Search Results (4,872)

In this study, Chinese medicinal herbs were evaluated as potential antibiotic substitutes for Chinese soft-shelled turtle (Pelodiscus sinensis). Forty-five herbs were initially screened for antibacterial activity against Salmonella enteritidis, Escherichia coli, and Shigella flexneri. Nine herbs exhibiting broad-spectrum inhibitory effects were selected and subjected to microbial fermentation, after which their antibacterial activities were reassessed and applied as dietary supplements in feeding trials. The results showed that fermentation altered the antibacterial activities of several herbs and enhanced their overall functional performance. Dietary supplementation with fermented Chinese herbal medicine did not adversely affect feed utilization but significantly improved hematological parameters, liver and kidney function indicators, antioxidant capacity, and nonspecific immune responses. Furthermore, turtles fed fermented herbal diets exhibited higher survival rates following bacterial challenge. Intestinal microbiota analysis based on 16S rRNA gene sequencing indicated that fermented herbal supplementation modulated microbial community structure by reducing potential pathogens and increasing beneficial bacterial taxa associated with intestinal health. These findings suggest that microbial fermentation effectively enhances the biological efficacy of Chinese medicinal herbs. Fermented herbal feed additives represent a promising green alternative to antibiotics for soft-shelled turtle aquaculture. The global ban on prophylactic antibiotics drives the need for safe, effective feed alternatives. Microbial fermentation of Chinese herbs (FCM) is proposed to enhance efficacy and detoxification, but its comprehensive effects in aquaculture require deeper investigation. This study evaluated compound unfermented (CM) and fermented (FCM) Chinese herbal supplements on the Chinese soft-shelled turtle (Pelodiscus sinensis). Initial screening showed fermentation generally enhanced the antibacterial activity of the herbs against common enteric pathogens (S. enteritidis, E. coli, S. flexneri). Results indicated that the FCM diet significantly improved physiological status, leading to higher red blood cell counts, better liver/kidney function (reduced ALT/AST, UREA), and stronger immune/antioxidant responses (increased Lysozyme and T-AOC) compared to CM or control diets. Critically, the FCM group achieved the highest survival rates across all single and combined pathogen challenges, demonstrating superior protective efficacy. Furthermore, FCM effectively modulated the gut microbiota, enriching beneficial fermentative bacteria. In conclusion, microbial fermentation significantly amplifies the health-promoting and protective benefits of Chinese herbal supplements in soft-shelled turtles, positioning FCM as a promising green alternative for disease control in aquaculture. Full article

Soybean (Glycine max) is a critically important crop for oil, protein, feed, and food security in China. Expanding soybean cultivation into high-latitude regions represents one of the most direct and effective strategies to increase total production. In the present study, we employed KASP (Kompetitive Allele-Specific PCR) marker technology to systematically analyze 18 variant loci across 14 flowering-time genes in 443 soybean germplasm accessions adapted to high-latitude conditions in Arctic Village (Beiji Cun), Mohe City (>53° N), northeastern China. Our results revealed clear functional-tier-dependent selection gradients: key mutation sites (frequency > 96%) in upstream photoreceptors and core circadian clock genes, such as E2 and GmPRR3a, were nearly fixed in the population, whereas downstream flowering genes such as GmFT5b and GmFT2b remained under dynamic selection. Combinatorial analysis of early-maturity allelic variants identified 178 distinct genotype combinations, including six dominant types (n ≥ 10). Field phenotypic analysis demonstrated that the cumulative number of early-maturity alleles was significantly negatively correlated with flowering time, with specific allele combinations such as FT5a^A + FKF1b-hap3^T exhibiting particularly strong flower-promoting effects. A set of 80 highly enriched super-early-maturity accessions, including extreme materials such as MHL22002, were identified, providing valuable genetic resources and a theoretical framework for elucidating the flowering regulatory mechanisms of high-latitude soybean and for breeding super-early-maturing varieties. Full article

