Search Results (415)

Background/Objectives: Identifying the true perpetrator among monozygotic (MZ) twins has long posed a challenge in forensic genetics and for police investigations because MZ twins are likely identical in their short tandem repeat (STR) profile. In this study, we propose a workflow to address this issue, anchored in a case study involving MZ twins. Methods: The workflow includes shotgun sequencing of reference samples from one twin and trace samples, followed by a targeted amplicon-based approach (AmpliSeq™ Custom Panel) to validate the identified variants. Results: Biological traces from the crime scene, identified as blood, were available for analysis along with reference material from one twin, collected as a buccal swab. The samples underwent shotgun sequencing, and the resulting reads were aligned to the human reference genome. The sequencing yielded 2.91 and 2.85 billion mapped positions (corresponding to a breadth of coverage of 91% and 89%), with mean depths of coverage of 39.7× and 25.8× for the trace and reference samples, respectively. To minimise the risk of detecting somatic variants in the two different tissues, a stringent heterozygosity balance threshold (Hb: 0.4–0.6) was applied, and 2,047,077 single nucleotide variants (SNVs) were identified, of which 28 showed inconsistencies between the trace and reference samples. These candidate variants were subjected to validation using an AmpliSeq™ Custom Panel. Conclusions: No detectable SNV differences were observed between the reference and trace samples, and it was not possible to determine whether the trace originated from the reference twin or from his monozygotic co-twin. Full article

Aggressive behavior in Muscovy ducks (Cairna moschata) has become a predominant concern in intensive farming systems, leading to reduced animal welfare and production losses. To unravel the molecular mechanisms underlying this behavior, transcriptomic profiling was performed on the hypothalamus, a key regulatory hub for aggressive responses. A total of 120 healthy 60-day-old female Muscovy ducks were continuously monitored for 24 h/day over one month using Media Recorder 2.0 software. Based on instantaneous and continuous behavioral observations, the ducks were categorized into three groups: aggressor (Experimental group I, actively attacking conspecifics), victim (Experimental group II, receiving aggression), and non-aggressive (Control group, no aggressive interactions). Hypothalamic tissues were collected from each group (n = 4 per group) for Illumina HiSeq 2000 high-throughput transcriptome sequencing. Functional annotation and enrichment analysis of differentially expressed genes (DEGs) were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, followed by quantitative real-time PCR (qRT-PCR) validation. GO analysis identified 626 DEGs in the aggressor group and 649 DEGs in the victim group compared to the control group, with 26 DEGs directly involved in aggressive behavior regulation. Integration of GO and KEGG annotations revealed 69 candidate genes associated with aggressive behavior, enriched in two GO terms (behavior [GO:0007610] and sensory perception of pain [GO:0019233]) and the ERBB signaling pathway (map04012). qRT-PCR validation of 14 randomly selected candidate genes (e.g., NPY, ERBB4, MAPK9, PRDM12) confirmed that their expression patterns were consistent with transcriptomic data, verifying the reliability of the sequencing results. These findings provide novel insights into the molecular genetic basis of aggressive behavior in Muscovy ducks and lay a foundation for developing targeted strategies to mitigate aggression in intensive farming systems. Full article

Double-haploid (DH) technology is a well-established method for speeding up the development of inbred lines in breeding programs. The major loci qhir1 and qhir8 are widely used in marker-assisted selection (MAS) to increase the haploid induction rate (HIR) in maize. However, previous studies have shown that HIR can be unstable within populations, even in the presence of these two loci. To identify novel loci associated with HIR, we performed QTL-seq analysis on 337 S₂ haploid inducers (qhir1+/qhir8+) derived from crossing K8 with BHI306. The population exhibited HIR ranging from 0% to 31.16%. We sequence-bulked DNA from 30 extremely high-HIR lines (15.72–31.16%) and 30 extremely low-HIR lines (0–3.84%), identifying candidate intervals on chromosomes 2 (qHI2), 3 (qHI3), 6 (qHI6), and 8 (qHI8). Based on the QTL-seq results, 147 high-confidence SNPs/InDels (R² > 0.3) led to the analysis of 58 genes across three QTLs. We retrieved ten missense mutation SNPs from three genes (GRMZM2G359746 (qHI2), AC198725.4 (qHI3), and GRMZM2G091276 (qHI8)), which are located on chromosomes 2, 3, and 8. Regression analysis of these SNPs showed an R² range of 0.27 to 0.72. The two most highly associated SNPs were located in exon 2 of GRMZM2G359746 (qHI2) and in exon 5 of GRMZM2G091276 (qHI8), respectively. Marker–trait association analysis revealed that lines carrying favorable alleles at both loci, together with qhir1+ and qhir8+, exhibited significantly higher average HIR (12.77%) compared to those with unfavorable alleles (6.66%). These findings provide valuable markers for enhancing maternal haploid inducer breeding programs in maize. Full article

