Small heat-shock proteins (sHSPs, the HSP20 family) are ATP-independent molecular chaperones that hold partially unfolded substrates and protect the proteome during heat and other abiotic stresses; every member is defined by a conserved α-crystallin domain (ACD). Finger millet (Eleusine coracana) is a climate-resilient, calcium-rich allotetraploid cereal of the semi-arid tropics whose HSP20 repertoire had not been catalogued. The present study is an entirely computational (in silico) analysis of the chromosome-scale reference genome of finger millet (NCBI GenBank assembly GCA_032690845.1, cultivar KNE 796-S). Mining the predicted proteome with the ACD profile (Pfam PF00011) and confirming every candidate by NCBI CD-search recovered 76 non-redundant ACD-bearing HSP20 genes (EcHSP20-1–EcHSP20-76). Based on phylogeny and TargetP-predicted localization, the members were classified into ten subfamilies: seven cytosolic/nuclear classes (C-I to C-VII, 60 members) together with chloroplastic (11), mitochondrial (3) and endoplasmic-reticulum (2) groups. The proteins ranged from 110 to 355 amino acids (12.1–39.2 kDa) with theoretical pI of 4.85–9.69. The 76 loci were distributed over 14 of the 18 chromosomes and were conspicuously absent from chromosomes 8 A, 8B, 9 A and 9B, with pronounced clustering on chromosomes 1, 2, 3 and 6. Duplication analysis detected 149 paralogous pairs (49 homoeologous, 80 segmental/dispersed and 18 tandem); 147 of 148 pairs for which substitution rates could be calculated returned Ka/Ks < 1 (mean 0.20), indicating strong purifying selection consistent with retention after whole-genome/allopolyploid duplication. Promoter analysis (PlantCARE) revealed enrichment of abscisic-acid-responsive (ABRE), MYB/MYC drought-related, STRE, DRE, low-temperature (LTR) and methyl-jasmonate/salicylic-acid elements, whereas canonical heat-shock elements (HSE) were not recovered. Expression profiling against a public drought transcriptome (SRP081350) showed that about half of the genes (39 of 76) are transcribed in leaf tissue, the expressed fraction being dominated by the cytosolic class C-I. This first finger-millet HSP20 catalogue provides a verified, reproducible framework and nominates computationally predicted candidate genes for future functional work on thermotolerance in cereals.
Soybean (Glycine max L. Merrill) productivity is strongly influenced by genotype × environment (G × E) interaction, while simultaneous improvement of yield, seed quality, and associated traits remains a major breeding objective. Twenty-two soybean genotypes were evaluated across eight environments representing four locations and two kharif seasons in Maharashtra, India, to identify genotypes combining desirable multi-trait performance, stability, and adaptability. Significant variation was found for all the traits studied, seed yield ranged from 0.26 to 1.68 kg plot− 1 and protein content from 33.25 to 41.83
The aim of this study was to access variability of different cultivars of winter oilseed rape for yield, yield components and seed quality traits by multivariable statistical method. Traits including seed yield, silique length, number of seeds per siliques, weight of 1000 seeds, content of oil in the seeds, two unsaturated fatty acids (linoleic, linolenic) and glucosinolate content in seed meal (gluconapine, glucobrassicanapine, progoitrine and total glucosinolates) were investigated. Seven cultivars of oilseed rape were evaluated in a randomized block design, with four replicates at two locations in two growing seasons. The tested genotypes displayed wider genetic variability for studied traits in all environments. The results of canonical variate analyses explained from 79.2
U-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.
Liver fibrosis, as a common pathological process in various chronic liver diseases, severely impacts patients' quality of life and prognosis. The core mechanisms driving its progression involve the activation of hepatic stellate cells (HSCs), sustained inflammatory responses, and cellular metabolic reprogramming. Within this process, hypoxia-inducible factor-1 (HIF-1), a key transcription factor enabling cellular adaptation to hypoxic environments, has been shown to play a significant role. Current research further demonstrates that HIF-1 participates in multiple molecular mechanisms of liver fibrosis by regulating HSC activation, promoting inflammation, and modulating metabolic pathways. However, the precise regulatory networks of HIF-1 in liver fibrosis and effective intervention strategies remain poorly understood.Therefore, this article systematically reviews the molecular regulatory network of HIF-1 in liver fibrosis, with a particular focus on its role in cell apoptosis and metabolic reprogramming. Furthermore, it summarizes recent advances in therapeutic strategies targeting HIF-1 and its related signaling pathways, including the development and application of HIF-1 inhibitors, natural products, and small-molecule drugs. In summary, by integrating the latest basic and clinical research findings, this review aims to provide theoretical support and identify future research directions for targeted therapy of liver fibrosis, thereby facilitating the clinical translation of relevant treatment approaches.