Background: Retinal and optic nerve disorders are a leading cause of irreversible visual impairment worldwide. Advances in molecular genetics—including next-generation sequencing, genome-wide association studies, and gene-based therapeutic technologies—have reshaped understanding of both inherited and complex retinal diseases. However, translating genetic discovery into sustained clinical benefit remains biologically and practically constrained. Methods: A structured literature search was conducted using PubMed and Scopus to identify relevant studies published between 2015 and 2025. The search focused on molecular genetics, epigenetic modulation, mitochondrial biology, and translational applications in inherited retinal dystrophies and selected complex retinal diseases, prioritizing high-impact original research and systematic reviews addressing diagnostic innovation and therapeutic development. Results: Inherited retinal dystrophies represent the most advanced model of precision ophthalmology, with diagnostic yields approaching 70–80% in well-characterized cohorts. Gene augmentation and genome-editing strategies have demonstrated proof-of-concept efficacy, yet clinical benefit depends on residual cellular viability, delivery efficiency, and durability of expression. Emerging platforms include AAV-mediated gene transfer, in vivo CRISPR-based editing, RNA-directed splice modulation, and mitochondrial-targeted approaches. Persistent barriers include unresolved non-coding and structural variants, variant interpretation uncertainty, and endpoint selection in clinical trials. In contrast, complex retinal diseases such as glaucoma, age-related macular degeneration, and pathological myopia reflect polygenic susceptibility interacting with environmental and aging-related factors. Although polygenic risk scores refine probabilistic prediction, their utility is limited by ancestry bias and incomplete predictive performance. Epigenetic and mitochondrial mechanisms further modulate disease expression but remain largely non-actionable in routine practice. Conclusions: Retinal genetics has progressed from gene discovery to early therapeutic implementation. Future advances will depend on improved variant detection, functional validation, biomarker-guided staging, and integration of genomics with imaging and longitudinal modeling to achieve durable and equitable precision ophthalmology. Full article

As sessile organisms, plants must continuously perceive and integrate external environmental cues with internal developmental signals to optimize growth, reproduction, and survival. Central to this adaptive capacity is the ubiquitin-proteasome system (UPS), the primary pathway for selective protein degradation in eukaryotes. Within the UPS, BTB (Broad-Complex, Tramtrack, and Bric-à-brac) proteins serve as critical substrate adaptors for the Cullin3 (CUL3)-based E3 ubiquitin ligase complex. These proteins play indispensable roles in plant growth, development, hormone signaling, and responses to abiotic stresses. Recent advances have revealed the remarkable functional versatility of BTB proteins, implicating them in the regulation of photomorphogenesis, root architecture, flowering time, stress resilience, and yield-related traits. With 80 BTB-encoding genes in Arabidopsis thaliana and key orthologs identified in major crops—including of rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays)—BTB proteins act as molecular “bridges” that integrate developmental programs with environmental stress signals. This review summarizes the structural features, classification, and multifaceted functions of plant BTB proteins, with an emphasis on their roles in growth regulation, abiotic stress tolerance, light signaling, and agricultural productivity. We further discuss their mechanisms in ubiquitin-dependent proteolysis, transcriptional regulation, and signal integration, offering insights into their potential as targets for engineering climate-resilient crops and advancing sustainable agriculture. Full article

Acoustic divergence is widely recognized as a key driver of speciation and niche differentiation in vocal animals. In echolocating horseshoe bats (Rhinolophus), the larynx is specialized for producing high-duty-cycle signals used in foraging, navigation, and species recognition. While the ecological role of echolocation is established, the molecular mechanisms regulating laryngeal frequency remain unclear. We compared the laryngeal transcriptomes of three closely related, sympatric Rhinolophus species with distinct resting frequencies (RFs): R. episcopus (~46 kHz), R. siamensis (~66 kHz), and R. osgoodi (~85 kHz). This comparison identified 511 differentially expressed genes. High-frequency species upregulated genes involved in cytoskeletal dynamics and muscle contraction, such as cell adhesion molecules and motor proteins, while low-frequency species upregulated genes related to cellular homeostasis and metabolic maintenance. Weighted gene co-expression network analysis revealed two RF-correlated modules: a high-frequency module enriched in aerobic respiration and carbon metabolism and a low-frequency module enriched in lipid metabolism. Protein–protein interaction analysis identified ACTC1, vital for muscle contraction, as a hub gene. Evolutionary analysis showed that ACTC1 is highly conserved, with no significant positive selection, indicating that transcriptional regulation, rather than coding-sequence divergence, is the primary driver of the observed functional differences. These findings suggest that RF variation likely results from transcriptional remodeling in laryngeal superfast muscles. This study provides the first transcriptomic evidence linking laryngeal gene expression with acoustic divergence and offers new insights into the genetic basis of bat echolocation. Full article

