Search Results (3,959)

Background: Major geopolitical events and structural shocks are thought to play a significant role in shaping HIV epidemics by influencing individual behaviours, reshaping social networks, and impacting HIV prevention and treatment programs. Here, we describe individual-level measures of estimated time since HIV infection (ETI) from viral next-generation sequencing data among female sex workers and their clients in relation to significant geopolitical events in Ukraine. Methods: The Dynamics Study is a cross-sectional integrated biological and behavioural survey conducted among female sex workers and their clients in Dnipro, Ukraine (December 2017 to March 2018). We were able to successfully sequence a portion of the HIV pol gene on dried blood spot specimens among n = 5/9 clients and n = 5/16 female sex workers who tested positive for HIV (total n = 10/25) using an in-house drug resistance genotyping assay. The “HIV EVO” Intrapatient HIV Evolution web-based tool was used to infer ETI from viral diversity. Results: The median ETIs for female sex workers and their clients were 5.4 years (IQR = 2.9, 6.6) and 6.5 years (IQR = 5.4, 10.8), respectively. Nearly all HIV acquisition events (n = 7/10; 70%) were estimated to have occurred between the Great Recession (2008–2009) and the War in Donbas (May 2014–February 2022). In general, ETI suggests that HIV acquisition occurred earlier among clients (2012 [IQR = 2007, 2013]) compared to sex workers (2013 [IQR = 2012, 2016]). Conclusion: Our findings suggest that most HIV acquisition in this small subset of female sex workers and clients living with HIV occurred during periods of economic decline. Molecular studies on timing of HIV acquisition against timing of major geopolitical events offer a novel way to contextualize how such events may shape transmission patterns. Full article

Background/Objectives: Fat-soluble 25-hydroxyvitamin D (25-OHD) may be endogenously synthesized or obtained from dietary sources. Notably, it is crucial in calcium homeostasis, gene regulation, and immune system modulation, being even more relevant during prenatal stages, as the embryo utilizes vitamin D obtained from maternal plasma. Moreover, 25-OHD has been recently demonstrated to affect hematological parameters. We aimed to determine the correlation between maternal plasma 25-OHD levels, other blood parameters, and fetal anthropometric outcomes. Methods: Pregnant women attending an obstetrics and gynecology clinic during their gestation period were recruited, and data during follow-ups until the birth of their child were collected (IRB Approval Code: 07-XD-096). Data from 103 pregnant women were analyzed. Results: Compared to participants with normal levels, pregnant women with inadequate plasma 25-OHD levels exhibited a higher red blood cell count (4.3 ± 0.51 vs. 4.1 ± 0.42; p = 0.012) and lower mean corpuscular volume (86.4 ± 8.47 vs. 90.4 ± 6.74; p = 0.003), mean corpuscular hemoglobin (28.1 ± 3.34 vs. 29.6 ± 2.70; p = 0.008), plasma folate (12.6 ± 5.91 vs. 15.6 ± 5.86; p = 0.006), and vitamin B12 (289 ± 174 vs. 352 ± 147; p = 0.001) levels. Fish consumption frequency was positively associated with plasma 25-OHD levels. Conclusions: 25-OHD deficiency was correlated with alterations in hematological markers, plasma folate, and vitamin B12 levels. Given the high prevalence of 25-OHD deficiency in women of fertile age, government policies and healthcare professionals should emphasize vitamin D consumption adequacy in fertile women and expectant mothers. Full article

Background: Diabetes insipidus (DI) in newborns is an extremely rare condition, with the age of presentation strongly suggesting a genetic background of the disease. The differential diagnosis should include arginine vasopressin deficiency (AVD) and arginine vasopressin resistance (AVR). Some novel diagnostic tools such as copeptin evaluation and genetic tests are vital for early diagnosis. Case report: We present the case of a 1-month-old boy with polyuria observed since birth. Laboratory tests showed persistent hypernatremia, elevated plasma and low urine osmolality. An attempt at oral administration of desmopressin had no effect; additionally the copeptin level was increased. A genetic study (NGS of the AVP, AVPR2 and AQP2 genes) was considered and a new pathogenic variant in the AVPR2 gene (hemizygous c.157del) was detected. After the genetic test result was obtained, treatment with hydrochlorothiazide was started. The patient is now 3 months old, developing normally, and the weight and height are normal. Conclusions: Newborns with DI should be subjected to extensive multidisciplinary diagnostics, including endocrine and renal causes. Copeptin evaluation and prompt genetic diagnosis allows for the early diagnosis and implementation of appropriate treatment. Full article

