Search Results (50)

Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4–104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future. Full article

Background: Pangolins are critically endangered mammals, and a comprehensive understanding of their genetic diversity is crucial for effective conservation. The mitochondrial genome serves as a vital molecular marker for phylogenetic and population genetic studies. Obtaining genetic material from these elusive animals non-invasively remains a challenge. This study aimed to sequence and characterize the complete mitochondrial genome of Manis javanica and explore the phylogenetic relationships among pangolin species. Methods: The complete mitochondrial genome was sequenced from a saliva-derived sample. Standard procedures for DNA extraction, amplification, and sequencing were employed. The genome was assembled and annotated using bioinformatic tools. Phylogenetic analysis was conducted based on the cytochrome c oxidase subunit I (COXI) gene sequences from nine pangolin species, with the resulting tree constructed using the maximum-likelihood method. Results: The complete mitochondrial genome of M. javanica (GenBank accession: PP110760) is a circular molecule of 16,573 bp, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The overall base composition showed a lower GC content (43.83%) than AT content (56.17%). Phylogenetic analysis based on COXI sequences delineated the nine species into three distinct genera: Manis, Phataginus, and Smutsia. Within the genus Manis, Manis pentadactyla was identified as the closest relative to M. javanica. The newly described species Manis mysteria was found to be closer to Manis culionensis and Manis crassicaudata than to other congeners. Furthermore, the analysis indicated that African pangolins diverged earlier than Asian pangolins. Conclusions: This study successfully demonstrates the feasibility of extracting and sequencing the complete mitochondrial genome from saliva samples, providing a valuable non-invasive method for future genetic studies on pangolins. The genomic data and phylogenetic results offer significant molecular insights that will benefit the genetic management and conservation of critically endangered pangolin resources. Full article

N. chui is an economically important marine fish species distributed along the coastal waters of China, renowned for its delicate flesh texture and high-quality dried swim bladder. However, its scientific name and taxonomic relationship with N. coibor have long remained controversial, hindering accurate resource assessment and germplasm management. To address this issue, we sequenced and annotated the first complete mitochondrial genome of N. chui (GenBank accession: PZ024444). The circular mitogenome is 16,504 bp in length and contains 37 typical genes, with gene arrangement, nucleotide composition (A + T content: 52.07%), and codon usage patterns consistent with general teleost characteristics. Phylogenetic analyses based on 13 concatenated protein-coding genes revealed that N. chui and N. coibor form a maximally supported monophyletic clade (bootstrap support = 100%), with a pairwise genetic distance of 0. These mitochondrial results strongly suggest that the two nominal taxa are very closely related and may represent the same species. However, formal taxonomic synonymy cannot be established on mitochondrial evidence alone and requires further evaluation through examination of type material and comparative morphological study. Gene-specific selection pressure analyses showed that most mitochondrial protein-coding genes were subject to purifying selection, with ATP8 exhibiting the highest mean ω among genes with ω < 1, whereas ND5 and ND6 showed elevated ω values that warrant cautious interpretation. This study provides essential mitochondrial genomic resources for future research on species delimitation, phylogeny, and conservation of this important sciaenid fish. Full article

PYL proteins are core components of the abscisic acid (ABA) signaling pathway and are involved in plant responses to biotic and abiotic stresses. In this study, a total of 19, four, and eight PYL genes were identified in Saccharum spontaneum, the Saccharum spp. hybrid R570, and Sorghum bicolor, respectively. Phylogenetic analysis classified these PYL genes into three distinct groups. Cis-acting element analysis, Gene Ontology annotation, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment and gene expression profile indicated that members of the PYL gene family are mainly associated with hormone signaling and stress-related biological processes. The ScPYL8 gene (GenBank accession number: OR838856) was isolated from sugarcane cultivar QT3. Expression of the ScPYL8 gene was induced under stresses of cold, PEG, SA, MeJA, ABA, and brown stripe disease (Bipolaris setariae). The gene was expressed in roots, stems and leaves, with the highest expression level in leaves. Subcellular localization analysis showed that the ScPYL8 protein localized to the cytoplasm and nucleus. ScPYL8 overexpression in tobacco activated the reactive oxygen species defense system and regulated the ABA and jasmonic acid signaling pathways, enhancing its resistance against Fusarium solani var. coeruleum. These findings provide insights into the expression, function, and evolutionary characteristics of the PYL gene family in sugarcane, offering valuable genetic resources for future molecular breeding. Full article

