Molecular Genetics and Genomics最新文献

The single-stranded RNA viruses exhibit stupendously high evolutionary rate spanned several orders of magnitude. The accurate and reliable estimates of the virus evolutionary rate are of importance for the robust interpretation of outbreak investigations and are critical for understanding short-term virus transmission patterns. In the previous studies, the substitution rate of the Japanese encephalitis virus (JEV) and time to the most recent common ancestor (MRCA) were reported, however, the estimates are substantially different between some of the studies. Importantly, temporal signal in data was not evaluated by a formal test. The purpose of our study is to estimate the substitution rate and the age of the JEV common clade (GI-GV) and of two JEV genotypes (GI and GIII) supported by a formal Bayesian analysis of temporal signal in the open reading frame (ORF) nucleotide data. Additionally, we assessed temporal signal in the data from the previous work to explain the observed discrepancy between the reported JEV evolutionary rate estimates. Results showed that the mean substitution rate of the JEV GI-GV was 2.41 × 10^- 4 nucleotide substitution per site per year (s/s/y) with 95% highest posterior density (HPD) interval of 1.67 × 10^- 4-3.14 × 10^- 4 or approximately 2.5 nucleotide substitutions per ORF (10,296 nucleotides) per year. That is one of the lowest substitution rates among the species closely related to JEV and other well-studied members of mosquito-borne flaviviruses. The mean substitution rate of GI and GIII was evaluated to be 4.13 × 10^- 4 s/s/y (95% HPD interval, 3.45 × 10^- 4- 4.82 × 10^- 4) and 6.17 × 10^- 5 s/s/y (95% HPD interval 3.84 × 10^- 5-8.62 × 10^- 5), accordingly, with the ages of clades of 153 (95% HPD, 87-237) and 216 (95% HPD, 139-317), respectively. The mean root height of JEV is 1234 years (95% HPD, 407-2333).

The glycosylation patterns of flavonol glycosides (FGs) in soybean leaves are associated with productivity and insect resistance. The structure of FGs is conditioned by four flavonoid glycoside glycosyltransferase (FGG) genes, Fg1 (6"-glucoside present), Fg2 (6"-rhamnoside present), Fg3 (2"-glucoside present), and Fg4 (2"-rhamnoside present). We previously cloned and characterized the Fg1 to Fg3 genes. This study was conducted to comprehensively identify FGG genes by isolating the Fg4 gene. Leaves of the cultivar, Clark (Fg4 allele), contained FGs with rhamnose at the 4"-position, whereas those of the cultivar A.K. (fg4 allele), were devoid of 4"-rhamnoside. Their F₂ population segregated in three Clark-type: 1 A.K.-type ratios, suggesting that a single gene controlled the existence of 4"-rhamnoside. Based on genetic mapping, we cloned a candidate gene, Glyma.06G235000, with three amino acid substitutions between cultivars. Recombinant protein of Clark acted on kaempferol 3-O-rhamnosyl-(1→6)-galactoside and generated a product with a similar retention time to kaempferol 3-O-rhamnosyl-(1→4)-[rhamnosyl-(1→6)-glalactoside]. Furthermore, it acted on kaempferol 3-O-glucoside/galactoside and generated products with similar retention times to kaempferol 3-O-rhamnosyl-(1→2)-glucoside/galactoside. The A.K. protein did not function presumably due to G293R mutation. The cleaved amplified polymorphic sequence (CAPS) marker to detect the mutation co-segregated with FG composition. These results suggest that Glyma.06G235000 corresponds to the Fg4 gene and that the protein attaches rhamnose to the 2"- or 4"-position, depending on the substrates. Information of all FGG genes may be useful for developing cultivars with the desired FGG composition.