Non-obstructive azoospermia is a severe form of male infertility characterized by impaired spermatogenesis. Given the strong evidence linking obesity and chronic inflammation to male reproductive dysfunction, we aimed to investigate the role of adipokines METRNL (Meteorin-like protein) and RARRES2 (Chemerin) in non-obstructive azoospermia pathogenesis. We conducted a retrospective study using the testicular biopsy samples of 35 patients (12 cases were obese, 23 cases had normal body mass index) with non-obstructive azoospermia and 18 patients with obstructive azoospermia and/or vas deferens agenesis. We compared the testicular METRNL and RARRES2 mRNA expressions of obese and non-obese non-obstructive azoospermia cases with controls (obstructive azoospermia cases with intact spermatogenesis). We detected significantly increased RARRES2 expression in both obese and non-obese non-obstructive azoospermia patients. Even though statistically non-significant, we observed a higher RARRES2 expression trend in histologically more severe non-obstructive azoospermia cases. We also detected a significant inverse correlation between RARRES2 expression and Johnsen score, an indicator of seminiferous tubule integrity and spermatogenesis status. Conversely, we found no significant difference in METRNL expression across the study groups. Broader studies are needed to validate our results and investigate the mechanisms of increased RARRES2 (chemerin) expression in the azoospermia cases with defective spermatogenesis.
Traditional breeding of chilli pepper (Capsicum annuum L.) is constrained by long generation intervals, limiting the rate of annual genetic gain. Recent advances in predictive breeding, genomic prediction, and image-based high-throughput phenotyping have created new opportunities for integrated breeding pipelines in Capsicum annuum. Speed breeding (SB) shortens the generation cycles through extended photoperiods and optimized light regimes, enabling rapid recycling of breeding populations. This review synthesizes the integration of SB with doubled haploid (DH), genomic selection (GS), and high-throughput phenotyping (HTP) to propose a crop-specific predictive breeding framework for chilli pepper improvement. Under optimized SB protocols, flowering time and seed maturation can be substantially accelerated, while DH technology enables rapid fixation of elite recombinants despite persistent genotype-dependent limitations. Genomic selection improves prediction accuracy for complex quantitative traits, including stress tolerance and disease resistance, whereas HTP platforms facilitate rapid and non-destructive phenotypic evaluation. Recent Capsicum studies further demonstrate the importance of multi-environment genomic prediction for addressing genotype-by-environment interactions in breeding programs. However, challenges including low DH efficiency, environmental sensitivity, and limited transferability between controlled and field conditions remain significant constraints. Overall, the integrated SB-DH-GS-HTP framework provides a scientifically grounded strategy for improving breeding efficiency and accelerating the development of climate-resilient chilli cultivars.
This study aimed to evaluate the effects of FTO (rs9939609) and ADRB3 (rs4994) gene variants, dietary intervention, and physical activity on gestational weight gain and perinatal outcomes in women with obesity and early gestational diabetes (GDM). In this prospective study, 115 pregnant women with obesity and early GDM were enrolled. All participants received standardised dietary counselling and recommendations regarding physical activity. Gestational weight gain, biochemical parameters, physical activity levels, genetic variants, and maternal and neonatal outcomes were assessed throughout pregnancy. Appropriate gestational weight gain was achieved by 73
Strigolactones are plant hormones that regulate diverse developmental processes and stress responses, but their potential role in epigenetic regulation remains poorly understood. Previous transcriptomic analyses of strigolactone mutants in various species revealed extensive transcriptional reprogramming, suggesting destabilisation of higher-order regulatory mechanisms rather than changes in discrete gene networks. Here, we investigated whether disruption in strigolactone biosynthesis or perception is associated with altered DNA methylation patterns. Whole-genome bisulfite sequencing was performed on 7-day-old seedlings of Arabidopsis thaliana wild-type and the strigolactone biosynthesis mutant max3 and the perception mutant d14. A comparative analysis identified differentially methylated regions in CG, CHG, and CHH sequence contexts. While CG methylation changes showed no directional bias, non-CG contexts exhibited a pronounced enrichment of hypermethylated regions in both mutants, with the strongest effect observed in the CHH context. CHH hypermethylation was preferentially enriched at promoter-associated regions, primarily overlapping non-coding and pseudogene loci and showed substantial overlap between max3 and d14, indicating a shared epigenetic response in both mutants. Gene-body-associated regions displayed a similar but weaker pattern. These results demonstrate that impairment of the strigolactone pathway is consistently associated with selective CHH hypermethylation rather than global methylation changes. Because CHH methylation in plants is commonly associated with RNA-directed DNA methylation, the observed pattern is consistent with altered RdDM-associated regulation; however, direct involvement of the RdDM machinery remains to be established. This study provides a genome-wide framework for exploring how strigolactones may be associated with epigenetic regulation in plants.