Background: The WRKY transcription factor family represents one of the most crucial transcription factor families in plants, regulating diverse physiological processes. The heartwood of Dalbergia odorifera is a prized material for both high-quality rosewood and traditional medicinal applications, exhibiting exceptional economic value. However, the roles of WRKY transcription factors in the growth and development of D. odorifera, particularly their correlation with heartwood formation, remain unexplored. Methods: WRKY transcription factors were identified through bioinformatics analysis using the published genome data of D. odorifera. Phylogenetic comparative analysis was performed based on the Arabidopsis classification system. Collinearity analysis was conducted to investigate the evolutionary dynamics and expansion mechanisms of the WRKY gene family, and differential expression analysis was performed across tissues. Results: A total of 94 WRKY genes were unevenly distributed across 10 chromosomes and systematically designated as DodWRKY1 to DodWRKY94 according to their chromosomal positions. The WRKY family was classified into three major clades (Groups I, II, and III), with Group II further subdivided into five subgroups (IIa–IIe). Purifying selection served as the primary force shaping the WRKY family, with whole-genome or segmental duplication acting as the dominant expansion mechanism; these duplication events contributed to functional divergence, whereas genes within the same subgroup retained conserved structural features and motif compositions. DodWRKY14 (subgroup IIb) and DodWRKY58/68 (subgroup IIc) were highly expressed in the transition zone, suggesting a potential involvement in heartwood formation. Conclusions: This study provides a comprehensive characterization of the DodWRKY family and identifies candidate genes associated with heartwood formation, thereby establishing a foundation for further investigation into the molecular mechanisms underlying heartwood development. Full article

Background/Objectives: Genome-wide association studies (GWAS) based on single-step genomic BLUP (ssGBLUP) commonly assume equal single nucleotide polymorphism (SNP) variances, which may not reflect the biological architecture of complex traits. Alternative weighting strategies can increase detection power but may affect stability. This study evaluated how different SNP weighting approaches influence genomic region detection and biological interpretation of ribeye area (REA) and subcutaneous fat thickness (SFT) in Guzerá cattle. Methods: Phenotypic records from 2729 animals and genotypes from 1405 individuals (43,039 SNPs after quality control) were analyzed. Heritabilities were estimated using Restricted Maximum Likelihood (REML), and GWAS were conducted under five approaches: unweighted method (UM), quadratic method (QM), and three Non-Linear A strategies with weighting constants (1.125, 1.2, and 1.5). Genomic windows of 20 adjacent SNPs explaining ≥0.5% of the additive genetic variance (AGV) were considered significant. Recurrent regions were prioritized, and functional enrichment analyses (KEGG, GO, and MeSH) were performed. Results: Heritability estimates were moderate for REA (0.26 ± 0.05) and SFT (0.22 ± 0.04). Weighted approaches increased detection sensitivity. For REA, UM identified 10 windows, whereas QM and A_1.5 detected 24 and 31 windows. For SFT, UM identified 8 windows, while QM and A_1.5 detected 30 and 23 windows. Recurrent chromosomes included 2, 4, 6, 12, 16, 19, and 22 for REA, and 2, 3, 5, 7, 11, 17, and 22 for SFT. Key genes included AKT3, NOS2, and MSTN. Enrichment highlighted pathways related to muscle growth and lipid metabolism. Conclusions: SNP-weighted GWAS increased detection sensitivity but involved trade-offs between signal amplification and stability. Integrating weighting strategies improves biological interpretation and supports robust candidate gene identification for genomic selection. Full article