Klebsiella quasipneumoniae, an emerging member of the Klebsiella genus, has recently garnered attention as a clinically significant pathogen capable of causing severe human infections. Despite its pathogenic potential, it is frequently misidentified as Klebsiella pneumoniae due to their close genetic and phenotypic similarities, leading to diagnostic challenges and potential implications for treatment and epidemiological surveillance. This study addresses a critical gap in our understanding of K. quasipneumoniae by applying high-resolution genomic tools to distinguish it from its more well-characterized K. pneumoniae, assessed their AMR profiles and evaluate the limitation of conventional identification methods. Whole genome of a gram-negative K. quasipneumoniae (Klebsiella ST1699) bacterium found in an edible fish bought from a retail market in Assam, India. Whole Genome Sequencing (WGS) using the Illumina sequencing and species identification by Mash Screen confirmed the authenticity of K. quasipneumoniae. We assembled the 5.21 Mb complete genome of Klebsiella ST1699 and harboured several Antimicrobial Resistance Genes (ARGs) viz., blaLAP-2, blaOKP-B-1, fosA, tet(A), Sul2, dfrA14. OqxA and OqxB, and identified as a novel sequence type 1699 K. quasipneumoniae (ST 1699) from the edible fish in the retail market, Assam, India. We also performed comparative genome analysis with 6 other strains of K. quasipneumoniae genome sequences in the NCBI database. K. quasipneumoniae represents a clinically relevant and underrecognized pathogen with significant antimicrobial resistance. Improved molecular diagnostics are essential for accurate identification and effective infection control. Misidentification may contribute to underreporting and inappropriate therapeutic strategies, underscoring the need for heightened awareness and surveillance. Our findings have implications for diagnostic accuracy, resistance surveillance, and the development of targeted therapeutic strategies.

To investigate the mechanism by which melatonin influences melanin production in goat melanocytes, and to provide a theoretical foundation for the genetic principles underlying animal hair color formation, dorsal skin tissues were collected approximately 5 cm behind the shoulder of 4-day-old Jiaohe black goats. Melanocytes were localized using immunohistochemistry and immunofluorescence techniques, isolated from hair follicle tissues through enzyme digestion, and treated with different concentrations of melatonin. Cell viability, proliferation, apoptosis, and melanin synthesis were assessed using CCK8, EdU, flow cytometry, and melanin content assays, respectively. Melanocytes were subjected to transcriptome sequencing, differential gene screening, and functional enrichment analyses. The expression of relevant genes and proteins was verified using real-time quantitative PCR and western blotting, respectively. Melanocytes were determined to be located above the hair follicle papilla and in the outer root sheath, and were successfully isolated and cultured. Melatonin inhibited melanocyte proliferation, promoted apoptosis, and inhibited melanin synthesis. After RNA sequencing, 952 and 1300 differentially expressed genes (DEGs) were screened by comparing the two groups respectively, which were mainly enriched in Melanogenesis and the Wnt signaling pathway. Validation experiments confirmed that melatonin inhibited the expression of genes and proteins related to the Wnt/β-catenin signaling pathway. Notably, treatment with an agonist of the Wnt/β-catenin pathway attenuated the inhibitory effect of melatonin. This study reveals that melatonin can reduce melanocyte viability, inhibit proliferation, promote apoptosis, reduce melanogenesis, and affect melanin synthesis through the Wnt/β-catenin signaling pathway. This study provides a theoretical basis for understanding the regulatory role of melatonin in hair color formation in animals.

Synodontis, of great edible and ornamental value, is the most species-rich genus of the catfish family Mochokidae, but comparative studies based on its mitogenome data are still lacking. Therefore, we sequenced and analyzed the complete mitogenomes of Synodontis decorus and Synodontis petricola and compared them with those of other Mochokidae or Synodontis species; these were determined to be 16,574 and 16,529 bp, respectively. A phylogenetic analysis further confirmed the position of Synodontis in Mochokidae and showed that the genus Synodontis is polyphyletic. These results are beneficial to a further understanding of the phylogenetic evolution of the Mochokidae family and Synodontis genus and provide a basis for species identification and conservation genetics.

Understanding gene function in vertebrate development requires tools that allow precise and timely manipulation of gene expression. Zebrafish (Danio rerio), with its transparent embryos and rapid development, offers an ideal model to study vertebrate biology. This review explores how morpholino oligonucleotides (MOs), a widely used tool for transient gene knockdown, have been employed to investigate the roles of carbonic anhydrases (CAs) and carbonic anhydrase-related proteins (CARPs) in zebrafish. CAs are metalloenzymes, while CARPs are inactive isozymes that play critical roles in pH regulation, ion transport, CO₂ metabolism, and protein interactions influencing diverse biological functions. Many of the MO knockdown studies presented here have been extensively conducted in our laboratory over the past decade, revealing novel roles for CAs in neural development, reproduction, and swim bladder formation. These studies also confirm roles previously reported in humans, such as pigmentation, acid-base homeostasis, neural development, and motor coordination. We discuss technical aspects of MO design, delivery, and validation, and address common challenges such as off-target effects, transient gene silencing, and the necessity of rescue experiments. In addition, the review includes a comparative analysis of MOs versus CRISPR/Cas9-based genome editing, underscoring their respective advantages and limitations for functional genomics. In conclusion, this review provides not only a methodological guide but also biological insights into CA function in zebrafish, highlighting how antisense technology continues to inform vertebrate development and disease modeling. The lessons learned here may inform the study of other gene families and support translational research in carbonic anhydrase-related human disorders.

