Search Results (989)

Recent advances in forensic genetics are rapidly transforming the field from traditional DNA profiling toward integrative and predictive genomic approaches. While short tandem repeat (STR)-based typing remains the gold standard for human identification, emerging technologies such as massively parallel sequencing (MPS), forensic genetic genealogy (FGG), and artificial intelligence (AI)-driven bioinformatics are expanding the scope of forensic investigations, with MPS also widely established in clinical genomics, further supporting its application in complex and unresolved cases. This article presents a structured narrative and conceptual review of next-generation forensic genomics, based on selected peer-reviewed studies, technical guidelines, and recent review articles relevant to MPS-based marker analysis, FGG, DNA phenotyping, ancestry inference, AI-supported bioinformatics, validation, and ethical/legal issues. We discuss the transition from STRs to single nucleotide polymorphisms (SNPs) and microhaplotypes enabled by MPS, emphasizing their applications in mixture deconvolution, kinship analysis, and degraded DNA samples. The role of FGG in cold case resolution is examined, alongside methodological, legal, and ethical considerations related to the use of public genetic databases. Furthermore, we explore recent developments in DNA phenotyping and ancestry inference, focusing on predictive models of externally visible characteristics (EVCs) and their forensic utility. Particular attention is given to the growing impact of AI and machine learning in data interpretation, probabilistic genotyping, and pattern recognition across complex genomic datasets. Finally, we address current limitations, including technical standardization, population biases, data privacy concerns, and the need for robust validation frameworks. Rather than providing a systematic review, this work aims to synthesize current developments into an operational framework for integrated forensic genomics, distinguishing forensic intelligence, probabilistic interpretation, confirmatory testing, and evidentiary use. By integrating technological, analytical, and ethical perspectives, this review proposes a conceptual framework for integrated forensic genomics, in which genomic data are used not only for identification but also for forensic intelligence generation. Full article

β-Casein A1 and A2 (β-CN-A1 and β-CN-A2) are the two predominant β-CN proteoforms in bovine milk. β-CN-A1 has been associated with a greater propensity to release opioid peptides, such as β-casomorphin-7 (β-CM-7) and β-casomorphin-5 (β-CM-5), during gastrointestinal (GI) digestion, which may have adverse biological effects. This has stimulated growing interest in milk from cows carrying the β-CN A2A2 genotype (A2 milk), which requires reliable characterization methods. In this work, we developed a rapid, selective, and sensitive capillary electrophoresis–mass spectrometry (CE-MS) method for the accurate identification and quantification of β-CM-7 and β-CM-5 in milk hydrolysates from in vitro GI digestion of bovine milk. The method showed good linearity (R² > 0.99, over 0.5–100 mg/L for β-CM-7 and 0.25–100 mg/L for β-CM-5), limits of detection (0.25 and 0.10 mg/L), and repeatability (<0.2% for times and <1.4% for areas), and tandem mass spectrometry (MS/MS) allowed confirmation. The method was applied to A1A1 and A2A2 milk digested using the standardized INFOGEST protocol, followed by solid-phase extraction. β-CM-7 was detected and quantified only in A1A1 digests (0.98 mg/L), whereas β-CM-5 was not detected (<0.10 mg/L). These results indicate a differential release of β-CMs from A1 and A2 milk and support the method’s suitability for β-CM profiling, which may help assess A2 milk quality control and β-CM health impact. Full article

Short tandem repeat (STR) expansions are a major cause of neurodegenerative disorders; however, their genetic and clinical heterogeneity complicates diagnosis. STR detection remains limited in routine short-read next-generation sequencing (NGS) workflows. We evaluated the diagnostic yield and clinical utility of computational STR genotyping in a large Turkish neurodegenerative disease cohort. ExpansionHunter was applied to NGS data from 3150 patients and 146 controls, targeting 15 disease-associated STR loci. To improve genotyping of poorly captured exonic regions in exome data, the default locus coverage threshold was reduced from 10× to 3×. Candidate expansions were visually inspected using REViewer and validated by conventional molecular methods. Computational analysis detected 28 pathogenic and 160 intermediate expansions. Of these, 23 were confirmed as pathogenic, and eight initially classified as intermediate were reclassified as pathogenic after conventional validation, resulting in 31 pathogenic cases across 28 families: HTT (n = 8), ATXN2 (n = 5), ATXN1 (n = 4), DMPK (n = 3), PABPN1 (n = 3), TBP (n = 2), and single cases in AR, ATN1, and CACNA1A. Lowering the coverage threshold markedly increased genotyping rates at low-coverage loci in exome data, particularly in ATXN2. Genetic findings were largely consistent with clinical pre-diagnosis and the additional diagnostic yield was 0.95%. These findings support integrating STR analysis into routine neurogenetic diagnostics. Full article

