Search Results (139)

Background: Gynostemma pentaphyllum (Thunb.) Makino is an important medicinal plant within the Cucurbitaceae family. Despite its economic and pharmacological importance, genomic resources for this species remain limited. Methods: We sequenced and assembled the complete mitochondrial genome of G. pentaphyllum. Comparative analyses were conducted to investigate the genomic structure, gene content, RNA editing events, and intracellular gene transfer (IGT) from chloroplasts. Additionally, phylogenomic relationships, synteny, and the selective pressure on mitochondrial genes were evaluated against related species within Cucurbitaceae. Results: The ~324 kb mitogenome has a multipartite architecture of six circular-mapping molecules. It encodes the typical complement of mitochondrial protein-coding genes, tRNAs, and rRNAs found in angiosperms. Extensive C-to-U RNA editing, including events that generate functional start and stop codons, points to substantial post-transcriptional regulation. We also detected multiple chloroplast-derived fragments, including several intact genes, indicating active intracellular gene transfer. Phylogenomic analyses of conserved mitochondrial genes place G. pentaphyllum firmly within Cucurbitaceae, clustering it with Thladiantha cordifolia and Momordica charantia, whereas synteny comparisons reveal pronounced structural rearrangements with respect to these close relatives. While most genes evolve under strong purifying selection, rps1, sdh3, and sdh4 show signatures of accelerated evolution; furthermore, haplotype networks based on conserved loci further corroborate the close affinity with T. cordifolia. Conclusions: This study provides the first high-resolution mitogenome resource for G. pentaphyllum and candidate mitochondrial markers for species authentication, evolutionary studies, and breeding in Gynostemma and related cucurbits. Full article

Background/Objectives: The further application of high-coverage whole genome sequencing in fields such as paleogenomics, forensic investigations, and conservation genomics is impeded by two major barriers: extremely high costs and stringent sample requirements. Utilizing low-coverage sequencing offers a practical solution to these constraints; however, this approach introduces a primary challenge—the necessity to reconstruct distorted genomic information for downstream analysis. Methods: Analytical experiments conducted on low- to medium-coverage sequencing data confirmed the accuracy of several existing methods for inferring relationships up to the third degree and distinguishing unrelated individuals. Subsequently, efforts were made to evaluate allele-frequency-independent methods within animal genomics, where analyses are likely to encounter challenges such as uncertain allele frequencies, diverse sample types, and suboptimal sample quality. Kinship inference was performed on a total of 33 pairs of animal samples across three species, comprising nine parent–offspring pairs and four full-sibling pairs. Results: The analysis revealed that two efficient algorithm implementations (READ and KIN) successfully identified all unrelated pairs. Notably, among the various algorithms utilized, only KIN exhibited confusion between first- and second-degree relationships when subjected to. Conclusions: This study has filled a critical gap in the existing literature by conducting a comprehensive evaluation of various algorithms on low-coverage sequencing data derived from authentic human and animal samples, accompanied by detailed ground truth—a vital task that has been overlooked. Full article

The Criaderas and Solera system represents one of the most sophisticated aging methodologies in winemaking, producing distinctive Sherry wines through dynamic blending and biological aging processes. This traditional Spanish system, combined with the unique metabolic activities of flor yeast (Saccharomyces cerevisiae), creates wines of exceptional complexity and consistency. This comprehensive review synthesizes current literature on the Criaderas and Solera system, focusing on biological aging mechanisms, flor yeast dynamics, industrial applications, and contemporary challenges. Recent advances in genomic, proteomic and metabolomic studies of flor yeasts have been analyzed, alongside modern analytical approaches to the characterization of Sherry wine. The Criaderas and Solera system enables consistent wine quality through fractional blending across multiple aging levels. Flor yeasts exhibit specialized metabolic adaptations, including enhanced ethanol oxidation capacity, biofilm formation abilities, and stress resistance mechanisms. Modern applications extend beyond traditional winemaking to include biotechnological uses, immobilization techniques, and sustainable production methods. Current challenges include climate change impacts, maintaining genetic diversity, adapting to new technologies and meeting evolving consumer preferences. The integration of traditional knowledge with modern biotechnology offers promising opportunities for optimizing Sherry production. Understanding flor yeast ecology and metabolic pathways provides insights for developing innovative applications while preserving the authenticity of this centuries-old winemaking tradition. Full article

