Search Results (565)

Rural black-odorous waterbodies (RBOWBs) represent a critical environmental challenge in China, yet the vertical stratification of sedimentary bacterial communities and its underlying drivers remain poorly understood. This study combined 16S rRNA gene amplicon sequencing across five sediment depths (0–125 cm) with shotgun metagenomic analysis of surface sediments to investigate bacterial diversity, composition, and functional potential in typical rural black-odorous systems of Dongming County, Shandong Province. Results showed a clear decline in bacterial richness with increasing sediment depth, with the surface layer (0–25 cm) exhibiting 1.2–1.9 times higher diversity than deeper strata. Community composition displayed distinct vertical zonation: Chloroflexi and Thiobacillus dominated surface layers and were linked to carbon hydrolysis and desulfurization, whereas Bacillus and nitrifying bacteria prevailed in deeper anoxic layers. Metagenomic analysis revealed high genetic potential for carbohydrate metabolism, amino acid biosynthesis, and sulfur-nitrogen cycling, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) being particularly abundant. Statistical correlations identified total phosphorus (TP₁), dissolved oxygen (DO), and pH of the overlying water—rather than sediment intrinsic nutrients—as the primary environmental factors associated with microbial functional stratification. These findings provide a mechanistic understanding of vertical microbial zonation in rural black-odorous sediment and offer a microbiological basis for developing depth-resolved sustainable remediation strategies. Full article

Cyanobacteria of the genus Tychonema are common inhabitants of freshwater bodies in a temperate zones. In Lake Baikal, Tychonema sp. was first reported in 2014. It grows excessively on the bottom on almost all substrates types, forming epiphytic and epizoic biofilms, and its role in the mass mortality events affecting of endemic Baikal sponges is discussed. The cyanobacterial strain BBK16 (=IPPAS B-2063^T), isolated from a biofilm on a log pier in the Bolshiye Koty settlement in 2016, was used for further taxonomic characterization. Key morphological features of strain BBK16 include its growth as a creeping mat, highly motile trichomes that are sometimes narrowed and hooked at the ends, and the presence of rounded-conical apical cells with a calyptra. Strain ultrastructure (fascicular parietal thylakoids and type D cell division) differs from Tychonema species with radial thylakoids but aligns with other genera in the Microcoleaceae family. A comprehensive analysis, including 16S rRNA gene phylogeny, conserved protein phylogeny, and whole-genome comparisons, confirmed its placement within the genus Tychonema. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain BBK16 and T. bourrellyi FEM GT703 were 90.7%, 91.1% and 43.3%, respectively, indicating values below the standard thresholds for species delineation. Based on combined morphological, genomic, and ecological evidence, we propose the name Tychonema litorale sp. nov. for strain BBK16, a novel species described in accordance with the International Code of Nomenclature for Algae, Fungi, and Plants. Full article

Background: Tic spectrum disorder (TSD), encompassing Tourette syndrome and chronic tic disorder, is a childhood-onset neurodevelopmental condition with complex genetic and environmental contributions. Heritable components have been implicated in TSD, but no clear genetic mechanisms have been identified. Significant aspects of TSD etiology remain unclear, with key uncertainties concerning the role of environmental influences in its development. In this study, we aimed to identify environmentally induced epigenomic and transcriptomic changes contributing to TSD pathology by investigating genetically similar monozygotic twins discordant for TSD. Methods: To investigate environmentally driven mechanisms, we analyzed peripheral blood from eleven monozygotic twin pairs, either discordant or concordant for TSD, using RNA sequencing and DNA methylation analysis. Results: Differential expression analysis identified a dozen differentially expressed genes between TSD and non-TSD individuals, most of which were long non-coding RNAs or pseudogenes. Expression of the small RNA gene RNY1 was significantly associated with tic severity, suggesting involvement of immune-related processes. DNA methylation (DNAm) analysis revealed ~30,000 probes with a nominal p < 0.05, however none of these were significant after multiple testing correction. Expression quantitative trait methylation (eQTM) analysis identified 236 methylation-associated genes. Gene set enrichment analysis demonstrated broad downregulation in TSD individuals for pathways related to translation, RNA processing, and neurobiological functions, with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including ribosome, nucleocytoplasmic transport, pluripotency signaling, and nicotine addiction. Conclusions: These results suggest that environmentally influenced gene expression may contribute to TSD pathogenesis through dysregulation of immune and neuronal pathways. Despite a small sample size, the monozygotic twin design provides strong control for genetic background and identifies significant differences that contribute to the understanding of the underlying molecular mechanisms of TSD. Full article