Background: Acanthosomatidae (Hemiptera: Pentatomoidea), commonly known as parent bugs, is a comparatively small pentatomoid family whose biological distinctiveness is exemplified by the repeated evolution of maternal egg–nymph guarding in several lineages; however, mitogenomic data for this group remain limited. Acanthosoma murreeanum is an important representative of Acanthosoma, yet its complete mitochondrial genome and comparative mitogenomic characteristics have not been comprehensively studied. Methods: Here, we obtained the complete mitochondrial genome of A. murreeanum through sequencing, assembly, and annotation. We then characterized its mitogenomic structure, nucleotide composition, codon usage, RNA structural features, control-region organization, nucleotide diversity, evolutionary rates, and phylogenetic position. In addition, control-region characteristics were compared among available acanthosomatid mitogenomes to evaluate structural variation in the AT-rich region. Results: The sequenced mitochondrial genome of A. murreeanum is a circular molecule of 15,718 bp, comprising the standard set of 37 mitochondrial genes and a control region of 1104 bp. The genome exhibits a strong A + T bias (74.04%) and retains the typical mitochondrial gene order without gene rearrangement. Most protein-coding genes start with standard ATN codons, except COX1, which begins with TTG, whereas COX2 and ND5 terminate with incomplete stop codons. Most predicted tRNA genes displayed the conventional cloverleaf configuration, whereas trnS1 lacked a complete DHU arm and instead formed a simple loop. The control region was characterized by a 60 bp tandem-repeat unit and several conserved sequence motifs. Comparative analysis showed that control-region length, AT content, repeat-unit size, and motif composition varied among sampled Acanthosomatidae, while A. murreeanum and A. haemorrhoidale shared similar 60 bp tandem-repeat organization. Among the mitochondrial PCGs, ATP8 exhibited the highest level of variation, whereas COX1 was the most conserved. The Ka/Ks values of all genes were lower than 1, suggesting that these genes have evolved under purifying selection. Phylogenetic analyses based on maximum-likelihood and Bayesian-inference methods consistently supported a sister relationship between A. murreeanum and A. haemorrhoidale. Conclusions: This study provides a new mitogenomic resource for Acanthosomatidae and represents the first detailed comparative mitogenomic analysis within Acanthosoma. The results suggest that A. murreeanum retains a conserved mitochondrial genomic architecture, whereas variation in the AT-rich control region provides additional evidence for lineage-specific mitogenomic differentiation. These results provide useful insights into mitogenome evolution and phylogenetic relationships within Acanthosoma and closely related acanthosomatid groups. Full article

Mycotoxin contamination in wheat products has consistently been a key issue of concern in food safety, and urinary biomonitoring provides an effective approach for assessing internal human exposure. In this study, a sensitive ultra-performance liquid chromatography–tandem mass spectrometry method was developed and validated for the simultaneous determination of 28 mycotoxins in wheat products and human urine. For the two matrices, the extraction solvent, acid concentration, solid-phase extraction cartridge type, and enzymatic hydrolysis parameters were optimized. Under the optimized conditions, all target compounds showed excellent linear relationships within the tested concentration ranges (R² > 0.99). In wheat products, the spiked recoveries ranged from 70.2% to 120%, the repeatabilities ranged from 1.6% to 9.1%, and the limits of detection and limits of quantification were 0.001~8.3 μg/kg and 0.002~25.0 μg/kg, respectively. In urine, the spiked recoveries ranged from 79.3% to 120%, the repeatabilities ranged from 0.7% to 9.4%, and the limits of detection and limits of quantification were 0.0001~1.0 μg/L and 0.0002~3.0 μg/L, respectively. Analysis of real samples showed that at least seven mycotoxins were detected in wheat product samples, and at least five were detected in urine samples. In wheat products, the detection rates of deoxynivalenol, enniatin B, enniatin A₁, enniatin B₁, tenuazonic acid, and tentoxin were all 100%, whereas in urine, the detection rate of fumonisin B₁ reached 100%, and tenuazonic acid showed the highest mean concentration in both matrices. In conclusion, the developed ultra-performance liquid chromatography–tandem mass spectrometry method is suitable for the simultaneous quantification of 28 mycotoxins in wheat products and human urine, and its preliminary application demonstrates good practical applicability. Full article