Apoptosis and pyroptosis-mediated neuronal death represent major pathogenic mechanisms underlying Alzheimer's disease (AD). Given the potential crosstalk between these two forms of cell death, investigation of a single death pathway may be insufficient to identify robust diagnostic biomarkers for AD. Therefore, this study aimed to explore hub genes involved in both apoptosis and pyroptosis as potential diagnostic biomarkers for AD. First, 23 common cell death-related genes (CDRGs) were identified through bioinformatic analysis. Functional enrichment analyses using GO, KEGG, and GeneMANIA revealed significant associations between AD and biological processes including apoptosis, pyroptosis, and neuronal death. Subsequently, machine learning algorithms combined with ROC curve analysis identified CASP3, IL1B, NLRP3, and PYCARD as candidate biomarkers with potential diagnostic and therapeutic implications for AD. These findings were further validated by the in vitro experiments, which confirmed that the expression levels of these four biomarkers were consistent with the predicted results. Additionally, in patients with AD, CASP3, IL1B, NLRP3, and PYCARD were negatively correlated with macrophages. Collectively, these results suggest that the identified biomarkers may co-regulate apoptosis and pyroptosis through macrophages, thereby contributing to the pathogenesis of AD.
Reduced sperm count, impaired motility, and abnormal morphology are characteristics of oligoasthenoteratozoospermia (OAT). Genetic factors play an important role in spermatogenic failure, but the molecular basis of OAT is still not fully understood. Whole-genome sequencing (WGS) was performed in 17 infertile men with normal karyotypes and no Y-chromosome microdeletions, including 10 patients with azoospermia and 7 with OAT. Among the OAT group, three patients carrying prioritized rare variants with potential relevance to spermatogenesis were selected for detailed analysis and presentation in the current study. Variants were called using DeepVariant, and they were annotated by Ensembl Variant Effect Predictor (VEP). Variants were prioritized based on low allele frequency (< 1
The DUF668 gene family, distinguished by a plant-specific conserved domain, is significantly involved in growth and stress responses. An extensive genome-wide study of the DUF668 gene family in potato (Solanum tuberosum L.) was conducted. A total of 11 DUF668s (StDUF668-1 to StDUF668-11) were recognized and analysed for their physicochemical characteristics, chromosomal distribution, gene structures, conserved motif profiles, secondary and tertiary structures and evolutionary relationships. The StDUF668s exhibited diverse structures, with intron-exon variations contributing to their functional diversity. The analysis of promoter sequences revealed multiple cis-acting regulatory elements related to phytohormones, stress responses, and developmental processes, indicating their potential modulatory roles. Expression profiling was conducted across various potato tissues and under different hormonal and stress conditions which demonstrated that StDUF668s play a role in crucial biological processes, involving abiotic and biotic stress responses. Furthermore, qRT-PCR-based expression profiling in response to salt and osmotic stress conditions validated that StDUF668s are involved in abiotic stress responses. Protein-protein interaction and miRNA targeting analyses highlighted the molecular pathways associated with the functions of DUF668s in potato. This study advances our understanding of the DUF668 gene family and provides a valuable resource for future research aimed at improving potato stress tolerance and growth.