Influenza A virus (IAV) remains a major global health threat, and host-directed antivirals may help overcome rapid viral mutation and drug resistance. Here, we performed a genome-wide siRNA screen in A549 cells using cell viability as an integrated endpoint to identify host determinants of IAV (PR8/H1N1) infection. Using plate-normalized viability ratios, we identified 2134 genes with >40% viability change after infection (2048 UP and 86 DOWN; two-tailed t-test, n = 3; p < 0.05, FDR < 0.1). MetaCore pathway analysis showed enrichment of programs linked to host response and tissue injury control, including RAS-related signaling and multiple metabolic pathways such as estradiol, ubiquinone/mitochondrial redox, and benzo[a]pyrene/xenobiotic metabolism. DAVID Gene Ontology analysis further highlighted biological processes relevant to infection, including endocytosis, transcription, and translation, consistent with host pathways supporting viral replication. Benchmarking against meta-analyzed RNAi and CRISPR resources revealed that shared hits were enriched for translation, nucleocytoplasmic transport, and ER-Golgi trafficking, supporting external validity, whereas the large unique UP fraction was dominated by hormone metabolism, detoxification, and mitochondrial redox/CoQ pathways, consistent with viability-specific, tolerance-associated host response programs. Integrating the screen with DrugBank identified 174 druggable host genes corresponding to 345 candidate compounds. Together, these findings provide a systematic resource of host factors influencing H1N1 infection, improve understanding of influenza virus–host interactions, and offer a foundation for future development of host-directed antiviral strategies and drug repurposing efforts. Full article

Iguanodectes geisleri and I. adujai are freshwater fish from South America. Their taxonomic status and phylogenetic relationships are uncertain due to limited molecular data. High-throughput sequencing was applied to obtain and annotate for the first time the complete mitochondrial genomes of I. geisleri and I. adujai to clarify their phylogenetic positions. Mitochondrial genome sequences of 73 Characoidei species were retrieved from GenBank, with Gyrinocheilus aymonieri and Microphysogobio alticorpus designated as outgroups. Phylogenetic trees were constructed using a mitochondrial protein-coding gene dataset and Maximum Likelihood and Bayesian Inference methods. The complete mitochondrial genome measured 16,774 and 16,802 bp, respectively. Both genomes exhibited highly conserved structures. Despite morphological similarities and a close phylogenetic relationship, differences were detected in genomic structure, base composition, codon usage bias, and the control region between the two species. The two species comprise a strongly supported monophyletic clade and are sister species but represent distinct, independent branches. I. geisleri and I. adujai have been recognized as distinct species based on morphological differences, and this study provides molecular confirmation of their separate taxonomic status. The study provides molecular data for the taxonomic identification of fishes of the genus, Iguanodectes, and foundational mitochondrial genomic data for Characiformes. The study advances research on the genetic evolution of this group and resource conservation. Full article

Background: Isotomidae is one of the most common Collembola families, comprising 1484 species belonging to four subfamilies: Isotominae, Proisotominae, Anurophorinae, and Pachyotominae, while the subfamilial classification remains contentious and lack of molecular phylogenetic evidence. Methods: We sequenced and assembled the mitochondrial genomes (mitogenomes) of three species (Parisotoma sp., Folsomia sp. 1, and Folsomia sp. 2. Combining these with 10 mitogenomes available from GenBank, we reconstructed the phylogeny of Isotomidae based on a dataset of 13 species representing all four subfamilies. Results: These new mitogenomes, with lengths of 15,741 bp, 16,295 bp, and 16,765 bp, respectively, exhibit the typical metazoan gene set (13 PCGs, 22 tRNAs, 2 rRNAs) and show high structural conservation with other Collembola species. However, phylogenetic analyses based on concatenated protein-coding genes revealed significant incongruence with traditional classification. While Isotomidae was recovered as monophyletic, both Isotominae and Anurophorinae were recovered as paraphyletic. Specifically, Parisotoma sp. formed a distinct lineage closer to the derived subfamilies than to the core Isotominae, and the representative of Pachyotominae (Paranurophorus simplex) was recovered nested within Anurophorinae, suggesting potential subfamilial misclassification or paraphyly. Furthermore, Proisotoma minuta was identified as an independent sister lineage to the Anurophorinae + Pachyotominae clade. Conclusions: Our findings suggest that the current subfamily boundaries are not natural and that key diagnostic traits, such as furcal structure, likely reflect symplesiomorphies or various forms of homoplasy-including convergent evolution, parallelism, and evolutionary reversals—rather than unique synapomorphies defining monophyletic groups. This study provides essential genomic resources and highlights the need for an integrative taxonomic revision of Isotomidae that incorporates both molecular and morphological data, with particular emphasis on redefining subfamilies boundaries and reassessing diagnostic morphological traits. Full article

