best practices for interpreting different types of omics data using pathway enrichment analysis and emphasizes the importance of considering intrinsic features of various types of omics data. The article also explains key components that influence the outcomes of pathway enrichment analysis and provides guidance on reporting methodological details to improve reproducibility. It aims to serve as a primer for biologists to utilize omics resources and encourage bioinformatics tool developers to enhance the power of pathway enrichment analysis.
TRENDS IN GENETICS
(2023)
Article
Genetics & Heredity
Jianlei Gu, Jiawei Dai, Hui Lu, Hongyu Zhao
Summary: Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for understanding human diseases. This study proposed a data-driven framework to derive a list of Ubiquitously Expressed Genes (UEGs) and their global expression patterns, providing a valuable resource for further characterizing the human transcriptome.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Entomology
Mahnaz Rashidi, Nabil Killiny
Summary: The immune system of Diaphorina citri is weaker compared to other insects. However, it possesses a complete Toll system. Characterizing Toll signaling system genes and studying gene expression profiles in different life stages can help design innovative strategies for controlling this insect vector.
Review
Biochemistry & Molecular Biology
Tianxin Gao, Pei Wang, Teng Gong, Ying Zhou, Ancong Wang, Xiaoying Tang, Xiaolei Song, Yingwei Fan
Summary: The use of molecular imaging technologies in brain imaging is not only important for disease diagnosis and treatment, but also for in-depth study of brain functions. Reporter gene technology based on optical imaging has made breakthroughs in molecular-level brain function studies. The applications of magnetic resonance imaging (MRI), single-photon emission computed tomography (SPECT), and positron emission tomography (PET) reporter gene technologies in brain imaging are discussed, with a focus on cell therapies and gene therapies. These methods have shown potential for preclinical and clinical research, providing deeper imaging depths and wider imaging ranges.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Carly Boye, Sezgi Arpag, Michael Francis, Scott DeClemente, Aislin West, Richard Heller, Anna Bulysheva
Summary: Gene therapy has a wide range of applications but viral delivery methods have safety concerns. By using smaller plasmid DNA backbones, gene expression levels can be significantly increased using non-viral methods, as shown in rat tenocytes and myocardium. Delivery to the skin showed more moderate improvements.
BIOELECTROCHEMISTRY
(2022)
Article
Horticulture
Lu Tong, Shanhan Cheng, Honghao Lv, Chengzhi Zhao, Jie Zhu, Pingwu Liu, Zhiwei Wang, Limei Yang, Yangyong Zhang
Summary: The study analyzed the glucosinolate content and composition in the stems and leaves of 16 Chinese kale varieties using HPLC-MS, and examined the expression levels of glucosinolate biosynthesis pathway genes in varieties with different glucosinolate contents using qRT-PCR. It was found that aliphatic glucosinolates were the predominant type of glucosinolates in these varieties.
Article
Plant Sciences
Zhijing Xiao, Yanke Lu, Yi Zou, Chi Zhang, Li Ding, Kai Luo, Qiaoyu Tang, Yifeng Zhou
Summary: This study conducted genome-wide and comparative analyses of ATP sulfurylase in Cardamine hupingshanensis and investigated its expression under selenium stress. The results indicated that ChATPS1-2 play crucial roles in the response to selenium stress. In addition, molecular docking experiments revealed that ChAPS3-1 has stronger binding energies with various compounds. These findings provide important insights into the selenium assimilation mechanism and lay the foundation for further research on selenium metabolism in C. hupingshanensis.
Article
Biotechnology & Applied Microbiology
Quanchao Wang, Tiangui Cao, Chunde Wang
Summary: In this study, bioinformatics methods were used to identify and analyze Dmrt genes in 15 bivalves, resulting in the retrieval of 55 Dmrt genes. The phylogenetic tree showed that these genes can be divided into 5 classes. The Ka/Ks ratios suggested that these genes underwent purifying selection pressure. Additionally, the spatiotemporal expression analysis indicated that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. Overall, this study provides a molecular basis for further investigation of the functions of Dmrt genes and phylogenomic analyses in bivalves.