Rosa roxburghii Tratt (RR) and Rosa kweichonensis var. sterilis (RS) are both edible medicinal plants. However, they are often confused due to their similar phenotypic characteristics, which may limit their targeted development and utilization. Here, we integrated targeted metabolomics (UPLC-MS/MS) and transcriptomics (Illumina HiSeq) to systematically dissect the metabolic and transcriptional differences between the two species. Metabolomic profiling identified 558 differentially accumulated metabolites (DAMs), defined as metabolites with significantly different abundance between RS and RR, predominantly classified as flavonoids and phenolic acids. Among these, vitamin C (L-ascorbic acid) and argininosuccinic acid were prioritized as key DAMs based on their significant fold changes, high abundance, and functional relevance to bioactivity and stress tolerance. Transcriptomic analysis further revealed that vitamin C synthesis is primarily driven by the coordinated up-regulation of USP and GME genes in the L-ascorbic acid metabolic pathway, while argininosuccinic acid production, as an intermediate in the urea cycle, is mainly mediated by the up-regulated glnA gene. These findings not only clarify the molecular basis of metabolic divergence between RR and RS but also provide potential biomarkers for their identification, laying a solid foundation for their development as distinct functional foods. Full article

High-altitude lakes are sensitive sentinels of climate change, and yet the microbial processes driving biogeochemical cycles under warming remain poorly understood. Seasonal dynamics of sediment microbial communities in four glacial lakes within the cirques of the Seven Rila Lakes (Rila Mountains, Bulgaria) were investigated during June, August, and October 2024. Environmental monitoring showed pronounced seasonal variability with summer peaks in temperature, dissolved organic carbon and nitrogen, and increased inputs of labile organic matter. Multivariate analyses revealed strong seasonal structuring of microbial assemblages, with the largest shifts occurring between the early ice-free season and summer. Archaeal communities were dominated by Halobacteriota over time, whereas lake warming corresponded to a shift from early-season dominance of Actinomycetota and Bacillota to the summer prevalence of Pseudomonadota and Cyanobacteriota, as well as a proliferation of minor phyla Gemmatimonadota. At the genus level, summer enrichment of archaeal methanogen Methanosaeta and bacterial genera Paucibacter, Ca. Accumulibacter, Methylibium, Crenothrix, and Pseudanabaena was observed. Canonical correspondence analysis identified temperature and nutrient availability as the primary drivers of microbial community restructuring. Our results provide empirical evidence that warming and associated changes in organic matter inputs drive shifts in sediment microbial communities, with direct implications for carbon cycling and methane production. Additionally, the results highlight the sensitivity of high-altitude lakes to global warming and emphasize the critical role of microbial communities in modulating ecosystem responses to climate change. Full article

Background: Haemoglobinopathies are the most common monogenic disorders both in Greece and worldwide. The most effective strategies against them are carrier detection and prenatal testing following genetic risk assessment consultation for couples on the likelihood of their offspring being affected. Case Presentation: A novel alpha globin chain variant, named Hb Thessaloniki, was detected in Northern Greece. The underlying point variation HBA1:c.260T>C (ref. seq. NM_000558.5) was detected in the HBA1 gene, in heterozygosity, during a routinely performed population screening for haemoglobinopathies. The amino-acid residue Leu86 was replaced by a structure disrupting Pro residue, resulting in a hyperunstable product as shown by the isopropanol test and predicted by the Dynamut2 and Alphafold3 algorithms. The haematological phenotype, due to which genetic analysis was performed, presented with mild microcytosis and hypochromia and was also indicative of the presence of an unstable haemoglobin produced in small quantities (variant encoded by HBA1). Since the proband’s partner presented with a normal haematological phenotype, there is no risk of the couple giving birth to an affected offspring. Expanded analysis of the proband’s relatives identified biallelic variants (α^Parmaα/αα^{Τhessaloniki}) in the proband’s mother, who presented with no apparent clinical findings, expect for slightly reduced haematological indices. Conclusions: The novel Hb Thessaloniki identified, although theoretically hyperunstable, seems to have minor effects on erythrocyte function, as indicated by haematological findings on the proband and his close relatives. Future identification of co-inheritance with HBA pathogenic point variations or deletions may provide further information regarding genetic counselling. In parallel, the usage of structure–function relation-calculating algorithms may enhance our prediction capability for novel variants. Full article