Rapid isolation of therapeutic bacteriophages from environmental sources is essential for personalized phage therapy, particularly when appropriate phages are unavailable in existing banks. However, comprehensive characterization of all candidate phages is resource-intensive, especially when plaque morphologies are similar and fail to discriminate between distinct phages. Here, we present an upstream screening approach that utilizes co-culture growth curve analysis to rapidly triage phage isolates during the early isolation process. We extracted seven biologically meaningful features that capture lysis kinetics, lysis efficiency, and post-lysis dynamics from bacterial growth curves and applied unsupervised clustering algorithms for phage discrimination. Validation using T-phages at a multiplicity of infection of 0.01 demonstrated superior clustering performance (Adjusted Rand Index = 0.881 ± 0.057) compared to established metrics including the Virulence Index and Centroid Index. Application to phages isolated from sewage successfully identified all three genomically distinct species present (sampling score = 1.0), enabling targeted selection of representative phages for downstream characterization. This approach reduced candidates requiring detailed analysis by two-thirds (from 21 to 7 isolates) while maintaining complete species coverage, thereby providing an efficient and scalable screening tool that reduces workload for downstream analyses and accelerates discovery of novel therapeutic phages for clinical applications. Full article

In an era of global warming, sustainable agriculture, which emphasises the conservation of biodiversity and the rational use of natural resources, is growing in importance. One of the key elements is to increase the genetic diversity of crops through the use of crop wild relatives (CWRs) and local varieties, which provide a source of genes for resistance to biotic and abiotic stresses. Modern agricultural systems are characterised by low biodiversity, which increases the susceptibility of plants to diseases and pests. Growing mixtures of varieties, both intra- and interspecific, is a practical strategy to increase plant resistance, stabilise yields and reduce pathogen pressure. This manuscript has a review character and synthesises the current literature on the use of CWRs, local varieties, and variety mixtures in sustainable agriculture. The main research question of the study is to what extent plant genetic resources, including CWRs and local varieties, as well as the cultivation of variety mixtures, can promote plant resistance, stabilise yields and contribute to sustainable agriculture under climate change. The objectives of the study are to assess the role of genetic resources and variety mixtures in maintaining biodiversity and yield stability, and to analyse the potential of CWRs and local varieties in enhancing plant resistance. Additionally, the study investigates the impact of variety mixtures in reducing disease and pest development, and identifies barriers to the use of genetic resources in breeding along with strategies to overcome them. The study takes an interdisciplinary approach including literature and gene bank data analysis (in situ and ex situ), field trials of cultivar mixtures under different environmental conditions, genetic and molecular analysis of CWRs, the use of modern genome editing techniques (CRISPR/Cas9) and assessment of ecological mechanisms of mixed crops such as barrier effect, and induced resistance and complementarity. In addition, the study considers collaboration with participatory and evolutionary breeding programmes (EPBs/PPBs) to adapt local varieties to specific environmental conditions. The results of the study indicate that the integration of plant genetic resources with the practice of cultivating variety mixtures creates a synergistic model that enhances plant resilience and stabilises yields. This approach also promotes agroecosystem conservation, contributing to sustainable agriculture under climate change. Full article