Renal ischemia–reperfusion injury (IRI) is a major cause of acute kidney injury. Estradiol (E2) and the selective estrogen receptor modulator raloxifene (RAL) reduce organ dysfunction, potentially via heme oxygenase-1 (HO-1)–mediated antioxidant and anti-inflammatory effects. This study examined whether E2 and RAL protect against IRI through G protein-coupled estrogen receptor (GPER)–dependent activation of the nuclear factor erythroid 2-related factor 2 (Nrf2)/HO-1 pathway in ovariectomized (OVX) mice; OVX IRI mice were pretreated for four weeks with E2, RAL, RAL + ML385 (Nrf2 inhibitor), or RAL + G15 (GPER antagonist). Renal histology, inflammatory and oxidative markers, and nuclear Nrf2 levels were assessed; OVX IRI increased interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and malondialdehyde (MDA) and decreased superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH); nuclear Nrf2 was low in sham and OVX IRI groups. E2 and RAL improved renal function and histology, reduced inflammation and oxidative stress, restored GPER expression, increased nuclear Nrf2, and upregulated HO-1 and NAD(P)H:quinone oxidoreductase 1 (NQO1). Co-treatment with ML385 or G15 reversed RAL’s benefits, reduced nuclear Nrf2, and worsened injury; E2 and RAL exert renoprotective effects against OVX-related renal IRI in a manner consistent with GPER-dependent Nrf2 nuclear translocation, which suggests involvement of the downstream antioxidant gene activation pathway. Full article

Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder characterized by reduced circulating levels and/or impaired function of alpha-1 antitrypsin (AAT), a key serine protease inhibitor, in which loss of effective antiprotease protection results in unchecked neutrophil elastase activity and progressive lung tissue destruction. Although AATD accounts for approximately 1% of chronic obstructive pulmonary disease (COPD) cases and up to 2% of emphysema, AATD-related COPD remains largely underdiagnosed, despite guideline recommendations for systematic evaluation in patients with COPD, particularly in high-risk clinical settings. Pathologically, AATD-related COPD is not limited to the typical early-onset, lower-lobe-predominant emphysema, also including upper-lobe or mixed emphysema patterns, airway-predominant disease, small airways dysfunction, and bronchiectasis. Clinically, AATD-related COPD is distinguished from smoking-related COPD by its earlier onset, physiological impairment that is often disproportionate to smoking exposure, and its potential presence of certain extrapulmonary manifestations. Diagnosis and monitoring are also challenged by the frequent discordance between airflow limitation and gas transfer impairment, as well as the early involvement of small airways, limiting reliance on spirometry alone. A multimodal assessment incorporating more sensitive functional techniques and CT densitometry may provide a more precise evaluation of disease burden, progression, and prognosis. Management generally follows standard COPD principles, with intravenous AAT augmentation therapy remaining currently the only established disease-modifying therapy for selected patients with severe deficiency. The advent of new pharmacological and gene-based therapies emphasizes the importance of developing personalized management strategies that integrate genotype and longitudinal disease behavior. This narrative review summarizes current evidence on AATD-associated COPD, focusing on its genetic basis and pathophysiological features, clinical and functional heterogeneity, current and emerging diagnostic and monitoring approaches, and disease-specific management considerations. Full article

Quorum sensing (QS) represents a promising target for anti-virulence therapy; however, effective pharmacological intervention requires a detailed understanding of regulatory network architecture and environmental context. In Klebsiella pneumoniae, the orphan LuxR-type receptor SdiA lacks a cognate LuxI synthase and instead detects exogenous acyl-homoserine lactones (AHLs), positioning it as an inter-species signal integrator. Here, we demonstrate that SdiA functions as a context-dependent regulator whose impact on biofilm formation and virulence gene expression is gated by environmental AHL availability. Using isogenic ΔluxS, ΔsdiA, and ΔluxSΔsdiA mutants in a clinical bloodstream isolate, we show that under AHL-limited conditions, SdiA promotes baseline biofilm development, whereas in the presence of exogenous C6-HSL, it restrains excessive biofilm maturation. Two-way ANOVA confirmed significant genotype, treatment, and interaction effects, establishing that SdiA-mediated regulation is signal contingent. We further investigated the halogenated thiolactone meta-bromo-thiolactone (mBTL), previously described as a QS inhibitor in Pseudomonas aeruginosa. In K. pneumoniae, mBTL acts as a context-selective modulator rather than a simple inhibitor. Under AHL-limited conditions, mBTL phenocopied ΔsdiA, reducing biofilm formation and inducing overlapping transcriptional profiles. In contrast, under AHL-replete conditions, mBTL opposed SdiA-dependent gene expression, consistent with competitive antagonism of ligand-bound receptor. RNA-seq analysis revealed substantial concordance between ΔsdiA and WT + mBTL under AHL-free conditions, with the inversion of transcriptional directionality in the presence of C6-HSL. The findings redefine SdiA as a conditional quorum-sensing integrator and identify mBTL as a ligand-context-dependent modulator of LuxR-type signaling. Our results highlight the necessity of evaluating anti-virulence compounds across relevant signal environments and introduce receptor state-selective modulation as a strategic framework for targeting hybrid quorum-sensing systems in polymicrobial pathogens. Full article