Magnesium (Mg) alloys, particularly Mg AZ31, have emerged as promising biomaterials for orthopedic applications due to their biodegradability and favorable mechanical characteristics. Among these, the Mg AZ31+SPF alloy, subjected to hydrothermal (HT) treatment, has demonstrated enhanced bioactivity. Our previous research established that this surface modification supports the osteogenic differentiation of human mesenchymal stem cells (hMSCs) by modulating both canonical and non-canonical signaling pathways, including those implicated in osteogenesis, hypoxic response, exosome biogenesis, and lipid metabolism. In the present study, we extended our investigation to assess the effects of Mg AZ31+SPF+HT and Mg AZ31+SPF extracts on murine pre-osteoclasts (RAW 264.7 cells) over 3- and 6-day treatment periods. The primary objectives were to evaluate biocompatibility and to investigate potential impacts on osteoclastogenesis induction and miRNA expression profiles. Methods: To assess cytocompatibility, metabolic activity, DNA integrity, and morphological alterations in RAW 264.7 cells were evaluated. Osteoclast differentiation was quantified using TRAP staining, alongside the assessment of osteoclastogenic marker expression by qRT-PCR and ELISA. The immunomodulatory properties of the extracts were examined using multiplex BioPlex assays to quantify soluble factors involved in bone healing. Additionally, global miRNA expression profiling was performed using a specialized panel targeting 82 microRNAs implicated in bone remodeling and inflammatory signaling. Results: Mg AZ31+SPF+HT extract exhibited high biocompatibility, with no observable adverse effects on cell viability. Notably, a significant reduction in the number of TRAP-positive and multinucleated cells was observed relative to the Mg AZ31+SPF group. This effect was corroborated by the downregulation of osteoclast-specific gene expression and decreased MMP9 protein levels. Cytokine profiling indicated that Mg AZ31+SPF+HT extract promoted an earlier release of key cytokines involved in maintaining the balance between bone formation and resorption, suggesting a beneficial role in bone healing. Furthermore, miRNA profiling revealed a distinct regulatory signature in Mg AZ31+SPF+HT-treated cells, with differentially expressed miRNAs associated with inflammation, osteoclast differentiation, apoptosis, bone resorption, hypoxic response, and metabolic processes compared to Mg AZ31+SPF-treated cells. Conclusions: Collectively, these findings indicate that hydrothermal treatment of Mg AZ31+SPF (resulting in Mg AZ31+SPF+HT) attenuates pre-osteoclast activation by influencing cellular morphology, gene and protein expression, as well as post-transcriptional regulation via modulation of miRNAs. The preliminary identification of miRNAs and the activation of their regulatory networks in pre-osteoclasts exposed to hydrothermally treated Mg alloy are described herein. In the context of orthopedic surgery—where balanced bone remodeling is imperative—our results emphasize the dual significance of promoting bone formation while modulating bone resorption to achieve optimal implant integration and ensure long-term bone health. Full article

Athletic performance is modulated by a complex interaction of physiological, environmental, and genetic factors, with regular exercise triggering molecular changes that influence gene expression and tissue adaptation. Despite growing knowledge, the underlying molecular mechanisms remain only partially understood, highlighting the need for precise biomarkers to monitor training-induced physiological adaptations. Long non-coding RNAs (lncRNAs) regulate cellular processes, including adaptation to physical exercise. Twelve healthy elite female volleyball players (mean age 27 ± 5.4 years) participated in the study. This study evaluated the expression of selected lncRNAs (SNHG4, SNHG5, PACERR, NEAT1, HIX003209, and HOTTIP) during a 10-week training program and evaluated their potential as biomarkers of training adaptation. Blood samples were collected before and after the training period. LncRNA expression was measured by quantitative polymerase chain reaction. HOTTIP exhibited an increase in expression after training (over sixfold change, p = 0.009, adjusted p = 0.024) and demonstrated high diagnostic accuracy (AUC = 0.917), which improved to 0.97 when combined with creatine kinase. Other lncRNAs showed no significant changes, although a correlation between HOTTIP and SNHG4 was noted. HOTTIP is markedly upregulated following chronic exercise and, especially when combined with creatine kinase, shows promise as a molecular biomarker for monitoring training adaptation in elite female volleyball players. Full article

