Trends in Genetics
A database for post-genome analysis
References (11)
- A.G. Murzin et al.
J. Mol. Biol.
(1995) - S. Goto
Cited by (324)
Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina
2023, iScienceThe retina is a notable tissue with high metabolic needs which relies on specialized vascular networks to protect the neural retina while maintaining constant supplies of oxygen, nutrients, and dietary essential fatty acids. Here we analyzed the lipidome of the mouse retina under healthy and pathological angiogenesis using the oxygen-induced retinopathy model. By matching lipid profiles to changes in mRNA transcriptome, we identified a lipid signature showing that pathological angiogenesis leads to intense lipid remodeling favoring pathways for neutral lipid synthesis, cholesterol import/export, and lipid droplet formation. Noteworthy, it also shows profound changes in pathways for long-chain fatty acid production, vital for retina homeostasis. The net result is accumulation of large quantities of mead acid, a marker of essential fatty acid deficiency, and a potential marker for retinopathy severity. Thus, our lipid signature might contribute to better understand diseases of the retina that lead to vision impairment or blindness.
MicroRNAs Markedly Expressed in Apical Periodontitis Cooperatively Regulate Cytokines and Growth Factors Promoting an Anti-inflammatory Response
2023, Journal of EndodonticsMicroRNAs have been shown to play a role in the pathogenesis of apical periodontitis. Upregulation of miR-10a-5p and downregulation of miR-891a-5p were previously reported in apical periodontitis samples. This study aims to perform a functional characterization of miR-10a-5p, investigating its capacity to regulate the expression of inflammatory cytokines and growth factors, as well as a possible co-regulation mechanism with miR-891a-5p in the development of apical periodontitis.
miR-10a-5p mimics/controls and miR-891a-5p inhibitors/controls were introduced to human K-562 cells in the presence or absence of lipopolysaccharide. Total RNA was extracted from cell lysates, and target genes were examined via quantitative reverse transcription-polymerase chain reaction. Cell lysates were also subjected to proteomics analysis. Furthermore, mimics of miR-10a-5p and inhibitors of miR-891a-5p were co-transfected into K-562 cells. RNA sequencing and quantitative reverse transcription-polymerase chain reaction were carried out to examine their target genes.
Overexpression of miR-10a-5p led to downregulation of tumor necrosis factor-alpha and interleukin-1 beta mRNA and upregulation of transforming growth factor-beta 1 (TGFB1) mRNA expression, whereas interleukin 3 and TGF-β1 proteins were upregulated. Simultaneous overexpression of miR-10a-5p and inhibition of miR-891a-5p further increased TGFB1 mRNA transcript levels. RNA sequencing revealed that genes co-regulated by miR-10a-5p and miR-891a-5p may be involved in apical periodontitis-related pathways such as tumor necrosis factor, transient receptor potential, and vascular endothelial growth factor signaling pathways.
miR-10a-5p may modulate the expression of multiple inflammatory cytokines and growth factors such as tumor necrosis factor-alpha, IL-1β, interleukin 3, and TGF-β1. In addition, miR-10a-5p and miR-891a-5p cooperatively regulate TGFB1 gene expression, and the gene network of this co-regulation is integrated with many pathways in apical periodontitis.
Gene reduction and machine learning algorithms for cancer classification based on microarray gene expression data: A comprehensive review
2023, Expert Systems with ApplicationsDisease diagnosis and prediction methods in biotechnology and medicine have significantly advanced over time. Consequently, analyzing raw gene expression is crucial for identifying diseases such as cancer. Interestingly, microarrays are a tool that records gene expression from deoxyribonucleic acid (DNA) or ribonucleic acid. This technique exhibits intriguing characteristics, such as generating high-dimensional data with a small sample size. However, in the case of such dataset, the classification model is prone to overfitting. This limitation can be overcome by reducing the dimensions of the microarray datasets to a reasonable number. Machine learning (ML)-based data reduction has recently achieved considerable attention in genomic research. Therefore, this review examines recent studies that present state-of-the-art data reduction and classification algorithms for microarray gene expression data to diagnose tumors and analyzes their performance. To the best of our knowledge, this is the first review that provides a comprehensive view of data preprocessing, dimensionality reduction, including feature (i.e., gene) selection, feature extraction, and their hybrid, and ML algorithms. The paper is structured as follows. First, this review summarizes several data preprocessing methods applied to gene expression datasets. Then, a detailed review of various ML-based feature selection algorithms, including filter, wrapper, embedded, ensemble, and hybrid algorithms, is discussed. These algorithms are examined under three main classes—supervised, unsupervised, and semisupervised ML. Next, the feature extraction and hybrid of feature extraction and selection algorithms are thoroughly reviewed. Furthermore, a detailed review of broadly applied ML algorithms to simplify tumor and nontumor classification using microarray datasets is presented. Finally, the challenges and open questions related to gene expression datasets for accurate cancer classification and detection are highlighted.