The Pacific oyster (Magallana gigas) is a widely cultivated species, and its commercial value has been significantly enhanced by the widespread adoption of triploid oysters. Since triploid offspring inherit two chromosome sets from tetraploid males, this suggests that genetic improvement of tetraploid oysters is essential. The induction of the dark-shelled tetraploid ‘Haida No. 3’ line from selected diploid lines of Pacific oysters has been achieved. However, the genetic parameters of growth and shell color traits in this line remain unclear. This study involved analyzing the genetic parameters of 42 tetraploid full-sibling families using the restricted maximum-likelihood (REML) method, with a tetraploid inverse additive relationship matrix constructed by the polyAinv package. These results indicated that the heritability of growth traits was moderate, with values ranging from 0.19 ± 0.05 for shell width to 0.45 ± 0.09 for whole weight. For shell color traits, the heritability values for color L*, color a*, color b*, and ΔE were 0.42 ± 0.09, 0.46 ± 0.09, 0.55 ± 0.10, and 0.63 ± 0.12, respectively. The genetic correlations ( r_g ) between color L* and growth traits (excluding shell width) were moderate, ranging from 0.32 ± 0.15 to 0.42 ± 0.15. The low ΔE values observed across the tetraploid ‘Haida No. 3’ families indicate that the shell color purification has achieved the desired level of phenotypic consistency. Therefore, growth was identified as the primary breeding objective, with shell color regarded as secondary for the subsequent breeding program. The results provide useful information into selective breeding of fast-growing, black-shelled tetraploid oysters in aquaculture.
This study aims to investigate the methylation status and mRNA expression of key apoptotic genes, including death-associated protein kinase (DAPK 1), tumor necrosis factor receptor superfamily member 6 (FAS), SMAC, and tumor necrosis factor-related apoptosis-inducing ligand receptor 1 (TRAIL-R1) and its association with clinicopathological factors in cervical cancer cases. Methylation analysis was performed on 110 cervical cancer patients using qualitative methylation-specific polymerase chain reaction (MSP). Real-time PCR was used to analyze expression levels of selected genes. All samples were also analysed for the presence of high-risk HPV types (HPV 16 and 18) with specific primer. Additionally, association with clinicopathological and risk factors were evaluated. In-silico analysis was also done for further validation. The methylation status of DAPK, TRAIL R1, SMAC, and FAS was significantly different between cancer tissues and normal tissues. DAPK (0.001), FAS (0.001), and TRAIL R1 (0.02) were hypermethylated, and SMAC was found to be hypomethylated with the highest significance of < 0.0001. HPV 16 + samples were highly significant with DAPK (0.007) and FAS (0.013), and HPV 18 + samples were significant with DAPK (0.024), FAS (0.002) and TRAIL R1 (0.009). No HPV association was found with SMAC. Methylation was found to be inversely proportional to DAPK, TRAIL R1, and FAS expression. Aberrant promoter methylation of key apoptotic genes is significantly associated with cervical cancer and may contribute to its progression. Significant correlations with HPV infection and clinicopathological factors highlight their possible potential as predictive biomarkers. However, larger studies and functional validation are needed to confirm these findings and their clinical applicability.
Bell pepper (Capsicum annuum L. var. grossum Sendt.) is a major Solanaceous vegetable crop exhibiting wide variability in fruit size, shape and colour, which are critical market traits. The present study aimed to evaluate genetic diversity among 34 advanced breeding lines of bell pepper along with two check varieties (California Wonder and Solan Bharpur) using 30 agro-morphological descriptors (13 qualitative and 17 quantitative) under DUS (Distinctness, Uniformity, Stability) guidelines. The experiment was conducted during 2022 and 2023 at Dr YS Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, in a randomized complete block design (RCBD) with three replications. Significant variation was observed across morphological traits, with highest diversity index (H = 1.01) recorded for fruit shape in longitudinal section. Analysis of variance revealed substantial genetic variability and several genotypes (UHF-CAP-108, UHF-CAP-119, IIHR-131, UHF-CAP-106, UHF-CAP-113) significantly outperformed the better check variety Solan Bharpur for fruit yield per plant, producing medium-sized, blocky, glossy, dark green fruits with 3–4 lobes. Principal component analysis (PCA) identified six components explaining 83.08
Lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA), and chronic venous disease (CVD) are frequently underdiagnosed vascular conditions that contribute significantly to morbidity, mortality, and diminished quality of life, representing a considerable public health burden. The discovery of novel molecular biomarkers is crucial to improving early diagnosis, enabling accurate risk stratification, uncovering disease mechanisms, and facilitating the development of targeted therapies. This study aimed to investigate alterations in small nuclear RNAs (snRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with LEAD, AAA, and CVD. The snRNA expression profiles were analyzed using snRNA-seq data and the DESeq2 package. In parallel, miRNA-seq data were used to identify differentially expressed microRNAs (miRNAs) associated with snRNA dysregulation. Using a strict selection criterion, we identified 4 (RNU6-4P, RNU6-18P, RNU6-36P, and RNU2-48P) and 2 (RNVU1-19 and RNU1-146P) dysregulated snRNAs in patients with LEAD and CVD, respectively. Three miRNA-snRNA interactions involving miRNAs differentially expressed in these diseases were identified and confirmed in silico using the IntaRNA platform. Genetic variants located within dysregulated snRNAs indicate a potential functional association between selected snRNAs and vascular biology, particularly in relation to platelet function, blood pressure regulation, and smoking. Obtained findings underscore the potential of snRNAs as novel biomarkers and offer insights into their possible involvement in the vascular pathophysiological mechanisms underlying LEAD and CVD.