The transition period in dairy cows, spanning late pregnancy and early lactation, is associated with substantial metabolic and immunological challenges, leading to increased oxidative stress and inflammation. Selenium (Se), particularly in organic forms, supports antioxidant defenses, immune function, and metabolic regulation. This study investigated the effects of supplementing periparturient Holstein–Friesian cows with orally administered selenitetriglycerides (0.5 mg Se/kg body weight/day starting 12 days before the expected calving date and continuing until parturition) on antioxidant enzyme activity and on the hepatic expression of key inflammatory and metabolic genes. Serum selenium concentrations and erythrocyte glutathione peroxidase (GSH-Px) activity were assessed before and after parturition, and hepatic gene expression levels of tumor necrosis factor alpha (TNF-α), peroxisome proliferator-activated receptor alpha (PPAR-α) and delta (PPAR-δ) were assessed 24 h and 7 days postpartum. Supplemented cows showed significantly elevated serum Se levels and increased GSH-Px activity, reflecting improved antioxidant capacity. Moreover, hepatic expression of TNF-α and PPAR-δ was significantly reduced postpartum in the supplemented group, whereas PPAR-α expression remained stable. These findings indicate that selenitetriglycerides effectively enhance antioxidant defenses, moderate inflammation, and stabilize metabolic pathways during the periparturient phase, potentially reducing postpartum metabolic disorders and improving dairy-cow health. Full article

Background/Objectives: We analyzed clinical and radiological characteristics and prognostic factors specific to young patients with breast cancer (YBC) aged <30 years. Methods: This retrospective study included 132 women aged <30 years who underwent breast surgery between 2008 and 2013. The clinical and radiological findings of the patients were examined and compared according to recurrence or death status at follow-up. Disease-free survival (DFS) and overall survival (OS) rates were also assessed. Results: Most patients (mean age, 27.1 years) presented with palpable lesions (85.6%). Hormone receptor-positive/human epidermal growth factor receptor-negative cancer was the most common molecular subtype (59.8%), followed by triple-negative breast cancer (28.0%), with high Ki-67 expression (62.1%). Mammography and ultrasound detected abnormalities in 90.1% and 97.3% of patients, respectively, whereas magnetic resonance imaging detected abnormalities in all patients. During the follow-up period (8–10 years), 28.5% of the patients experienced recurrence and 11.5% died. The calculated DFS and OS at 5 years were 80.8% and 69.8% and 91.3% and 87.8% at 10 years, respectively. Statistically significant factors associated with DFS/OS included the BRCA1 gene mutation, with preoperative neoadjuvant chemotherapy, no hormone therapy, larger tumor size, negative hormone receptor status, high Ki-67 expression, and some radiological findings, including asymmetry with calcifications on mammography, no sonographic echogenic rind of mass, and mild vascularity on Doppler study. Conclusions: Our study highlights the aggressive nature of breast cancer in YBC aged <30 years, with relatively high rates of recurrence and mortality. Significant factors affecting prognosis may guide personalized treatment approaches and predict the prognosis. Full article

The emergence of multidrug-resistant Salmonella poses a significant threat to global public health and food safety, necessitating the urgent search for new strategies to replace conventional antibiotics. Phages are viruses that can directly target bacteria and have garnered attention in recent years for their development as antibiotic alternatives. In this study, 4458 samples were collected from farms, supermarkets, and human feces, yielding 65 strains of Salmonella, which were serotyped using multiplex PCR. Subsequently, a lytic phage was isolated and identified using the dominant serotype of Salmonella as the host bacterium. We further explored the biological characteristics of this phage through host range, growth properties, and genomic analysis. Finally, we analyzed the potential of the phage to block the cross-host transmission of Salmonella, combining PFGE Salmonella classification, strain sources, and phage lytic phenotypes. The results showed that phage gmqsjt-1 could lyse 69.23% (45/65) of Salmonella, of which 75.56% (34/45) were resistant strains. The optimal multiplicity of infection (MOI) for gmqsjt-1 was 0.01, with a latent period of about 10 min, maintaining high activity within the temperature range of 30 to 60 °C and pH range of 2 to 13. No virulence or resistance genes were detected in the gmqsjt-1 genome, which carries two tail spike proteins (contain FAD binding_2 superfamily, the Tail spike TSP1/Gp66 N-terminal domain, and the Pectin lyase fold) and a holin–lysozyme–spanin lytic system. Phylogenetic classification indicates that phage gmqsjt-1 belongs to a new genus and species of an unnamed family within the class Caudoviricetes. PFGE classification results show a high genetic relationship among human, farm animal, and food source Salmonella, and the comprehensive lytic phenotype reveals that phage gmqsjt-1 can lyse Salmonella with high genetic correlation. These results suggest that this novel lytic Salmonella phage has the potential to inhibit cross-host transmission of Salmonella, making it a promising candidate for developing alternative agents to control Salmonella contamination sources (farms), thereby reducing the risk of human infection with Salmonella through ensuring food system safety. Full article