The Na⁺/K⁺-ATPase (NKA) gene encodes a critical membrane transporter that maintains cellular ion homeostasis and plays a pivotal role in osmoregulation and salinity adaptation of aquatic organisms. In this study, we identified and validated SNP markers in the NKA gene associated with low-salinity tolerance in Scylla paramamosain. Four candidate SNPs (g.72037G>T, g.72122G>C, g.74293G>T, and g.74433G>T) were screened and genotyped in low-salinity tolerant and intolerant groups. Association analysis revealed that mutant genotypes at all four loci were significantly enriched in the tolerant group (p < 0.05), with odds ratios (OR) > 1. The tolerant group exhibited higher genetic diversity parameters than the intolerant group. Haplotype analysis showed the GGGG haplotype was dominant in the intolerant group, whereas the other haplotypes were mainly enriched in the tolerant group. The NKA expression in the mutant genotypes was significantly higher than that in the wild genotypes by qRT-PCR. For tolerant individuals, the fast-growing group exhibited higher mutation frequencies than the slow-growing group. Multi-locus analysis achieved substantially more discrimination accuracy than single-locus analysis. These findings demonstrated that these SNPs could be candidate molecular markers for breeding programs in S. paramamosain in low-salinity environments, helping to identify individuals with enhanced salinity tolerance and supporting sustainable aquaculture practices. Full article

The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities’ structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously “Proteobacteria”) (68–72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes. Full article

Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by inflammation and damage to salivary and lacrimal glands. Its etiology involves both genetic and environmental factors. Among susceptibility genes, IRF5 has been highlighted in European populations, but evidence in non-European groups remains limited. This study evaluated whether IRF5 variants rs2004640G/T, rs2070197T/C, rs10954213G/A, and rs59110799G/T are associated with pSS susceptibility, clinical manifestations, or the presence of autoantibodies in a Mexican population. The diagnosis was confirmed by rheumatologists using the 2016 ACR–EULAR classification criteria for pSS. Genotyping was performed using TaqMan probes in 231 controls and 132 pSS patients from central Mexico. Associations were analyzed through binary logistic regression under different genetic models, adjusting for age and geographic origin. Clinical correlations were examined with SNPStats, and haplotypes were constructed using Haploview. Results showed that all four IRF5 variants were significantly associated with pSS susceptibility. Moreover, rs2004640, rs2070197, and rs10954213 variants were associated with arthritis, a frequent clinical manifestation in pSS patients. This represents the first evidence in a Latin American population demonstrating that IRF5 variants contribute to increased risk of developing pSS. These findings suggest ethnicity-specific genetic influences and highlight the importance of expanding research beyond European cohorts. Replication in larger samples and functional analyses are needed to confirm these associations and clarify their biological relevance. Full article

The Chinese plum (Prunus salicina L.), ‘Zuili’, is a geographically protected cultivar that is valued for its high polyphenol levels and distinctive flavor. Light availability strongly influences sugar accumulation and secondary metabolism in plum fruit, yet the molecular processes associated with quality variation under protected cultivation remain unclear. Here, we compare three cultivation systems—multi-span greenhouse (M), retractable electric rain shelter (R), and conventional open field (CK)—to evaluate their effect on fruit quality using integrated transcriptomic and metabolomic analyses. Field trials showed that M treatment increased fruit sweetness by 28.10% versus CK (14.68 vs. 11.46 °Brix, p < 0.001) without yield loss and significantly improved vertical fruit diameter. RNA-seq analysis identified 7561 and 7962 upregulated genes in the M and R treatments compared to CK, respectively, with significant functional enrichment in pathways related to sucrose metabolism, light-response, and ethylene-mediated signaling. Untargeted metabolomic signaling identified 1373 metabolites, with shading treatments increasing the abundance of several sugar-conjugated compounds (e.g., epicatechin 3-O-(2-trans-cinnamoyl)-β-D-allopyranoside). Multi-omics integration revealed coordinated changes in gene expression and metabolite abundance, suggesting that controlled light environments are associated with the concurrent modulation of sugar metabolism and phenylpropanoid-related pathways. These patterns were supported by the upregulation of GT2-family glycosyltransferase genes and the accumulation of lignin-related flavonoid precursors, such as pinobanksin and pinobanksinol. Collectively, these results highlight statistically robust associations between light-regulated cultivation practices and fruit quality traits, providing a molecular framework for optimizing protected cultivation strategies to enhance both the sensory and nutritional attributes of P. salicina fruit without compromising yield. Full article