Introduction: Intermittent fasting (IF) is becoming increasingly popular as a method of weight management, but it is unknown whether it affects plasticiser intake with resultant changes in glycaemic control in diabetes and vitamin D (VitD) levels; therefore, this study was undertaken in a cohort of control and type-2 diabetic (T2D) subjects during Ramadan time-restricted feeding (TRF). Methods: In T2D subjects (n = 19) and controls (n = 31) undertaking TRF, 24 h urinary levels of phthalate metabolites, bisphenols and serum VitD were determined pre- and post-TRF by liquid chromatography–tandem mass spectrometry (LC-MS/MS). Anthropometric data and glycosylated haemoglobin (HbA1c) were measured. Results: T2D subjects were older (52 versus 36.73 years, p < 0.001), and had higher BMI (36.54 versus 27.67 kg/m², p < 0.001), body weight (101.77 versus 80.36 kg, p < 0.001), and HbA1c (8.38 versus 5.46%, p < 0.001) compared to controls, while VitD levels did not differ (60.43 versus 63.95 nmol/L, p > 0.05). Post-TRF, HbA1c was unchanged in T2D subjects and there was no difference in weight, BMI or VitD. Increased mono-iso-butyl phthalate (MiBP) in T2D subjects (10 versus 6.1 ng/mL, p = 0.001) and mono-n-butyl phthalate (MnBP) in T2D subjects (37 versus 13 ng/mL, p = 0.018) and controls (8.3 versus 5.4 ng/mL, p = 0.007) were observed post-TRF; however, significance was lost after adjusting for baseline differences in age, BMI, and HbA1c using a general linear model (GLM) repeated-measures ANOVA. Despite having no median differences in DEHP (di-2-ethylhexyl phthalate) metabolites pre- and post-TRF, analyses revealed a significant time × HbA1c interaction for [mono(2-ethyl-5-carboxypentyl) phthalate, MECPP: F(1,42) = 4.79, p = 0.03, mono(2-ethyl-5-hydroxyhexyl) phthalate, MEHHP: F(1,42) = 8.56, p = 0.006, mono(2-ethylhexyl) phthalate, MEHP: F(1,42) = 4.64, p = 0.03 and mono(2-ethyl-5-oxohexyl) phthalate, MEOHP: F(1,42) = 8.19, p = 0.007] and time × group interactions [MEHHP: F(1,42) = 14.27, p < 0.001, MEHP: F(1,42) = 6.35, p = 0.01 and MEOHP: F(1,42) = 10.30, p = 0.003]. Estimated marginal means (adjusted for age, BMI, HbA1c, and VitD) further confirmed higher concentrations of DEHP metabolites [MECPP, MEHHP, MEHP, and MEOHP] in T2D participants over time compared with controls. Additionally, monomethyl phthalate (MMP) trajectories were significantly influenced by the time × group interaction (F(1,42) = 4.28, p = 0.04), with post-TRF elevations observed in T2D subjects. Vitamin D status was observed to modify mono(3-carboxypropyl) phthalate (MCPP) and MEP trajectories over time. Conclusion: Ramadan TRF is associated with changes in plasticiser metabolite levels, with estimated increased levels in T2D subjects versus healthy controls. Metabolite levels were influenced by HbA1c and vitamin D, though BMI was not observed to be a contributing factor. Full article