Article
Pharmacology & Pharmacy
Mercedes Rose, Alain Filiatreault, Andrew Williams, Josee Guenette, Errol M. Thomson
Summary: Air pollution is associated with increased risk of metabolic diseases such as type 2 diabetes due to the dysregulation of the insulin-signaling pathway. This study aimed to investigate the effects of ozone on insulin-signaling genes in major metabolic tissues and explore the role of glucocorticoids. Results showed that ozone inhalation led to distinct mRNA profiles and altered phosphorylation states of insulin-signaling proteins, indicating tissue-specific regulation of insulin-signaling pathway genes through glucocorticoid-dependent and independent mechanisms.
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2023)
Article
Oncology
Piaopiao Li, Yingxia Li, Lei Ma
Summary: This study investigated the biological roles and mechanisms of chimeric genes in pigs using weighted co-expression network analysis. The results showed that most protein domains of chimeric genes were derived from fused pre-genes and were involved in negative regulation of cell proliferation and protein localization to centrosomes. Additionally, chimeric genes were related to the growth factor-beta superfamily and played a key role in regulating T cell pathways.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Physiology
Marcelo R. Luizon, Izabela M. C. A. Conceicao, Sarah Viana-Mattioli, Mayara Caldeira-Dias, Ricardo C. Cavalli, Valeria C. Sandrim
Summary: This study analyzed the expression profiles of circulating miRNAs in the plasma of pregnant women in the second trimester, identifying 23 upregulated miRNAs, with only miR-204-5p showing statistical significance as a potential predictive biomarker for the early development of PE. The target genes of miR-204-5p were found to be related to known pathophysiological pathways in PE, suggesting its potential role in the pathophysiology of the disease.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Genetics & Heredity
Chanchal Malik, Sudhanshu Dwivedi, Tilahun Rabuma, Ravinder Kumar, Nitesh Singh, Anil Kumar, Rajesh Yogi, Vinod Chhokar
Summary: This study explores the genes involved in flavonoid biosynthesis pathways in Asparagus racemosus through de novo transcriptome sequencing. The results reveal a limited number of genes related to flavonoid biosynthesis and validate the expression using quantitative Real-time PCR. The study also shows the upregulation of many genes associated with flavonoid biosynthesis under the induction of methyl jasmonate.
FRONTIERS IN GENETICS
(2023)
Article
Cell Biology
Qiunan Zuo, Youyu Wang, Deqing Yang, Shujin Guo, Xiaohui Li, Jiajia Dong, Chun Wan, Yongchun Shen, Fuqiang Wen
Summary: This study used WGCNA to explore the molecular pathogenesis of the emphysema phenotype of COPD, identifying gene modules associated with emphysema and highlighting immune response and ECM organization. The results shed light on potential genetic mechanisms underlying the pathogenesis of the emphysema phenotype of COPD, but further research is needed to confirm the involvement of identified genes.
Article
Genetics & Heredity
Wei Zhang, Mengsi Xu, Juanjuan Wang, Shiyin Wang, Xinhua Wang, Jingquan Yang, Lei Gao, Shangquan Gan
Summary: Using RNA sequencing, this study analyzed the transcriptome profiles of tail fat tissues in Altay sheep and Xinjiang fine wool sheep, revealing significant differences in gene expression related to fat metabolism between the two breeds. Pathway analysis showed that the majority of differentially expressed genes were enriched in pathways related to fat metabolism. Additionally, some genes were involved in multiple pathways.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Yaolei Mi, Ruikun He, Huihua Wan, Xiangxiao Meng, Di Liu, Wenjun Huang, Yanjun Zhang, Zubaida Yousaf, Hongwen Huang, Shilin Chen, Ying Wang, Wei Sun
Summary: In this study, the anthocyanidins of eight different Epimedium species with different floral pigmentation phenotypes were analyzed. The expression levels of catalytic enzyme genes DFR and ANS were significantly decreased in four species showing loss of floral pigmentation. Complementation and overexpression experiments confirmed the functional role of these genes at the protein level.
FRONTIERS IN PLANT SCIENCE
(2023)