As the laying cycle is prolonged, the egg albumen quality exhibits a declining trend. A Haugh unit (HU) is a standard measure of the albumen quality, which reflects viscosity and freshness. During the late laying period, the HU not only decreased significantly, but also exhibited greater variability among individuals. The magnum, as the primary site of albumen synthesis, plays a central role in this process; however, the mechanisms by which it regulates the albumen quality remain unclear. To address this, we obtained genomic and transcriptomic data from 254 individuals, along with single-cell RNA sequencing (scRNA-seq) data of the magnum tissue. Genome-wide association studies (GWAS) across five laying stages (66, 72, 80, 90, and 100 weeks of age) identified 77 HU-associated single-nucleotide polymorphisms (SNPs). Expression quantitative trait locus (eQTL) mapping linked these variants to the expression of 12 genes in magnum tissue. In addition, transcriptomic analysis using linear regression and random forest models identified 259 genes that significantly correlated with the HU. Single-cell RNA sequencing further revealed two key cell types, plasma cells and a subset of epithelial cells, marked by ADAMTSL1 and OVAL, which are functionally relevant to the HU. Through integrated Transcriptome-Wide Association Study (TWAS) and Summary-data-based Mendelian Randomization (SMR) analyses, we identified four robust regulators of the albumen quality: CISD1, NQO2, SLC22A23, and CMTM6. These genes are functionally involved in mitochondrial function, antioxidant defense, and membrane transport. Overall, our findings uncovered the genetic and cellular mechanisms underlying age-related decline in the albumen quality and identified potential targets for improving the egg quality in aging flocks. Full article

Studying comprehensive performance is fundamental for the effective utilisation of broomcorn millet (Panicum miliaceum L.) germplasm resources and breeding of new varieties. However, compared with other major crops, research on broomcorn millet germplasm resources is limited, and the trait variations of broomcorn millet are unclear. In this study, three qualitative and seven quantitative traits of 933 broomcorn millet core collections were analysed to provide the basis for improving utilisation of broomcorn millet germplasm resources. The seed colour was a strong phenotypic trait and had eight variants. The 933 resources exhibited three panicle types: lateral (74.5%), scattered (18.4%), and compact (7.1%). They exhibited two inflorescence colours: green (54.7%) and purple (45.3%). Pearson’s correlation analysis revealed that 1000-seed weight significantly correlated with plant height, length of panicle, and number of main stem segments. The period of duration positively correlated with 1000-seed weight but negatively correlated with the number of uniserial panicles. Cluster analysis based on the quantitative traits indicated that all resources were divided into three groups, and each group had its respective characteristics. The analysis of core germplasm resources of broomcorn millet in this study provided a basis to explore excellent genes and for breeding of excellent varieties. Full article

Groundwater, a critical source of drinking water, plays an essential role in global biogeochemical cycles, yet its microbial ecosystems remain insufficiently characterized, particularly in pristine karst aquifers. This study conducted high-resolution profiling of microbial communities and environmental parameters in two representative alpine karst aquifers in Slovenia: Idrijska Bela and Krajcarca. Monthly groundwater samples from the Krajcarca spring and Idrijska Bela borehole over a 14-month period were analyzed using whole-metagenome sequencing (WMS), UV-Vis spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), and isotopic analysis. The results revealed stable hydrochemical conditions with clear spatial differences driven by bedrock composition and groundwater residence time. Bacterial communities displayed strong correlations with hydrochemical parameters, while archaeal communities exhibited temporal stability. Functional gene profiles mirrored bacterial patterns, emphasizing the influence of environmental gradients on metabolic potential. No significant temporal changes were detected across two sampling campaigns (2016–2023), highlighting the resilience of these aquifers. This work establishes a valuable baseline for understanding pristine groundwater microbiomes and informs future monitoring and water quality management strategies. Full article

Background/Objectives: RAB11 (RABA) is a type of RAB GTPase. RAB GTPases are key components of membrane trafficking mechanisms, Rab11 is implicated in a variety of biological developmental processes and responses to biotic and abiotic stresses. Nevertheless, the role of Rab11 in the defense mechanisms of cotton against Verticillium dahliae (V. dahliae) remains to be elucidated. Methods: In the present study, by analyzing the transcriptome data of Gossypium hirsutum (G. hirsutum) infected with V. dahliae, in combination with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, the research focused on endocytosis. Further, through bioinformatics approaches, the endocytosis-related gene Rab11 was identified. We conducted a genome-wide identification and analysis of Rab11 in G. hirsutum. In addition, by integrating transcription factor (TF) prediction, prediction of protein–protein interactions (PPI) and quantitative real-time polymerase chain reaction (qRT-PCR), the gene expression of Rab11 at different infection periods of V. dahliae (0, 24 and 72 hpi) were analyzed and validated. Results: The analysis of transcriptome data revealed that the endocytosis pathway is implicated in the stress response of cotton to V. dahliae. Additionally, three Rab11 genes were identified as being involved in this stress response. Phylogenetic analysis revealed that the 65 genes in the Rab11 family could be divided into four subgroups, each with similar gene structures and conserved motif patterns. Conclusions: The downregulation of Rab11 in G. hirsutum is closely linked to its defense against V. dahliae. TF prediction coupled with PPI offers a roadmap for dissecting the signaling pathways, functional validation, and network construction of the three GhRab11 genes. Full article