Next-generation sequencing technology was employed to read and assemble the complete plastid genome of the ‘Mejhoul’ date palm cultivar (Phoenix dactylifera L.). The genome consisted of 158,436 base pairs (bp) with a GC content of 37.24%, and it included 95 protein-coding genes, 44 tRNA genes, and eight rRNA genes. The plastome of five ‘Mejhoul’ genotypes from Jordan was compared with three genotypes from the USA, Morocco, and the UAE. It revealed 91 single-nucleotide polymorphisms (SNPs) and 23 insertions–deletions (InDels); the majority of them (62%) were located in intergenic regions, while the remaining variants were located in intragenic regions, including tRNA and rRNA genes. When the plastomes of all eight ‘Mejhoul’ genotypes were aligned, along with major cultivars ‘Barhee’ and ‘Khalas’, 24 SNPs and 23 InDels could be found. This would enable the development of a cultivar-specific fingerprint test for authentication. The phylogenetic tree was constructed using seventeen date palm cultivars. The phylogenetic analysis places ‘Mejhoul’ as a lineage derived within Clade I rather than as an early-diverging cultivar, suggesting it shares a more recent common ancestor with ‘Deglet Noor’ and ‘Barhee’. Full article

Accurate species identification is essential for the quality control and standardization of herbal medicines. Agrimonia species, the authentic sources of Agrimoniae Herba, have long been used in traditional medicine, yet limited genomic resources have hindered the establishment of reliable molecular approaches for accurate species discrimination within this genus. Here, we report the newly assembled complete chloroplast genomes (155,156–155,302 bp) of four Agrimonia species, which exhibit the typical quadripartite structure and contain 112 unique genes. Comparative analysis revealed 684 variable sites, including 497 single nucleotide polymorphisms (SNPs) and 187 insertions/deletions (InDels), predominantly located in the single-copy regions. Based on these species-specific variations, we developed nine PCR-based molecular markers that distinguished the four species. The markers were validated using herbarium specimens and commercial herbal products, demonstrating reproducibility and practical applicability. Phylogenetic analysis supported the monophyly of the genus Agrimonia and resolved each species into distinct clusters within the subtribe Agrimoniinae. These results showed that chloroplast genome sequences of the genus Agrimonia can serve as effective super DNA barcodes for species identification. Our study provides fundamental genomic resources for Agrimonia and reliable molecular tools for species authentication, providing a basis for ensuring the authenticity and safety of Agrimoniae Herba. Full article

This study aimed to establish a multiplex PCR identification system capable of rapidly detecting adulteration in sheep and goat meat, while qualitatively identifying common adulterant meats (pork, chicken, and duck). Species-specific primers targeting mitochondrial DNA sequences were designed after screening for gene fragments with intraspecies conservation and interspecies specificity across five target species. The multiplex PCR conditions and system were systematically optimized and evaluated for specificity, reproducibility, sensitivity, and practical applicability using simulated mixed samples and heat-treated products. The results demonstrated that the system could successfully identify sheep meat, goat meat, and adulterant meat components in randomly combined target meat template DNAs with excellent reproducibility. The system maintained a high sensitivity, detecting target species even at low DNA template concentrations and in samples with low adulteration ratios. Moreover, target meat components remained detectable in heat-treated products, confirming the system’s robustness under realistic market conditions. This multiplex PCR identification system demonstrates strong specificity, good reproducibility, high sensitivity, and broad applicability. It provides an important tool for effectively monitoring sheep and goat meat adulteration and offers crucial technical support for ensuring the authenticity of sheep and goat meat. Full article

Background/Objectives: miR5200 is miRNA unique to Poaceae plants. Induced under short-day conditions, it modulates flowering time by regulating the florigen FT gene expression. However, to date, the genetic locus responsible for mature miR5200 formation remains experimentally unvalidated, and its biological function in abiotic stress responses remains unknown. This has hindered systematic elucidation of miR5200’s physiological role and molecular mechanisms. Methods: This study utilized wheat as the research material. First, through bioinformatics analysis at the genomic level, 13 potential candidate tae-miR5200 gene loci were screened. Subsequently, the authenticity of these gene loci was systematically validated by combining tobacco transient transfection-based GUS staining assay and quantitative real-time PCR (qRT-PCR) to detect expression levels. Building upon this foundation, the expression patterns of tae-miR5200 under abiotic stresses such as low temperature, drought, and salinity, as well as SA, ABA, IAA, GA₃, and MeJA treatments, were further investigated. Results: Experimental validation confirmed that 7 out of 13 potential gene loci are authentic and functional, and tae-miR5200 exhibited specific expression changes under different types of abiotic stress. Conclusions: This study confirms the authenticity of tae-miR5200 gene loci, effectively eliminating interference from bioinformatics-predicted false-positive loci in subsequent functional studies. It provides an experimental foundation for further investigation into the molecular mechanisms of tae-miR5200 in wheat responses to abiotic stress. Full article