Per- and polyfluoroalkyl substances (PFASs) are a large class of thousands of synthetic organofluorine chemical compounds used for many industrial applications. Humans are exposed to PFASs mainly through diet and contaminated drinking water. Studies show that PFASs induce several adverse effects on humans. A great number of human biomonitoring studies have been widely conducted with the aim of estimating exposure to PFASs. The matrices mainly investigated are blood, serum and breast milk. However, in many cases, the need for non-invasive sampling methods with a minimal impact on donors has become paramount to comply with modern ethical standards and regulations. For this reason, we developed a streamlined and efficient method for the analysis of eight perfluorocarboxylic and perfluorosulfonic acids (PFHpA; PFHxS; PFOA; PFHpS; PFNA; PFOS; PFDA; and PFUdA) in human urine samples by UPLC chromatography tandem mass spectrometry. Chromatographic and MS parameters were optimized; the method was validated for: repeatability (<20%), within-lab reproducibility (<20%), trueness (within the set 20% variation limit of agreement between the mean of the data set and the true value), efficiency (51–97%), linearity (R² > 0.99), limits of detection (0.0003 ng/mL), and limits of quantification (0.001 ng/mL). To our knowledge, this is the first published method in Italy for the detection of PFASs in human urine. Full article

The remarkable ecological success of fungi is supported by their capacity for rapid and often reversible molecular responses to fluctuating environments. While conventional evolutionary theory has largely emphasized mutation and selection as central drivers of adaptation, many environmentally responsive fungal traits are also shaped by molecular processes that generate reversible phenotypic variation on ecological or developmental timescales. This review synthesizes current knowledge on reversible genetic and epigenetic mechanisms underlying fungal phenotypic plasticity by integrating insights from programmed genetic rearrangements such as mating-type switching, transposable element activity, variation in tandem repeats and the behavior of accessory chromosomes, together with dynamic epigenetic processes including histone modifications, DNA methylation, chromatin remodeling and RNA mediated regulation. Together, these mechanisms form an interconnected framework that enables rapid and, in many cases, reversible phenotypic diversification, although their consequences range from transient regulatory shifts to partially or fully irreversible sequence-level changes. We highlight the molecular machinery that governs reversibility and its evolutionary implications for fungal pathogenesis, symbiosis, and biotechnology. By uniting genetic and epigenetic perspectives, this review advances a holistic framework in which reversibility is treated as a key property of fungal phenotypic plasticity, helping fungi balance stability with flexibility under environmental challenge. Understanding these mechanisms provides new insights into fungal evolution, and opens new avenues for antifungal intervention and the rational design of industrially valuable fungal strains. Full article

Background/Objectives: The Black Caribbean population of Honduras, also referred to locally as Negro Inglés, constitutes one of the country’s nine recognized indigenous and Afro-descendant peoples. Predominantly settled in the Bay Islands and sections of the Caribbean coast, this community traces its ancestry predominantly to West Africa and has remained culturally and linguistically distinct for more than three centuries. Despite its demographic and historical relevance, no population-specific short tandem repeat (STR) database has been established for this group. Methods: Allele frequencies for 23 autosomal STR loci were characterized in 100 unrelated Black Caribbean individuals from the department of Islas de la Bahía. DNA was extracted from blood on FTA cards and amplified with the PowerPlex Fusion 6C System (Promega Corporation). Statistical parameters were computed using Genepop v4.2, Arlequin v3.5 and GDA v1.0. Results: A total of 241 distinct alleles were detected across all 23 loci (mean 10.48 ± 3.85 alleles/locus). Expected heterozygosity ranged from 0.6541 (D13S317) to 0.9350 (SE33), with a mean of 0.8150 ± 0.0664—values consistent with a population of predominantly West African origin. No locus exhibited a significant departure from Hardy–Weinberg equilibrium after Bonferroni correction (α = 0.0022). The combined power of discrimination exceeded 99.9999% and the combined chance of exclusion surpassed 99.9999%. Conclusions: This first genetic characterization of the Honduran Black Caribbean population delivers an essential, population-specific reference dataset for forensic casework, paternity testing, and population genetics research. The data also deepen the understanding of Afro-descendant genetic diversity in Central America and constitute a critical step towards equitable forensic genetic services for all Honduran ethnic communities. Full article