Body weight (BW) is a critical economic trait closely linked to livestock meat production performance and producer profitability. In the present study, we measured individual BW of 1070 male Hu sheep at six growth stages (80, 100, 120, 140, 160, and 180 days of age) and conducted descriptive statistical analyses. Results showed that the coefficient of variation (CV) for BW at each stage was higher than 13%. Additionally, we investigated the expression patterns of the FGF9 gene and its associations with single nucleotide polymorphisms (SNPs) and BW. Quantitative real-time PCR (qRT-PCR) revealed FGF9 is significantly higher expressed in the hypophysis tissues that in the other tested tissues. Association analyses indicated that the SNP FGF9:c.382-1264C>T was significantly associated with BW across different measurement periods. Finally, we performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and cleavage under targets and tagmentation (CUT&Tag) techniques to identify the OCRs (open chromatin regions) and regulatory regions in the hypophysis tissues of Hu sheep, and we obtained an average of 221243, 52692, and 20957.5 peaks in the ATAC-seq, H3K27ac, and H3K4me3 data per sample. Simultaneously, by integrating the SNPs of FGF9 and hypophysis tissue’s epigenomic data, we found that the SNP FGF9:c.382-1264C>T was located in the adjacent OCR- and H3K27ac-modified peaks. Therefore, we propose that the SNP FGF9:c.382-1264C>T plays an important role in regulating body weight in sheep. Overall, this study generated a valuable epigenetic dataset (ATAC-seq, H3K27ac, and H3K4me3) in sheep hypophysis tissue and identified a novel functional regulatory variant for improving body weight in sheep. Full article

Drought stress significantly affects the yield and quality of agricultural crops. Plants have developed various adaptations to cope with drought stress. These adaptations involve the regulation of physiological and biochemical mechanisms regulated by many genes. Therefore, identification of cultivars with strong responses to drought stress will provide important contributions to breeding programs. In this study, Hayward and Matua kiwifruit cultivars were used and the plants were subjected to drought in vitro in nutrient media containing PEG 6000 (Polyethyleneglycol) at concentrations of 0, 1, 2, and 3%. The morphological parameters of the plants were examined during the culture period and WRKY TF was utilized to determine the molecular regulations induced by drought stress in plants. For this purpose, the expression levels of WRKY3, WRKY9, WRKY21, WRKY28, WRKY41, WRKY47, WRKY65 and WRKY71 genes were analyzed in leaf and root tissues of the cultivars. The findings showed that the plants in the 2% and 3% PEG media were significantly affected by drought stress, with a notably low root formation performance. The gene expression analysis revealed that the expression levels of genes in the leaf and root tissues of plants under drought conditions were higher compared to the control group. The data obtained from the analyses indicated that the Hayward and Matua cultivars exhibited strong responses to drought both morphologically and genetically. Full article

Antibiotic resistance (AR) in environmental Escherichia coli represents a growing public health challenge. This study evaluated the prevalence of AR among E. coli isolates recovered from surface water bodies within the Ameca River basin in Jalisco, Mexico, and examined associations with anthropogenic influence and seasonal variation. Over a 1-year period, water samples were collected monthly from 16 sites, including tributaries, wetlands, and main river channels with differing degrees of urban impact. E. coli isolates were confirmed by malB gene PCR and tested for susceptibility to six antibiotics using the Kirby–Bauer disk diffusion method. High resistance frequencies were observed for ampicillin (93.9%), tetracycline (92.4%), and streptomycin (89.6%), while gentamicin exhibited the lowest resistance rate (48.1%). Resistance prevalence was significantly higher at sites adjacent to urban settlements and during the rainy season (p < 0.05). These findings underscore the influence of land use and seasonal dynamics on AR dissemination in aquatic environments and highlight the need for improved wastewater management strategies to mitigate the spread of resistant bacteria. Full article