Cyber defense has evolved into an algorithmically intensive discipline where mathematical rigor and adaptive computation underpin the robustness and continuity of digital infrastructures. This review consolidates the algorithmic spectrum that supports modern cyber defense, from cryptographic primitives that ensure confidentiality and integrity to behavioral intelligence algorithms that provide predictive security. Classical symmetric and asymmetric schemes such as AES, ChaCha20, RSA, and ECC define the computational backbone of confidentiality and authentication in current systems. Intrusion and anomaly detection mechanisms range from deterministic pattern matchers exemplified by Aho-Corasick and Boyer-Moore to probabilistic inference models such as Markov Chains and HMMs, as well as deep architectures such as CNNs, RNNs, and Autoencoders. Malware forensics combines graph theory, entropy metrics, and symbolic reasoning into a unified diagnostic framework, while network defense employs graph-theoretic algorithms for routing, flow control, and intrusion propagation. Behavioral paradigms such as reinforcement learning, evolutionary computation, and swarm intelligence transform cyber defense from reactive automation to adaptive cognition. Hybrid architectures now merge deterministic computation with distributed learning and explainable inference to create systems that act, reason, and adapt. This review identifies and contextualizes over 50 foundational algorithms, ranging from AES and RSA to LSTMs, graph-based models, and post-quantum cryptography, and redefines them not as passive utilities, but as the cognitive genome of cyber defense: entities that shape, sustain, and evolve resilience within adversarial environments. Full article

Zika virus (ZIKV) caused Zika outbreaks and continues to post threats to public health. ZIKV infection may cause congenital abnormalities during pregnancy and neurological manifestations in adults. The recurrent public health threat of Zika in various geographical areas demonstrates a need for the development of effective therapeutics. Currently, there are no approved therapies for Zika. ZIKV is a single-stranded, positive-sense RNA virus, whose genome encodes three structural proteins and seven non-structural proteins. The surface envelope (E) protein is essential for host–cell recognition and viral entry; therefore, inhibition of E-mediated viral entry is a key strategy underlying antiviral treatments. Here, molecular docking-based virtual screening was used to screen small-molecule compound libraries to identify potential ZIKV entry inhibitors. Among the compounds identified, Pyrimidine-Der1 exhibited efficient inhibition of reporter ZIKV infection. The microscale thermophoresis assay confirmed its binding with the ZIKV E protein. This compound has effective inhibition of authentic ZIKV infection in a plaque inhibition assay against R103451, PAN2016, and FLR human strains (IC₅₀: ~3–5 μM). Additionally, it efficiently inhibited ZIKV infection at viral entry and fusion steps of the virus life cycle in a time-of-addition assay. Overall, Pyrimidine-Der1 is a promising ZIKV entry inhibitor, warranting further optimization and evaluation. Full article

Backgrounds: Accurate annotation of open reading frames (ORFs) is fundamental for understanding gene function and post-transcriptional regulation. A critical but often overlooked aspect of transcriptome annotation is the selection of authentic translation start sites. Many genome annotation pipelines identify the longest possible ORF in alternatively spliced transcripts, using internal methionine codons as putative start sites. However, this computational approach ignores the biological reality that ribosomes select start codons based on sequence context, not ORF length. Methods: Here, we demonstrate that this practice leads to systematic misannotation of nonsense-mediated decay (NMD) targets in the Arabidopsis thaliana Araport11 reference transcriptome. Using TranSuite software to identify authentic start codons, we reanalyzed transcriptomic data from an NMD-deficient mutant. Results: We found that correct ORF annotation more than doubles the number of identifiable NMD targets with premature termination codons followed by downstream exon junctions, from 203 to 426 transcripts. Furthermore, we show that incorrect ORF annotations can lead to erroneous protein structure predictions, potentially introducing computational artefacts into protein databases. Conclusions: Our findings underscore the importance of biologically informed ORF annotation for accurate assessment of post-transcriptional regulation and proteome prediction, with implications for all eukaryotic genome annotation projects. Full article

Modern crop breeding requires efficient tools for genetic identity and parentage verification to manage large-scale programs. To address this, we present GIPA (Genomic Identity and Parentage Analysis), a high-performance toolkit designed for these tasks. GIPA integrates key innovations: a sliding-window algorithm enhances accuracy by correcting genotyping errors, an intelligent system classifies samples by heterozygosity to streamline parentage analysis, and an integrated engine generates intuitive chromosome-level heatmaps. We demonstrate its utility in a soybean backcrossing scenario, where it identified a donor line with 98.02% genomic identity to the recipient, providing a strategy to significantly shorten the breeding program. In maize, its parentage module accurately identified the known parents of commercial hybrids with match scores exceeding 97%, validating its use for variety authentication and quality control. By transforming complex SNP data into clear, quantitative, and visual insights, GIPA provides a robust solution that accelerates data-driven decision-making in plant breeding. Full article