Objective: Growth traits are important economic characteristics in livestock. Genetic polymorphism has great influences on the improvement of goat growth traits. As an important member of the myogenic regulatory factor (MRFs) family, MyoG gene polymorphisms can alter the growth characteristics in goats. In this study, we aimed to investigate the regulation mechanism of the MyoG gene promoter region from the perspective of single nucleotide polymorphisms (SNPs) and transcription factors. Methods: Genomic DNA sequencing was carried out to detect SNPs in the −1000 bp upstream to 300 bp downstream of the MyoG gene promoter region in 224 Guizhou White goats (Capra hircus), and the genetic parameters of novel SNPs were calculated. The association between SNPs and growth traits, comprising body weight, body length, body height, chest circumference and cannon circumference, were analyzed using one-way ANOVA by IBM SPSS 23.0 software according to the general linear model. Transcription factor binding sites in the promoter region of the MyoG gene before and after mutation were predicted using bioinformatics software programs. Results: Four SNPs, including g.–709C>T, g.–461G>T, g.–377G>T and g.–249G>A, were identified in the 1 246 bp promoter region of the MyoG gene in Guizhou White goats. Based on χ² test, the g.–709C>T and g.–461G>T loci were consistent with Hardy–Weinberg equilibrium, while two other SNPs were deviated from Hardy–Weinberg equilibrium in Guizhou White goats. Association analysis revealed that the body weight of those with the CT genotype at the g.–709C>T locus was greater than of those with the CC and TT genotypes in Guizhou White goats (p < 0.05). At the g.–461G>T locus, the body weight of individuals with the GG genotype was significantly higher than that of those with GT genotype (p < 0.01). The body length of individuals with the GG genotype formed by the g.–249G>A locus was significantly higher than that of those with the GA genotype (p < 0.01). Online software programs found that four SNPs within the promoter region of the MyoG gene changed some transcription factor binding sites. Conclusions: Mutations of the MyoG gene promoter region may have a significant regulatory effect on the growth traits of Guizhou White goats. The small sample size may be one of the limitations for this study; nevertheless, these findings could provide a theoretical basis for further exploring the relationship between the four SNPs studied and the growth traits in Guizhou White goats, as well as the promoter function of the MyoG gene. Full article

Background/Objectives: Atrial fibrillation (AF), characteristic of chaotic atrial electrical activity along with ineffective atrial systole, remains the most frequent sustained cardiac dysrhythmia, with an overall lifetime risk for AF being approximately 15% to 40% in the global population. AF is associated with substantially enhanced risks for multiple adverse clinical outcomes, including thromboembolic cerebral stroke, dementia, chronic kidney disease, myocardial infarction, cardiac failure, and even premature cardiac demise. Although remarkable advances have been achieved toward unravelling the complex hereditary etiopathogenesis underpinning AF, it has become increasingly clear that inherited determinants predisposing to AF in a vast majority of individuals are still uncertain. Methods: A Chinese pedigree with idiopathic AF and another group of 236 cases suffering idiopathic AF along with 312 unrelated healthy volunteers were prospectively recruited. Exome-wide sequencing and Sanger sequencing assays were implemented in research participants. The functional effects of the discovered variations in the SOX5 gene were explored through dual-luciferase reporter analysis. Results: Two novel SOX5 mutants, NM_006940.6: c.355C>T; p.(Gln119*) and NM_006940.6: c.640G>T; p.(Glu214*), were identified in the AF pedigree and one of the 236 unrelated patients affected with AF, respectively. These two heterozygous truncating SOX5 variations were absent from the 624 control chromosomes. Quantitative luciferase reporter assays unraveled that both Gln119*- and Glu214*-mutant SOX5 lost the ability to transactivate GJA1. Additionally, the two variations abolished the synergistic transactivation of SCN5A by SOX5 and SHOX2. Conclusions: The current findings indicate SOX5 as a novel gene contributing to AF, which adds more insight to the molecular pathogenesis of AF, and provides a potential target for personalized precision medicine. Full article