Background: Hypoxic–ischemic (HI) brain injury triggers a dynamic, multi-phase response involving early microglial efferocytosis followed by extracellular matrix (ECM) deposition and scar formation. Arginase-1 (ARG1), a key enzyme in tissue repair, is implicated in both processes, yet its role in neonatal microglia remains poorly defined. We characterize ARG1-linked pathways in neonatal microglia, identifying distinct efferocytic and fibrotic phases post-HI. Methods: HI was induced in P9 mice using the Vannucci model, and brains were collected at 24 h (D1) and 5 days (D5). Spatially resolved single-cell transcriptomics (seqFISH) was performed using a targeted panel enriched for microglial, ARG1-pathway, efferocytosis, and profibrotic genes. Cell segmentation, clustering, and spatial mapping were conducted using Navigator and Seurat. Differential expression, GSEA, and enrichment analyses were used to identify time- and injury-dependent pathways. Results: Spatial transcriptomics identified 12 transcriptionally distinct cell populations with preserved neuroanatomical organization. HI caused the expansion of microglia and astrocytes and the loss of glutamatergic neurons by D5. Microglia rapidly activated regenerative and profibrotic programs—including TGF-β, PI3K–Akt, cytoskeletal remodeling, and migration—driven by early DEGs such as Cd44, Reln, TGF-β1, and Col1a2. By D5, microglia adopted a collagen-rich fibrotic state with an upregulation of Bgn, Col11a1, Anxa5, and Npy. Conclusion: Neonatal microglia transition from early efferocytic responses to later fibrotic remodeling after HI, driven by the persistent activation of PI3K–Akt, TGF-β, and Wnt/FZD4 pathways. These findings identify microglia as central regulators of neonatal scar formation and highlight therapeutic targets within ARG1-linked signaling. Full article

Dentathalia scutellariae (Hymenoptera: Athaliidae) is a major pest of Scutellaria baicalensis, a plant of significant economic and medicinal value. To date, no genomic resources have been available for this species, limiting research into its biology and control. Here, we reported a genome assembly of D. scutellariae with high accuracy and contiguity, sequenced by PacBio HiFi long-read and MGI-Seq short-read methods. The genome assembly is 157.00 Mb in length with a contig N50 of 4.04 Mb. The complete BUSCO score was 98.8%. The genome contained 14.73 Mb of repetitive elements, representing 9.38% of the total genome size. We predicted 14,904 protein-coding genes, of which 12,327 genes were annotated functionally. Gene family analysis of D. scutellariae revealed 422 expanded and 113 contracted gene families. Notably, genes within expanded families were significantly enriched in retinol metabolism and drug metabolism–cytochrome P450 pathways. We present the first high-quality genome assembly of D. scutellariae, which serves as a foundational genomic resource. This dataset will facilitate future studies on the molecular basis of D. scutellariae’s pest status, host adaptation, and the development of targeted control strategies. Full article

Fermented grains (FGs) for Chinese strong-flavor Baijiu (CSFB) serve as both microbial habitats and flavor sources, yet the correlations among fungal communities, physicochemical properties, and volatiles during long-term fermentation remain insufficiently understood. To address this gap, this study employed Illumina HiSeq high-throughput sequencing, physicochemical analysis, and GC-MS for systematic investigation. Fermentation was divided into early, middle, and late stages based on FGs’ physicochemical dynamics and eukaryotic microbial diversity. A total of 9 fungal phyla and 195 genera were detected, with 12 dominant genera (e.g., Thermoascus, Aspergillus, Kazachstania). Forty-seven volatiles were identified, showing increasing diversity and richness. Redundancy Analysis revealed total acids exerted the most significant effect on dominant fungal succession, while network analysis screened 10 key genera (e.g., Mortierella, Trichoderma) pivotal for community structure. Additionally, Trichoderma, Fusarium and other genera correlated with important flavors like 1-butanol and 1-hexanol. This study clarifies the complex interactions in FGs, provides theoretical support for CSFB quality improvement via biofortification or environmental control, and offers a reference for revealing the ecological mechanisms underlying FG microbial community assembly. Full article