Cannabis sativa L. (2n = 2x = 20) is a widely recognized species within the Cannabaceae family. Despite its utilization for medicinal, recreational, and industrial purposes, alongside its extensive historical background, the number of genetic and biotechnological studies of this plant species has decreased due to legal ramifications and prohibition campaigns associated with its use and cultivation. For many years, the development of novel varieties has been pursued solely by cultivators, as domestic growers have transitioned their work from cultivation to breeding Cannabis lineages. Recently, the application of genomics has facilitated a surge in methodologies aimed at marker-assisted selection, germplasm management, genetic differentiation, authentication of cultivated varieties or cultivars, and forensic applications such as safeguarding intellectual property rights. Nevertheless, the utilization of molecular markers for the advancement of commercial varieties through marker-assisted breeding (MAB) frameworks remains rare. This investigation was designed to evaluate a previously established informative microsatellite (SSR) array for the genotyping of drug-type Cannabis sativa cultivars derived from seeds of European origin. A total of 171 samples from 20 varieties were collected from European distributors and analyzed for genetic uniformity and population structure. The results were then compared with previously analyzed hemp samples and drug-type samples of Canadian origin, revealing the identification capabilities of our SSR genotyping method. Full article

Ginkgo biloba is one of the most consumed medicinal plants and broadly included as an ingredient in plant food supplements (PFS) and herbal infusions, being potential targets for economically motivated adulteration. This work aimed at comparing the use of DNA and phytochemical markers to authenticate the botanical origin of ginkgo-leaf extracts and PFS. Quantitative real-time PCR was used to detect ginkgo DNA, while ultra-high performance liquid chromatography with tandem mass spectrometry detection (UHPLC-MS/MS) determined its main phytochemicals (terpene lactones and flavonol aglycones). DNA was detected in all ginkgo leaf extracts, mainly water, while the highest levels of phytochemicals were obtained using ethanol or acetone as solvents. The results suggested that 4 out of a total of 19 PFS samples were adulterated, with two samples evidencing the addition of quercetin from sources other than ginkgo. The other two samples showed low amounts of ginkgo phytochemicals, which was corroborated by low DNA content, suggesting the use of reduced amounts of G. biloba leaf material. Full article

Background: Genomic information is becoming integral to nursing practice, yet undergraduate curricula often provide limited opportunities to apply this knowledge in realistic settings. Objective: To evaluate the impact of a clinical simulation-based intervention on nursing students’ learning of genetic counseling, with a focus on knowledge acquisition, communication skills, and student satisfaction. Methods: A sequential mixed-methods study was conducted with 30 third-year nursing students enrolled in the elective Genetics Applied to Health Sciences. Quantitative data comprised (i) pre-/post-simulation knowledge tests, (ii) a satisfaction questionnaire, and (iii) final course grades, which were compared with grades of a cohort from the previous academic year that had no simulation component (n = 28). Qualitative insights were gathered through field notes and semi-structured interviews with six purposively selected participants. During the intervention each student rotated through the roles of genetic-counseling nurse, patient, and observer, followed by a facilitated debriefing. Results: Post-simulation knowledge scores and final course grades were significantly higher than both baseline values and the historical comparison cohort. Students reported very high satisfaction, highlighting the authenticity of the scenarios and the usefulness of immediate feedback. Qualitative analysis showed that role rotation fostered deeper understanding of counseling complexities, improved empathic communication, and bolstered self-confidence when discussing hereditary risk. Conclusions: Embedding standardized-patient simulation into undergraduate genetics courses measurably improves students’ knowledge, communication proficiency, and satisfaction. These findings support incorporating similar simulation-based learning activities to bridge the gap between theoretical genetics content and real-world nursing practice. Full article

This review highlights the critical role of chemotaxonomy in the identification, authentication, and discovery of bioactive compounds in medicinal plants. By analyzing secondary metabolites using techniques like UV spectroscopy, FTIR, HPLC, GC-MS, NMR, LC-MS-Qtof, and MALDI-TOF MS, chemotaxonomy ensures accurate plant identification, supporting the safe and effective use of plants in herbal medicine. Key secondary metabolites used in chemotaxonomic identification include alkaloids, flavonoids, terpenoids, phenolics, tannins, and plant peptides. Chemotaxonomy also facilitates the discovery of novel compounds with therapeutic potential, contributing to drug development. The integration of chemotaxonomy with genomics and proteomics allows a deeper understanding of plant biosynthesis and the mechanisms behind bioactive compound production. However, challenges due to variability in metabolite profiles and the lack of standardized methods remain, and future research should focus on developing global databases, improving standardization, and incorporating artificial intelligence and machine learning to enhance plant identification and bioactive compound discovery. The integration of chemotaxonomy with personalized medicine offers the potential to tailor plant-based therapies to individual genetic profiles, advancing targeted treatments. This review underscores chemotaxonomy’s importance in bridging traditional knowledge and modern science, offering sustainable solutions for medicinal plant use and drug development. Full article