Codon usage bias is important for regulating protein translation efficiency and accuracy. The HSP90 gene, a pivotal gene in plants, maintains homeostasis in plant protein stress responses and organelle immune defense functions. We systematically examine codon usage preferences in six forage grass species and the regulatory mechanisms of the HSP90 gene in governing codon preference. A set of metrics is evaluated, including effective codon number (ENC), codon adaptation index, and relative synonymous codon usage. Neutral evolutionary trajectories reveal usage preferences for six plant codons, with natural selection serving as the primary driving factor. The correlation between the ENC–GC3 curve (ENC relative to third-position GC content in synonymous codons) and codon bias index reveals these genes to exhibit moderate codon bias. The phenomenon of evolutionary constraints is exemplified by a propensity for C/G-terminating codons, concomitant with a suppression of NUA/NCG codons (NUA is an abbreviation for UA dinucleotide, and NCG is an abbreviation for CG dinucleotide). Phylogenomic reconstruction reveals a conserved diversification pathway, positioning P. giganteum A. Rich. at the basal node of the evolutionary framework. This study identified through systematic assessment that natural selection is the primary evolutionary force driving the biased use of codons in grass HSP90 genes. This finding provides actionable insights for enhancing abiotic stress tolerance in forage germplasm through precise codon engineering. Full article

Sigma factors (SIGs) are nuclear-encoded regulators of chloroplast gene transcription. We conducted a genome-wide analysis in Brassica napus, identifying 23 SIG genes that were phylogenetically classified into six distinct subfamilies. Characterization of gene structure, conserved motifs, and chromosomal locations indicated family expansion primarily through segmental duplication under purifying selection. Promoter analysis identified cold-responsive elements enriched in BnSIG5A. Expression profiling showed that BnSIG5 subfamily members, particularly BnSIG5A, are strongly induced by cold stress. Analysis of Arabidopsis SIG5 mutants confirmed previously reported roles of AtSIG5 in cold tolerance. Heterologous expression in yeast, and the strong cold induction of BnSIG5A together with its chloroplast localization, suggest that BnSIG5A may play a conserved role, providing a foundation for future functional studies in B. napus. This work establishes a genomic framework for the SIG family in rapeseed and identifies BnSIG5A as a high-priority candidate for further investigation. Subcellular localization confirmed chloroplast targeting of BnSIG5A. Heterologous expression in yeast and analysis of Arabidopsis SIG5 mutants suggest conserved functions in cold tolerance, providing a foundation for future functional studies in B. napus. This work establishes a genomic framework for understanding SIG-mediated stress responses in rapeseed and identifies BnSIG5A as a promising candidate for further investigation. Full article