Background/Objectives: The widespread adoption of short tandem repeat (STR) marker technology in genetic analysis has led to the collection of substantial STR data from diverse populations. Allele-frequency data provide robust forensic utility and support accurate likelihood ratio calculations, highlighting the importance of regional databases. Methods: The presented study aimed to determine the allelic frequencies and statistical parameters for 16 autosomal genetic STR markers included in the NGM Detect^TM PCR Amplification Kit in a population sample of 220 unrelated individuals from the South-West region of the Republic of Bulgaria. Results: We found that the most polymorphic and informative marker for the Bulgarian population in the southwestern region is SE33, with the next most informative markers being D1S1656, D12S391, D18S51, and FGA. In contrast, D22S1045, D16S539, and D2S441 showed comparatively lower genetic variability and informativeness. At the same time, no deviations from the Hardy–Weinberg equilibrium were observed for the 16 loci studied. Conclusions: This work not only enriches knowledge of the genetic diversity of the Bulgarian population but also provides the Bulgarian and international justice systems with an objective, scientifically sound basis for expert decision-making. Full article

Generally, forest trees with medicinal value present diverse chemotypes considered key determinants of efficacy, safety, and commercial valuation. Such heterogeneity varies among tissues, genotypes, and seasons, and stress exposure. This review summarizes how regulatory controls and genome architecture affect the stability and synthesis of secondary metabolites in woody medicinally important taxa. Detailed haplotypic and chromosomal analyses have recently identified diverse and repeatable architectural drivers. Among these, LTR/transposon-mediated revamping, neofunctionalization, biosynthetic gene clusters, and tandem duplication play a special role in reshaping pathway capacity. The enzymatic regulation of these drivers translates this “capacity” into harvest-pertinent chemistry by employing conserved TF modules, hormone crosstalk, and emergent chromatin/epigenetic layers. Nevertheless, major parameters pertaining to the tissue-specific storage, transport, and compartmentalization of these chemotypes are contextualized with certain limitations. In this review, the integration of GWAS/eQTL/TWAS with multi-tissue is explained in addition to the replacement of a single reference with pangenome/haplotype frameworks, and explicit modeling of G × E further strengthen genotype-to-chemotype mapping. Therefore, in this review we summarize practical workflows for chemotype discovery utilizing staged validation models of heterologous reconstitution, isotope/spatial evidence, and chemistry. These findings were supported by data on saponins, alkaloids, iridoids, and defense response. Such an integration links mechanistic understanding to authentication, standardization, and sustainable utilization strategies in woody medicinal trees. Full article

Background/Objectives: Therapeutic drug monitoring (TDM) of immunosuppressants is essential in treating pediatric kidney diseases; however, repeated venipuncture is burdensome in children. We evaluated whether minimally invasive fingerstick capillary sampling combined with liquid chromatography–tandem mass spectrometry (LC-MS/MS) provides results analytically comparable to those of conventional venous sampling. Methods: Capillary whole blood (2.8 µL) was collected via fingersticks from pediatric patients receiving mycophenolate mofetil, with or without tacrolimus (TAC) or cyclosporine A (CsA). Drug concentrations were quantified using a previously validated simultaneous LC-MS/MS method and compared with conventional venous sampling using linear regression and Bland–Altman analyses. Results: Seventy-four paired samples from 21 patients were analyzed. Strong correlations were observed between capillary and venous samples for mycophenolic acid (MPA), TAC, and CsA (R² > 0.90). Hematocrit correction improved agreement for MPA. Bland–Altman analyses demonstrated acceptable bias across analytes. Conclusions: Fingerstick-based microvolume sampling combined with LC-MS/MS provides analytically reliable immunosuppressant quantification in pediatric patients. Although larger clinical validation is required, this minimally invasive approach may reduce procedural burden and may support future outpatient or home-based TDM strategies. Full article