Hereditary Hemorrhagic Telangiectasia (HHT), also known as Rendu–Osler–Weber syndrome, is a disorder of angiogenesis characterized by mucocutaneous telangiectasias and visceral arteriovenous malformations. This rare autosomal dominant disorder is caused by pathogenic variants in the ENG and ACVRL1 genes, and only 1–3% of case variants occur in SMAD4. HHT clinical manifestations include telangiectasias, epistaxis, and arteriovenous malformations in multiple organ systems. Clinical diagnosis is based on Curaçao Criteria. Here, we describe a pauci-symptomatic 10-year-old girl with an orbital and sinus infectious disease. Her clinical history was unremarkable, except for sporadic, self-limiting epistaxis episodes. She showed finger clubbing and low oxygen saturation levels on pulse oximetry, suggesting a chronic lung disease, and a large lung arteriovenous malformation. She also developed acute neurological symptoms, with evidence of multiple cerebral abscess lesions on MRI. HHT was therefore suspected and confirmed by genetic analysis, which revealed a de novo pathogenic variant in the ENG gene [c.1183G>T p.(Glu395Ter)] found in only 15% of the reads from NGS analysis, performed on peripheral blood lymphocytes, indicating a possible mutational mosaicism. This case outlines that HHT could present with unusual clinical symptoms highlighting the importance of diagnosis using both clinical criteria and genetic test. Full article

Background: Anthocyanins and proanthocyanidins (PAs), as flavonoid compounds with potent antioxidant activity, exhibit significant health-promoting and medicinal properties. Black wolfberry (Lycium ruthenicum Murr.) is renowned for its exceptional anthocyanin content; however, the regulatory mechanisms of anthocyanin biosynthesis remain poorly understood, limiting its biotechnological potential. This study aimed to elucidate the transcriptional regulatory function of LrMYB30 in anthocyanin biosynthesis in black wolfberry. Methods: The regulatory function of LrMYB30 was investigated using virus-induced gene silencing (VIGS), yeast one-hybrid assays, and dual-luciferase reporter assays in black wolfberry. Results: VIGS demonstrated that silencing LrMYB30 promoted anthocyanin accumulation while reducing PA content, establishing that the LrMYB30 transcription factor as a negative regulator of anthocyanin synthesis. Yeast one-hybrid and dual-luciferase reporter assays confirmed that LrMYB30 directly binds to and activates the promoter of LrANR, a key structural gene in PA biosynthesis. In contrast, LrMYB30 neither binds to nor suppresses the promoters of the critical anthocyanin biosynthesis genes LrUF3GT and LrDFR. Conclusions: Thus, LrMYB30 redirects the flavonoid metabolic flux from anthocyanin to PA synthesis through transcriptional activation of LrANR during later fruit development, reducing anthocyanin accumulation and delaying coloration. These findings reveal a novel regulatory mechanism in black wolfberry pigmentation and maturation, providing genetic targets for molecular breeding of high-anthocyanin cultivars. Full article

Background: Immune-regulatory genes such as CTLA-4, FOXO-3, and PTPN-22 influence immune tolerance and metabolic adaptation, but their interaction with environmental factors in type 1 diabetes (T1DM) remains unclear. Methods: In this observational associated study, we analyzed CTLA-4 (rs3087243, rs231775), FOXO-3 (rs2802292, rs9400239), and PTPN-22 (rs12730735) polymorphisms in 277 adults with T1DM, assessing associations with probiotic and vitamin D use, self-reported dietary patterns, metabolic control, autoimmune thyroid disease (AITD), and metabolic dysfunction-associated steatotic liver disease (MASLD). Results: Across the cohort, CTLA-4 rs3087243 G and FOXO-3 rs2802292 T alleles were associated with higher AITD risk (p = 0.016–0.03), significant in both dominant and additive models. The effect persisted by sex: CTLA-4 in women and FOXO-3 in men. Stratified analyses revealed metabolic advantages for CTLA-4 G and FOXO-3 T carriers (vegetarian diet, lower HbA1c, stress adaptation). FOXO-3 rs9400239 T was linked to MASLD (p ≈ 0.037–0.041), with similar trends for CTLA-4 rs231775, stronger in men. Vitamin D supplementation showed protective trends, particularly in FOXO-3 rs2802292 GG and CTLA-4 GG/AG carriers. Conversely, probiotic use was associated with higher AITD in FOXO-3 rs2802292 GT and CTLA-4 rs3087243 GG genotypes. Conclusions: CTLA-4, FOXO-3, and PTPN-22 variants may modulate the metabolic and autoimmune response to environmental factors including nutrients in T1DM. Full article