Comparative genomic analyses of Klebsiella pneumoniae K57 capsule serotypes isolated from bovine mastitis in China
2023, Journal of Dairy ScienceKlebsiella pneumoniae can cause severe clinical mastitis in dairy cows, with K. pneumoniae type K57 (K57-KP) being the most common capsular serotype. To identify virulence factors and antimicrobial resistance (AMR) genes of K57-KP with varying virulence, Galleria mellonella (greater wax moth) larvae were infected as a screening model to characterize virulence of 90 K57-KP strains, with 10 and 11 strains defined as virulent or attenuated, respectively, based on larval survival rates. Next, virulence of these 21 isolates was subsequently confirmed in adhesion and lactate dehydrogenase release assays, using bovine mammary epithelial cells cultured in vitro. Finally, genes associated with virulence and AMR were characterize with whole-genome sequencing. These 21 K57-KP strains were designated into 16 sequence types based on multi-locus sequence typing and allocated in phylogenetic analysis based on single nucleotide polymorphisms. There was great genetic diversity among isolates. In addition, adhesion-associated genes (e.g., fimA, sfaA, and focA) aminoglycoside-resistance genes (aph(6)-Id, strAB) were associated with virulence. This study provided new knowledge regarding virulence of K57-KP associated with bovine mastitis, which may inform development of novel diagnostic tools and prevention strategies for bovine mastitis.
The cotton mitochondrial chimeric gene orf610a causes male sterility by disturbing the dynamic balance of ATP synthesis and ROS burst
2022, Crop JournalPlant cytoplasmic male sterility (CMS) is maternally inherited and often manifested as aborted pollen development, but the molecular basis of abortion remains to be identified. To facilitate an investigation of CMS in cotton, the complete sequence of cotton mitochondrial (mt) genome for CMS-D2 line ZBA was determined. The mt genome was assembled as a single circular molecule with 634,036 bp in length. A total of 194 ORFs, 36 protein‐coding genes, six rRNAs, and 24 tRNAs were identified. Several chimeric genes encoding hypothetical proteins with transmembrane domains were identified. Among them, a previously unknown chimeric gene, orf610a, which is composed of atp1 and a 485-bp downstream sequence of unknown nature, was identified. RT-PCR and qRT-PCR validation indicated that orf610a was expressed specifically in a sterile line. Ectopic expression of orf610a in yeast resulted in excessive accumulation of reactive oxygen species and reduction in ATP content, in addition to inhibition of cellular growth. Transgenic A. thaliana overexpressing orf610a fused with a mitochondrial targeting peptide displayed partial male sterility. Interaction between ORF610a and the nuclear-encoded protein RD22 indicated an association between ORF610a and pollen abortion. Positive feedback during transcriptional regulation between nuclear regulatory factors and the mt CMS gene may account for the male sterility of ZBA.
Overexpression of lncRNA-Gm2044 in spermatogonia impairs spermatogenesis in partial seminiferous tubules
2022, Poultry ScienceLong noncoding RNAs (lncRNAs) have been demonstrated to regulate reproduction in mammals. Our previous study revealed that the expression level of lncRNA-Gm2044 was obviously elevated in nonobstructive azoospermia with spermatogonial arrest. Here, a transgenic mouse model of lncRNA-Gm2044 in spermatogonia using the Stra8 promoter was constructed to explore the roles of upregulated lncRNA-Gm2044 in male fertility. Testicular morphology and fertility weren't affected in transgenic mice expressing lncRNA-Gm2044. However, overexpression of lncRNA-Gm2044 in spermatogonia partially impaired spermatogenesis in the transgenic mice. Then, transcriptome sequencing was executed to find the potential signaling pathway repressing spermatogenesis in germ cells of lncRNA-Gm2044 transgenic mice. Through quantitative analysis of differentially expressed genes, 442 upregulated mRNAs and 147 downregulated mRNAs were displayed in male germ cells of Gm2044-transgenic mice (Gm2044-Tg) compared with non-transgenic mice (Non-Tg). Using gene ontology (GO) analysis, differentially expressed genes were shown to play vital roles in RNA_metabolic_process, Central_element, Enzyme_binding, and Intracellular_bridge. Using Kyoto encyclopedia of genes and genomes (KEGG) analysis, differentially expressed genes were shown to participate in RNA_transport, Cell_cycle, Renin-angiotensin_system, and Chemokine_signaling_pathway. Gene Set Enrichment Analysis (GSEA) revealed that Acrosome_assembly and Sperm_plasma_membrane were involved in the overexpression of lncRNA-Gm2044 blocking spermatogenesis. Furthermore, some of the most differentially expressed mRNAs were verified by RT-qPCR. In addition, we determined that the lncRNA-Gm2044 has no ability to translate into peptides by the bioinformatics method and molecular experiment. Thus, lncRNA-Gm2044 is a novel molecular target for the diagnosis and treatment of male infertility.