Background: It is essential to recover as much DNA as possible from evidence samples to ensure optimal DNA analysis in forensic casework. However, both DNA collection and purification procedures cause a substantial loss of genetic material. Thus, a large loss of DNA through the pre-PCR procedures, including swabbing and extraction, may significantly affect downstream analysis results. In this study, different cotton swabs and extraction kits used for forensic samples were compared separately. Methods: The recovery of cell-free DNA (control DNA) and cell-bound DNA (blood and saliva) was evaluated using five different extraction kits: Chelex^® 100 Resin, Wizard^® Genomic DNA Purification Kit, QIAamp^® DNA Micro Kit, QIAamp^® DNA Investigator Kit and DNeasy^® Blood & Tissue Kit. The DNA recovery efficiency of the different extraction kits was assessed using real-time quantitative PCR targeting nuclear and mitochondrial DNA targets. In addition, nine cotton swabs from four manufacturers (Selefa^®, Puritan^®, Texwipe^®, and Heinz Herenz) with different production lots were evaluated for DNA quantity and quality using real-time PCR and short tandem repeat (STR) analysis. Results: Overall, large differences in DNA recovery were observed between the different extraction kits. The QIAInvestigator kit demonstrated the highest recovery at low DNA amounts, which is particularly beneficial for minute forensic samples. The swab comparison revealed variations not only in DNA recovery between swab manufacturers but also between lots of the same swab brand, and the DNA quantity was not clearly correlated with downstream DNA profile quality. Conclusions: Our findings emphasise the importance of considering the choice of extraction kit, swab brand and batch-to-batch variation in forensic laboratory procedures, as they may influence DNA recoveries and affect the success rate in forensic casework. Full article

S. suis is a major zoonotic infectious disease whose serological diversity brings challenges to vaccine development. Based on the whole-genome data of 169 S. suis strains, this study conducted a systematic bioinformatics analysis of the surface antigen protein HP0197 that reveals its distribution characteristics, sequence diversity, domain composition and antigenic epitope distribution. The results showed that the HP0197 gene, which has a detection rate of 91.72%, can be divided into seven major phylogroups (I–VII) and the following two structural types: short form (HP0197-S) and long form (HP0197-L). All sequences contained signal peptides, transmembrane structures, LPXTG anchoring motifs, as well as conserved GAGBD and G5 domains, among which tandem repeats of the G5 domain existed in the long HP0197-L type. Tertiary structure prediction indicated that HP0197 has a spatial architecture of “conserved at both ends and flexible in the middle”, in which B-cell epitopes are mainly enriched near the GAGBD and G5 domains, suggesting these regions are the key targets for inducing cross-immune protection. It systematically elucidates the diversity and structural characteristics of the HP0197 protein from the perspective of population genetics, which provides a theoretical basis for optimizing existing subunit vaccines, designing broad-spectrum multi-epitope vaccines and exploring novel anti-infection strategies. Full article

Satellite DNA (satDNA) is a family of tandemly repeated non-coding sequences in eukaryotic genomes involved in shaping genome architecture and regulation of various biological functions. Within a species, all satDNA families collectively form the satellitome. Satellitomes of Allium species has been explored only superficially, largely due to enormous genome sizes, high transposable element content, and a general lack of reference genomic resources. The emergence of reference genome assemblies now makes it possible to conduct a more in-depth study. Here, we applied a comprehensive bioinformatics approach to study the satellitomes of Allium cepa and Allium fistulosum. Using two complementary bioinformatics pipelines along with available reference genome assemblies, we have created the most complete collection of consensus satDNA sequences of A. cepa and A. fistulosum so far, consisting of 83 and 97 consensus sequences, respectively. The in silico analysis of the genomic distribution allowed the identification of 11 novel candidates for cytogenetic marker panels, including chromosome-specific satDNA families. Validation of satDNA using PCR and FISH confirmed the reliability of the created satellitomes. Furthermore, comparative analysis of satDNA genomic organization and abundance provided insights into the evolution of these species satellitomes. These findings provide a foundational resource that will help illuminate the evolutionary dynamics of Allium satellitomes and pave the way for future cytogenetic studies of Allium species. Full article