The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus. Full article

C2H2-type zinc-finger transcription factors (ZFPs) play essential roles in plant stress signaling and development; however, their putative functions in safflower have not been systematically characterized. Leveraging the reference genome of the safflower cultivar ‘Jihong-1’ (Carthamus tinctorius L.), we investigated the C2H2 family and identified 62 CtC2H2 genes. Comparative phylogeny with Arabidopsis revealed six subfamilies characterized by shared features such as exon–intron organization and conserved QALGGH motif. Promoter analysis identified multiple light- and hormone-responsive cis-elements (e.g., G-box, Box 4, GT1-motif, ABRE, CGTCA/TGACG), suggesting potential multi-layered regulation. RNA-seq and qRT-PCR analysis identified tissue-specific candidate genes, with CtC2H2-22 emerging as the most petal-specific (6-fold upregulation), alongside CtC2H2-02, CtC2H2-23, and CtC2H2-24 in seeds (~3-fold), and CtC2H2-21 in roots (3-fold). Under abiotic stresses, CtC2H2 genes also demonstrated rapid and dynamic responses. Under cold stress, CtC2H2 genes showed a rapid temporal pattern of expression, with early increase for genes like CtC2H2-45 (>4-fold at 3–6 h) and a delayed increase for CtC2H2-23 at 9 h. A majority of CtC2H2 genes (8/12) were upregulated by ABA treatment, with CtC2H2-47 suggesting 3.5-fold induction. ABA treatment also led to a significant increase (2.5-fold) in total leaf flavonoid content at 24h, which is associated with the significant upregulation of flavonoid pathway genes CtANS (5-fold) and CtCHS (3.3-fold). Simultaneously, UV-B radiation induced two distinct expression patterns: a significant suppression of four genes (CtC2H2-23 decreased to 30% of control) and a complex fluctuating pattern, with CtC2H2-02 upregulated at 48 h (2.8-fold). MeJA elicitation revealed four complex expression profiles, from transient induction (CtC2H2-02, 2.5-fold at 3 h) to multi-phasic oscillations, demonstrating the functional diversity of CtC2H2-ZFPs in jasmonate signaling. Together, these results suggest stress and hormone-responsive expression modules of C2H2 ZFPs for future functional studies aimed at improving stress adaptation and modulating specialized metabolism in safflower. Full article

Recurrent pregnancy loss (RPL), also termed recurrent spontaneous abortion, is defined as the failure of ≥2 consecutive pregnancies before 20 weeks of gestation. Approximately 5% of pregnant couples experience RPL. The hyaluronan-binding protein 2 (HABP2) gene is involved in coagulation and plays an important role during pregnancy. In >50% of RPLs, the etiology remains unexplained. We collected 765 blood samples from 388 female RPL patients and 377 healthy female controls. To investigate the relationships between HABP2 polymorphisms and RPL, we examined six HABP2 variants (rs3832698 A>del, rs10885478 G>A, rs932650 T>C, rs7923349 G>T, rs1157916 G>A, and rs2240879 T>C) to clarify their association with RPL risk. The rs2240879 CC genotype was significantly associated with an increased RPL risk (p = 0.028). In haplotype analysis, the combination of rs3832698 del and rs2240879 T (del-T) was associated with elevated risk (p = 0.043); this risk persisted in combinations with additional polymorphisms (rs3832698 A>del, rs10885478 G>A, rs932650 T>C, rs7923349 G>T; del-A-T-T, p < 0.001; rs3832698 A>del, rs10885478 G>A, rs932650 T>C, rs7923349 G>T, rs1157916 G>A, rs2240879 T>C; del-A-C-T-G-T, p = 0.024). The rs3832698 and rs1157916 genotypes were significantly associated with prothrombin time (p = 0.020 and p = 0.012, respectively). We identified associations between HABP2 polymorphisms and RPL; rs2240879 was linked to an increased RPL risk. Additionally, rs3832698 was associated with an altered prothrombin time. These findings suggest that HABP2 represents a biomarker for RPL susceptibility. Full article