Susceptibility to SARS-CoV-2 infection and severity of COVID-19 have high heterogeneity, but the underlying factors for such heterogeneity were largely unknown. This study aimed to investigate whether genetically determined immune phenotypes contribute to the variability in COVID-19 outcomes, by integrating large-scale GWAS data to assess genetic correlations, causal associations, and pleiotropic gene functions. Based on the summary statistics from GWAS analyses for immune phenotypes and COVID-19 outcomes, comprehensive analyses were performed to elucidate the associations between immune phenotypes and COVID-19 pairs. The genetic correlations between COVID-19 outcomes and immune phenotypes were commonly observed, and 60 immune phenotypes were significantly correlated with four COVID-19 outcomes (64 pairs) (FDR < 0.05). Treg T cell panel and B cell panel have relatively more significant pairs in number. Pairwise gene-based analyses identified numerous pleiotropic genes for significant pairs identified. The gene set enrichment analysis revealed the involvement of the identified pleiotropic genes in complex immune processes. We observed significant causal effects of six immune phenotypes from 4 trait panels on any one of the two COVID-19 outcomes, and of which CD19 on naïve-mature B cell was the only significant immune phenotype shared by the two COVID-19 outcomes. The findings greatly improved our understanding of the interaction between immune response and COVID-19 outcome, and also contribute to the detection of susceptible individuals and the design of therapeutic strategies from the perspectives of immunology. In conclusion, our study provides genetic evidence that immune phenotypes, particularly B cell and Treg traits, play a causal role in susceptibility to SARS-CoV-2 infection and progression to severe COVID-19.

Esophageal squamous cell carcinoma (ESCC) is a malignant cancer. At present, platinum-based chemotherapy drugs are mainly used to treat ESCC patients. However, certain patients have developed significant resistance to cisplatin, which greatly limits the effectiveness of treatment. Hence, it is urgent to probe the mechanism of cisplatin chemotherapy resistance in ESCC. To clarify the association between AL137246.1 level and cisplatin resistance in ESCC patients, a total of 30 pairs of cisplatin-sensitive and cisplatin-resistant ESCC tissues were collected, and 30 non-cancerous tissues were used as controls. Survival analysis was used to detect the relationship between AL137246.1 level and ESCC prognosis. Then, Eca109 and Kyse70 cells were treated with cisplatin to induce the ESCC cisplatin resistance model. For understanding the detailed molecular process involving AL137246.1 in the development of cisplatin resistance in ESCC, the binding relationship between GLI2 and ABCC1 promoter was determined by dual luciferase and ChIP assays. RIP was applied to test the interaction between AL137246.1 and GLI2. Cell viability and proliferation were detected by CCK8 and Edu assays, respectively. Cell apoptosis was detected by flow cytometry. The results indicated that AL137246.1 level was reduced in ESCC and indicated a poor prognosis of ESCC. AL137246.1 overexpression was associated with increased sensitivity to cisplatin in ESCC cells, which was reversed by ABCC1 upregulation. Mechanistically, GLI2 led to the transcriptional activation of ABCC1 in ESCC. In conclusion, AL137246.1 inhibited the expression of ABCC1 by binding to GLI2, thereby enhancing the sensitivity of ESCC to cisplatin. This study suggested that AL137246.1, as a potential molecular target, has important application prospects in improving the sensitivity of ESCC to cisplatin chemotherapy.

Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.

Aging is a major biological process underlying increased risk of chronic and neurodegenerative diseases, yet its molecular mechanisms remain incompletely defined. Our study systematically investigates the conserved functions and pathways of W06A7.4 in Caenorhabditis elegans and its human homolog TMEM144 in the regulation of aging, combining genetic manipulation in model organisms, analysis of human clinical samples, and functional assays in cell lines. The results demonstrate that W06A7.4 promotes longevity in C. elegans through synergistic effects with dietary restriction, reduction of oxidative damage, modulation of IIS and mTOR signaling, and maintenance of mitochondrial membrane potential. In human samples and cellular models, TMEM144 expression increases with age and in Alzheimer's disease. Our results suggest that TMEM144 may be involved in the regulation of glucose transport and mitochondrial respiration via the downstream protein TIMMDC1. These findings advance our understanding of evolutionarily conserved aging pathways and identify W06A7.4/TMEM144 as promising molecular targets for anti-aging and neurodegenerative disease interventions.