Background: Wild jujube (Ziziphus jujuba var. spinosa) exhibits remarkable tolerance to saline-alkali stress, yet its molecular mechanisms remain poorly understood. 3-ketoacyl-CoA synthase (KCS) is a key enzyme involved in the biosynthesis of very-long-chain fatty acids (VLCFAs), which constitute pivotal precursors for membrane lipids involved in stress adaptation. Methods: Through genome-wide analysis and molecular biology techniques, 20 ZjKCS genes were identified. Results: The ZjKCS genes were grouped into nine subfamilies, exhibiting highly conserved gene structures, motifs, and functional domains within each subfamily. Two pairs of collinear gene pairs were identified, with the ZjKCS12-ZjKCS18 pair retaining core conserved functions despite intense purifying selection. ZjKCS genes are rich in cis-acting elements associated with light transduction, phytohormone responses, and abiotic stress adaptation. Tissue-specific expression patterns of ZjKCS under light, ABA (abscisic acid), and MeJA (methyl jasmonate) treatments were analyzed by quantitative real-time PCR (qRT-PCR). Under saline-alkali stress, ZjKCS genes were significantly upregulated, with most showing strong sustained induction during later treatment stages. Conclusions: These findings indicate that the ZjKCS family participates in saline-alkali stress and abiotic stress adaptation, potentially by enhancing VLCFA synthesis to reinforce and remodel membrane lipid structure. This study provides a foundation for elucidating lipid-mediated stress resistance mechanisms in stress-tolerant fruit trees. Full article

Mixograph properties represent important quantitative traits that are controlled by multiple genes and influenced by environmental factors. In this study, we conducted quantitative trait locus (QTL) mapping for key Mixograph paraments using a recombinant inbred line (RIL) population derived from a cross between Yangxiaomai and Zhongyou 9507. Based on a high-density genetic map, six stable QTLs were identified on chromosomes 1A, 1B, and 1D across four environments, with individual phenotypic variation explained, ranging from 2.26 to 28.70%. Among these, QTh.ahau-1A, QMt/QPa.ahau-1B, and QTw.ahau-1D.1 are potentially novel loci. Furthermore, four functional Kompetitive Allele-Specific PCR (KASP) markers were developed based on tightly linked SNPs and validated in 110 advanced breeding lines, confirming their significant association with the target traits and utility for marker-assisted selection (MAS). Additionally, six candidate genes were predicted, which encoded proteins such as a hydroxyproline-rich glycoprotein, a CCCH-type zinc finger protein, protease, kinase, a phosphoglucan water dikinase, and a TRP-like family protein. Collectively, these findings provide valuable genetic loci, functional molecular markers, and candidate gene resources for improving wheat processing quality through MAS-based breeding. Full article

Underutilised, nutrient-dense legumes in their sprouted form provide promising substrates for developing functional fermented foods capable of influencing gut microbial activity and metabolite production. This study evaluated the effects of probiotic lactic acid bacteria-fermented beverages derived from sprouted Bambara groundnut (Vigna subterranea) and cowpea (Vigna unguiculata) on gut microbiota composition and short-chain fatty acid (SCFA) production using an in vitro colonic fermentation model. The beverages were fermented with either Bifidobacterium animalis BB-12 (BCBF24) or Lactiplantibacillus plantarum 75 (BCL7524). During colonic fermentation, at 0, 12, 24, and 38 h, faecal slurries were collected for SCFA analysis using gas chromatography–mass spectrometry (GC-MS) and deoxyribonucleic acid (DNA) sequencing (Oxford Nanopore Technologies). Microbial diversity decreased, indicating selective enrichment of taxa. BCL7524 induced a major shift, significantly (p < 0.05) enriching Bacillota and driving Megasphaera to ~42% dominance within 24 h. This reflected cross-feeding from L. plantarum to lactate-utilising Megasphaera spp. Spearman correlation linked Megasphaera to a broad SCFA profile, including isobutyric, isovaleric, valeric, and hexanoic acids, with a significant (p < 0.05) positive correlation observed for hexanoic acid. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated proteolysis and mapped hexanoic acid to fatty acid biosynthesis pathways, suggesting chain-elongation activity contributing to hexanoate formation. In line with this, BCL7524 produced significantly (p < 0.05) higher levels of hexanoate (3–14 mM) and valerate (10–15 mM), supporting chain-elongation activity within the community. In contrast, BCBF24 enriched Actinomycetota and Bifidobacterium, correlating with acetate production (18–23 mM). This study demonstrates that specific synbiotic beverages can modulate gut microbial ecology and metabolic output under in vitro conditions. Full article