Background/Objectives: The arrangement and positioning of genes on chromosomes are non-random in plant genomes. Adjacent gene pairs often exhibit similar co-expression patterns and regulatory mechanisms. However, the genomic and epigenetic features influencing such co-expression, particularly in perennial crops like tea (Camellia sinensis), remain largely uncharacterized. Methods: Firstly, we identified 771 specific neighboring gene pairs (SNGs) in C. sinensis (YK10) and investigated the contributions of intergenic distance and gene length to SNGs’ co-expression. Secondly, we integrated multi-omics data including transcriptome, ATAC-seq, Hi-C and histone modification data to explore the factors influencing their co-expression. Thirdly, we employed logistic regression models to individually assess the contributions of nine factors—ATAC-seq, H3K27ac, Hi-C, GO, distance, length, promoter, enhancer, and expression level—to the co-expression of SNGs. Finally, by integrating co-expression networks with metabolic profiles, several transcription factors potentially involved in the regulation of catechin metabolic pathways were identified. Results: Intergenic distance was significantly negatively correlated with co-expression strength, while gene length showed a positive correlation. Furthermore, these two features exerted synergistic effects with threshold characteristics and functional significance. SNGs marked by either ATAC-seq or H3K27ac peaks displayed significantly higher expression levels, suggesting that epigenetic regulation promotes co-expression. In addition, correlation analysis revealed that the expression of certain SNGs was closely associated with catechin accumulation, particularly epicatechin gallate (EGC) and epigallocatechin gallate (EGCG), highlighting their potential role in modulating tissue-specific catechin levels. Conclusions: Collectively, this study reveals a multilayered regulatory framework governing SNG co-expression and provides theoretical insights and candidate regulators for understanding metabolic regulation in tea plants. Full article

Background: Drynaria roosii is a typically epiphytic fern characterized by the intriguing phenomenon that nest leaves (NLs) and sporotrophophyll leaves (SLs) are metatypical, with NLs persisting in a hardened form. Few reports have concentrated on the physiological characteristics of these two leaf types and the metabolite differences in their associated rhizomes (NRs and ORs). Methods: A comparative analysis of the two leaf types and their connected rhizomes was conducted based on photosynthetic parameters, leaf ultrastructure, Illumina HiSeqTM 2000 transcriptome sequencing, widely targeted metabolomics, and the spatial distribution of flavonoid components. Results: The results indicated that SLs exhibited significant advantages in photosynthetic parameters, with a net photosynthetic rate exceeding that of NLs by 228%. A total of 7236 differentially expressed genes (DEGs) were identified between SLs and NLs, with the majority of DEGs involved in developmental processes (491 DEGs), stress response (420 DEGs), and responses to abiotic stimuli (337 DEGs). A total of 1409 components were detected and authenticated, revealing that ORs contained relatively high levels of flavonoids, quinones, tannins, alkaloids, terpenoids, and vitamins. Furthermore, the spatial distribution of flavonoid components indicated a dispersive distribution in both NRs and ORs. Conclusions: This comprehensive study of NLs and SLs, along with their connected rhizomes, provides vital reference for scientific cultivation management and rational harvesting prior to medicinal use. Full article

This study investigates FLNC mutations in Chinese cardiomyopathy patients. Background: Inherited cardiomyopathies, including dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), restrictive cardiomyopathy (RCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC) are major heart failure causes. FLNC, critical for muscle structure, is implicated in myofibrillar myopathy and isolated DCM (3–4% cases) with ventricular arrhythmias. Missense variants are linked to HCM and protein aggregation. A cohort of 25 patients with pathogenic/likely pathogenic FLNC mutations (2022–2025, Beijing Anzhen Hospital) underwent whole-exome sequencing (WES) using IDT kit 1.0/Hiseq 4000. Variants were classified via the American College of Medical Genetics and Genomics (ACMG) guidelines. Clinical data (echocardiography, CMR, labs) and follow-up data (prognosis, meds, and family history) were collected. The statistics used SPSS (p < 0.05). The mean age was 38 ± 14.6 years (13 males). There were 25 FLNC mutations: 12 single nucleotide polymorphisms (SNPs), 5 deletions, 2 duplications, and 3 deletion-insertions, classified as 6 pathogenic, 16 likely pathogenic, and 3 variants of uncertain significance (VUS). Diagnoses: 24% dilated cardiomyopathy (DCM), 8% hypertrophic cardiomyopathy (HCM), and 4% left ventricular non-compaction. Nonsense mutation carriers exhibited significantly higher tricuspid regurgitation prevalence compared to frameshift mutation carriers (6/9 vs. 2/10; p = 0.04). Echocardiography revealed reduced left ventricular ejection fraction (LVEF) (41.5 ± 14.1%), with statistically significant differences in fractional shortening (p = 0.024) and aortic root diameter (p = 0.028). Pedigree analysis confirmed that a frameshift mutation (LP) co-segregated with familial DCM and was associated with severe phenotypes, including sudden cardiac death. Furthermore, nonsense FLNC mutations correlated with increased tricuspid regurgitation severity, smaller aortic root dimensions, and reduced pulmonary artery flow velocity. Full article