Each year, hundreds of female koalas are presented to koala hospitals suffering from a range of morbidities, many of which require euthanasia for animal welfare reasons. These koalas represent a possible resource for genetic recovery by means of oocyte retrieval for genome banking or use in assisted reproductive technology. To examine the feasibility of koala oocyte recovery, this study conducted a preliminary survey of follicular activity and disease presence in fixed ovarian tissues from koala cadavers in South East Queensland. Ovarian activity and pathology were assessed by gross examination and histology. Bursal pathology was categorized into koalas with no, small (<10 mm diameter), moderate (10–20 mm diameter), or large (>20 mm diameter) sized bursae, whereas uterine pathology was diagnosed by an experienced reproductive pathologist. Antral follicles were observed in 94.4% of ovaries recovered from koalas with no bursal or uterine pathology (n = 18/44), 95.2% of the ovaries of koalas with bursal but no uterine pathology (n = 11/44), 100% of the ovaries of koalas showing only uterine pathology (n = 4/4) and 89.5% of ovaries from koalas with both bursal and uterine pathology (n = 11/44). Of the fixed ovarian tissue suitable for PCR Chlamydia detection (35/44), none were positive. As proof of concept, oocytes were also collected and evaluated from six koala cadavers within 2 h post-mortem. Although further studies are required to determine the quality and viability of the retrieved koala oocytes, our preliminary survey provides strong evidence that ovarian activity mostly continues unabated, irrespective of reproductive pathology, and that oocytes can be recovered successfully. Full article

The tumour suppressor protein p53 plays a central role in safeguarding genomic integrity through the regulation of DNA repair, cell cycle arrest, and apoptosis. Mutations in TP53, particularly within its DNA-binding domain, are among the most frequent genetic alterations in human cancers and are strongly associated with chemoresistance and poor prognosis. In this study, all TP53 mutations reported in the COSMIC database were systematically mapped onto all experimentally resolved TP53 three-dimensional structures available in the Protein Data Bank, supplemented with AlphaFold-predicted models to achieve full structural coverage. Mutations were classified according to their structural context—protein core, interface regions, ligand- and zinc-binding sites, and intrinsically disordered regions—and evaluated using complementary sequence- and structure-based predictive tools. The analysis revealed distinct mutational hotspots, differential distribution across structural regions, and context-dependent effects on stability and DNA-binding capacity. Notably, a subset of mutations exhibited consistent predictions of high destabilisation across all structural contexts, underscoring their potential as drivers of functional inactivation. By providing a comprehensive structural map of TP53 alterations, this work offers a valuable resource for understanding mutation-specific mechanisms of p53 dysfunction and for guiding the development of precision therapeutic strategies aimed at restoring its tumour-suppressive functions. Full article

Germplasm resources embody the genetic diversity of plants and form the foundation for breeding and the ongoing improvement of elite cultivars. The establishment of germplasm banks, along with their systematic evaluation, constitutes a critical step toward the conservation, sustainable use, and innovative utilization of these resources. Liriodendron, a rare and endangered tree genus with species distributed in both East Asia and North America, holds considerable ecological, ornamental, and economic significance. However, a standardized evaluation system for Liriodendron germplasm remains unavailable. In this study, 297 Liriodendron germplasm accessions were comprehensively evaluated using 34 phenotypic traits and whole-genome resequencing data. Substantial variation was observed in most phenotypic traits, with significant correlations identified among several characteristics. Cluster analysis based on phenotypic data grouped the accessions into three distinct clusters, each exhibiting unique distribution patterns. This classification was further supported by principal component analysis (PCA), which effectively captured the underlying variation among accessions. These phenotypic groupings demonstrated high consistency with subsequent population structure analysis based on SNP markers (K = 3). Notably, several key traits exhibited significant divergence (p < 0.05) among distinct genetic clusters, thereby validating the coordinated association between phenotypic variation and molecular markers. Genetic diversity and population structure were assessed using 4204 high-quality single-nucleotide polymorphism (SNP) markers obtained through stringent filtering. The results indicated that the Liriodendron sino-americanum displayed the highest genetic diversity, with an expected heterozygosity (He) of 0.18 and a polymorphic information content (PIC) of 0.14. In addition, both hierarchical clustering and PCA revealed clear population differentiation among the accessions. Association analysis between three phenotypic traits (DBH, annual height increment, and branch number) and SNPs identified 25 highly significant SNP loci (p < 0.01). Of particular interest, the branch number-associated locus SNP_17_69375264 (p = 1.03 × 10⁻⁵) demonstrated the strongest association, highlighting distinct genetic regulation patterns among different growth traits. A minimal set of 13 core SNP markers was subsequently used to construct unique DNA fingerprints for all 297 accessions. In conclusion, this study systematically characterized phenotypic traits in Liriodendron, identified high-quality and core SNPs, and established correlations between key phenotypic and molecular markers. These achievements enabled differential analysis and genetic diversity assessment of Liriodendron germplasm, along with the construction of DNA fingerprint profiles. The results provide crucial theoretical basis and technical support for germplasm conservation, accurate identification, and utilization of Liriodendron resources, while offering significant practical value for variety selection, reproduction and commercial applications of this species. Full article