The mrk operon gene clusters encode type 3 fimbriae, involving in biofilm formation. Hence, we aimed to find out the distribution of mrk genes among uropathogenic Klebsiella pneumoniae (UPKP) strains. Moreover, mrk genes, hypermucoviscosity (HMV) characteristic and antimicrobial resistance (AMR) patterns and profiles were successfully, provided. From August 2023 to January 2024, 104 positive urine samples were collected. Standard microbiological and biochemical tests were employed to confirm the UPKP strains. Kirby-Bauer disc diffusion method was recruited to conduct antimicrobial susceptibility test (AST). The HMV characteristic in UPKP isolates was assessed using the string test. Finally, multiplex polymerase chain reaction (mPCR) was used to identify mrk genes distribution. Chi-square (χ2) and Fisher’s exact tests were utilized for statistical analysis. The mrk gene distribution varied among the UPKP isolates comprising mrkA (1.92
The addition lines derived from oat (Avena sativa L.) × maize (Zea mays L.) crosses constitute a unique tool for studying gene expression and the structure of chromatin, as well as a source of agronomically desirable traits in the context of new intergeneric hybrid cultivars. Therefore, for a better understanding of the introgression of maize chromatin into the oat genome, a comprehensive analysis of oat × maize lines was conducted. The presence of maize chromatin was confirmed in three tested lines by PCR-based amplification of the maize retrotransposon Grande-1, and verified by genomic in situ hybridization. Interestingly, the addition lines containing cytologically-detectable maize chromosomes showed a possible disturbance of the Rabl-like centromere-telomere polarization typical for oat. Moreover, the maize chromatin was consistently positioned near the nuclear periphery. The maize chromatin introgression caused a prolonged DNA replication phase, altering cell cycle dynamics, and may led to mitotic abnormalities, such as the formation of micronuclei and anaphase chromosome bridges. The introgression lines also showed morphological and physiological changes: smaller seeds, hampered seedlings' growth, and reduced yield parameters (number of flowers/seeds per plant/panicle and seed weight). These findings shed more light on the consequences of the maize chromatin introgression into the oat genome and the stability and utility of the obtained hybrids.
The global obesity epidemic involves a multifaceted interplay between genetics, environment, and the interactions between them. The discovery of leptin in 1994 changed our understanding of body weight regulation and triggered extensive genetic studies into monogenic and polygenic obesity. Despite initial therapeutic hopes, leptin’s efficacy in obesity was limited by leptin resistance. However, glucagon-like peptide-1, an incretin hormone, has become an important tool for managing obesity. Glucagon-like peptide-1 receptor agonists aid in weight loss and glycemic control while also providing metabolic and cardiovascular benefits. This article presents the shift from leptin biology to the therapeutic application of glucagon-like peptide-1 receptor analogs, focusing on their unique mechanisms, gene polymorphisms, and the hormonal interactions that regulate energy homeostasis. It outlines the shift from leptin-based theories to therapies focused on glucagon-like peptide-1 as we have gained understanding of the gut–brain–adipose axis, paving the way for targeted therapies in obesity management.
Array Comparative Genomic Hybridization (aCGH) enables genome-wide detection of copy number variants (CNVs), representing a major advance in diagnosing neurodevelopmental disorders and congenital anomalies. We performed aCGH in 1,468 patients referred for genetic evaluation due to neurodevelopmental delay, dysmorphic features, and congenital malformations. Pathogenic CNVs were detected in 24.5