Gymnodiptychus integrigymnatus is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of G. integrigymnatus. The complete mitochondrial genome of one individual of G. integrigymnatus was sequenced using the Illumina HiSeq X Ten sequencing platform and comprehensively characterized. The mitochondrial genome was 16,714 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a typical control region. The genome composition showed a positive A + T skew (0.029) and a negative G + C skew (−0.198). All tRNAs were predicted to form typical cloverleaf secondary structures, except for tRNA-Ser (GCT), which lacked the DHU stem. Phylogenetic reconstruction based on 13 PCGs revealed that the subfamily Schizothoracinae was not a monophyletic group. Two major clades were identified within this subfamily: one comprising primitive taxa (Percocypris, Aspiorhynchus, and Schizothorax) and the other consisting of specialized and highly specialized groups. Gymnodiptychus integrigymnatus was distinct from both its congeners and the specialized clade and was instead recovered within a highly specialized group of the Schizothoracinae subfamily. This study offers novel perspectives on the taxonomy and phylogenetic relationships within the Schizothoracinae subfamily, with a specific focus on G. integrigymnatus, thereby enhancing the understanding of the systematics and phylogeny of the Schizothoracinae subfamily. Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat, with ST101 identified as a major circulating clone in Saudi Arabia. We used whole genome sequencing and plasmid reconstruction to investigate the molecular characteristics of CRKP ST101 isolates from Saudi Arabia (2018–2021), analyzing antimicrobial resistance genes (ARGs), virulence factors, and plasmid structure and replicon types. Clinical isolates were obtained from the Ministry of National Guard Health Affairs (MNGHA) hospitals in Saudi Arabia between 2018 and 2021. Whole-genome sequencing was performed using the Illumina MiSeq^® platform, followed by comprehensive bioinformatic analysis of ARGs, virulence factors, and plasmid content. All ten isolates belonged to ST101 and harbored extensive antimicrobial resistance (AMR) and virulence determinants. Nine isolates (90%) carried bla_OXA-48, with three co-harboring bla_NDM-1, representing dual-carbapenemase producers. These carbapenemase genes were located on plasmids with distinct replicon types, including IncL/M, IncHI1B/IncFIB, and IncFIA/IncR. All isolates were multidrug-resistant (MDR), with half classified as extensively drug-resistant (XDR). Four isolates exhibited hypervirulent profiles, harboring aerobactin and yersiniabactin siderophores. This study provides comprehensive genomic characterization of CRKP ST101 in Saudi Arabia, revealing complex resistance mechanisms mediated by diverse plasmid types. The findings highlight the importance of genomic surveillance to track the evolution and dissemination of high-risk MDR and XDR lineages and inform targeted infection control strategies. Full article

Bone mesenchymal stem cells (BMSCs) are multipotent progenitors with significant potential for bone tissue engineering and regenerative medicine. This study compared the mitochondrial imaging and transcriptome of BMSCs under two-dimensional (2D) and three-dimensional (3D) culture conditions during osteogenesis. 2D BMSCs were induced toward osteogenesis for 7, 14, and 21 days, while 3D BMSCs were induced for 21 days. Osteogenic mineralization was assessed by Alizarin Red S (ARS) staining, and whole-transcriptome sequencing (RNA-Seq) was performed to elucidate gene expression profiles. Furthermore, mitochondrial morphology in live cells was monitored at 0, 7, 14, and 21 days of 2D osteogenic differentiation to observe the mitochondrial changes. High-Sensitivity Structured Illumination Microscopy (HIS-SIM) imaging showed that mitochondrial morphology in BMSCs underwent a shift toward elongated and interconnected networks over time. The transcriptional profile showed that genes associated with skeletal morphogenesis, bone development, and extracellular matrix organization were significantly upregulated in 3D culture systems. These findings indicate that 3D culture is associated with a transcriptional profile enriched in pathways commonly observed during in vivo osteogenesis, which can inform scaffold-based bone-regeneration strategies. Full article