This study describes the first complete chloroplast genome of Ranunculus cf. penicillatus and provides new insights into the genetic composition and evolutionary relationships of the Ranunculus genus. The genome was assembled and characterized using high-throughput sequencing technologies, revealing a circular structure encompassing 158,313 base pairs. Comparative analysis with the chloroplast genomes of related species within the Ranunculus genus highlights notable variations in structural organization, which can elucidate potential adaptive evolutionary mechanisms. Phylogenetic analyses conducted using the maximum likelihood approach resulted in the placement of Ranunculus cf. penicillatus within a well-defined clade, revealing its relationship with other taxa. This study not only enriches the existing plastid genomic data of the genus Ranunculus but also serves as an additional resource for future studies on the phylogenetics, systematics, and conservation biology of this diverse group of aquatic plants. The findings highlight the importance of complete chloroplast genomes in the Ranunculus section Batrachium, an evolutionarily young group of aquatic plants, for understanding plant diversity and evolution. The genome can be accessed on GenBank with the accession number PV690257. Full article

This study presents the first complete mitochondrial genome characterization of Elops machnata (Teleostei: Elopiformes: Elopidae), a basal teleost lineage critical for understanding early actinopterygian evolution. The assembled mitogenome, deposited under GenBank accession number PV294982, spans 16,712 bp and exhibits the canonical vertebrate mitochondrial gene organization, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Base composition analysis revealed 22.71% A, 17.36% C, 29.82% T, and 30.11% G, with a slight AT bias (A + T = 52.53%). Codon usage analysis of the 13 protein-coding genes identified CUA (L), CGA (R), GCC (A), and GGA (G) as the most frequent codons, with a pronounced preference for adenine at the third codon position. Amino acid composition analysis across 23 Elopomorpha species revealed consistently high leucine contents, and tRNA secondary structure prediction showed 21 tRNAs forming typical cloverleaf structures, except for trnS1(gct), which lacks the dihydrouridine (DHU) arm. Phylogenetic reconstruction using maximum likelihood and Bayesian inference methods, based on concatenated mitochondrial protein-coding genes from 23 Elopomorpha species, placed E. machnata in a well-supported clade with Elops hawaiensis, confirming their close evolutionary relationship. This study not only provides essential genomic resources for E. machnata but also resolves key gaps in the mitochondrial genome and improves phylogenetic understanding of Elopomorpha. Full article

Considering the taxonomic uncertainties of Neotropical deer species, as well as the threat status of many of them, new studies and strategies for their maintenance are urgently needed. Obtaining live cells is of great importance for the conservation of wild species in order to allow cytogenetic and molecular studies to be carried out and for the construction of genomic resource banks. In order to increase the genetic diversity stored in these banks, the possibility of collecting skin fragments from dead animals (e.g., run over, hunted, deaths related to disease or natural causes) becomes a valuable source and a last alternative for obtaining material from these individuals. However, the interval between the death of the animal and the collection of tissue can directly interfere with the quality of the sample obtained and it is therefore essential to identify the maximum time during which viable cells are still found. Thus, this study sought to establish a protocol for the collection, storage, cryopreservation, and cultivation of skin obtained postmortem from individuals of the species Subulo gouazoubira (gray brocket deer) and Mazama rufa (red brocket deer). The collection of tissue fragments at different postmortem intervals (0 h, 1 h, 2 h, 3 h, 4 h, 5 h, 6 h, 7 h, 8 h, 9 h, 10 h, and 11 h) was evaluated. The tissues were analyzed for fibroblast cell viability immediately after collection. Their ability to undergo cryopreservation was evaluated based on techniques that can be directly applied to samples obtained in the field and their subsequent thawing and success of cell cultures was performed in the laboratory. Regarding the genetic integrity of the cells, the number of metaphases was observed by the mitotic index. The cell viability presented by the samples always remained above 60%. It was possible to establish cell cultures even with the tissues obtained 11 h after the death of the individuals; however, they required twice as many days to reach bottle confluence compared to the cultures performed with the tissues obtained 0 h after the death of the individuals. The results suggest that the best rates of cell viability, time to reach confluence, and number of metaphases per cell (mitotic index) are found in skin fragments collected up to 5 h after the death of individuals when their carcasses are kept at room temperature. Full article