Search Results (4,179)

This review aims to provide a broad, multidisciplinary perspective on how dynamic genomics and systems biology are transforming modern healthcare, with a focus on cancer especially liver cancer (HCC). It explains how integrating multi-omics technologies such as genomics, transcriptomics, proteomics, interactomics, metabolomics, and spatial transcriptomics deepens our understanding of the complex tumor environment. These innovations enable precise patient stratification based on molecular, spatial, and functional tumor characteristics, allowing for personalized treatment plans. Emphasizing the role of regulatory networks and cell-specific pathways, the review shows how mapping these networks using multi-omics data can predict resistance, identify therapeutic targets, and aid in the development of targeted therapies. The approach shifts from standard, uniform treatments to flexible, real-time strategies guided by technologies such as liquid biopsies and wearable biosensors. A case study showcases the benefits of personalized therapy, which integrates epigenetic modifications, checkpoint inhibitors, and ongoing multi-omics monitoring in a patient with HCC. Future innovations, such as cloud-based genomic ecosystems, federated learning for privacy, and AI-driven data analysis, are also discussed to enhance decision-making and outcomes. The review underscores a move toward predictive and preventive healthcare by integrating layered data into clinical workflows. It reviews ongoing clinical trials using advanced molecular and immunological techniques for HCC. Overall, it promotes a systemic, technological, and spatial approach to cancer treatment, emphasizing the importance of experimental, biochemical–functional, and biophysical data-driven insights in personalizing medicine. Full article

The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their “generally recognized as safe” (GRAS) status remains challenging. Here, we have subjected the annotated draft genome sequences of four human skin-derived bacterial strains, namely Bacillus subtilis MBF10-19J, Micrococcus luteus MBF05-19J, Staphylococcus hominis MBF12-19J, and Staphylococcus warneri MBF02-19J, to bioinformatic analyses to detect the genes associated with important probiotic traits, as well as undesirable characteristics such as antibiotic resistance, virulence factors, and toxic metabolites. Each bacterium harbors at least one type of adhesin-encoding gene, while only S. hominis MBF12-19J and S. warneri MBF02-19J contain the putative genes encoding enzymes for metabolism improvement. In vitro assays, including antibiotic susceptibility and antimicrobial activity testing, revealed strain-specific safety characteristics that complement the genomic findings. With regard to antibiotic resistance determinants, S. hominis MBF12-19J showed the most favorable profile, S. warneri MBF02-19J and M. luteus MBF05-19J appeared suitable when used with appropriate caution, and B. subtilis MBF10-19J exhibited amoxicillin resistance, i.e., warrants careful evaluation. Further in vivo validation is needed to determine whether these strains do indeed comply with GRAS evaluation frameworks. Full article

Animal-derived E. faecium poses a public health risk due to its capacity to acquire antimicrobial resistance (AMR) and virulence genes. However, the pathogenicity and cross-host transmission potential of strains originating from unique environments, such as the Qinghai–Tibet Plateau, remain poorly understood. In this study, a strain of E. faecium was isolated from yak feces. We constructed a phylogenetic tree and identified AMR and virulence genes via whole-genome sequencing. Antimicrobial susceptibility testing was performed to determine its resistance phenotype. An in vivo mouse infection model was established to assess pathogenicity, and transcriptomic analysis was utilized to investigate the host’s molecular response mechanisms in infected intestinal tissue. The results indicated that this yak-derived strain is closely related to human clinical isolates, suggesting a risk of cross-host transmission. The strain harbored the AMR genes AAC(6′)-Ii, msrC, and eatAv and exhibited resistance to penicillin, kanamycin, erythromycin, and clindamycin. The strain harbored key virulence genes, such as bopD, Acm, and ClpP. Infection with this strain caused characteristic inflammatory damage in mouse intestinal tissue, as revealed by histopathological examination, including epithelial necrosis, vascular congestion, and inflammatory cell infiltration. Transcriptomics further delineated a complete “Recognition–Response–Damage” signaling axis: pathogen recognition through Toll-like receptors and NOD-like receptors activates the NF-κB and MAPK signaling pathways. This activation is accompanied by significant upregulation of various inflammatory factors and recruits immune cells via chemokine signaling, ultimately leading to tissue damage. Our findings provide insights into the pathogenic pathway of this strain from genetic determinants to phenotypic manifestations, providing a theoretical foundation for assessing the public health risk posed by animal-derived E. faecium and for developing targeted intervention strategies. Full article

The huge number of possible permutations of genes, proteins and small molecules make the random emergence of cellular networks problematic. How, therefore, do interactomes come into existence? What selects for their stability and functionality? I hypothesize that interactomes originate from molecularly complementary modules (MCMs) that are selected for stability and retain their interactivity when mixed and matched with other such modules to create novel molecules and complexes displaying emergent properties not present in the individual components of the network. Because evolution can only proceed by working upon existing variants, and these variants emerge from selection of MCMs, the resulting systems must exhibit the characteristics of pleiofunctional, epistatic interactomes (PEIs). The resulting systems should display “molecular paleontology”, providing clues as to the historical process by which these MCMs were incorporated into the system. The MCM mechanism of PEI evolution is illustrated here by two case studies. The first concerns the prebiotic emergence of the glutathione–ascorbate anti-oxidant system and its later incorporation into regulation of glucose transport and catecholamine receptor activity. The second concerns the MCM evolution of the ribosome as, perhaps, the first PEI, and its role as a module for the later construction of the first cellular genomes. Full article

Background: Multimodal AI integration across genomics, radiomics, and pathomics is rapidly evolving in oncology, but evidence remains heterogeneous and unevenly distributed across modalities. Objective: To map empirical studies integrating two or more -omic modalities, summarize integration and validation approaches, and identify gaps informing future directions toward surgomics. Methods: We conducted a scoping review in accordance with PRISMA-ScR, searching PubMed, Ovid, Wiley Online Library, and Google Scholar for English-language studies published from January 2020 to 5 March 2025. We charted study characteristics, modalities combined, fusion strategies, AI model categories, validation approaches, and reported performance metrics as presented by the original studies. Results: From 184 records, 11 studies met inclusion criteria (n = 1078 total participants across reported studies), most focusing on radiomics–pathomics integration; fewer incorporated genomics, and tri-modal fusion was uncommon. Studies varied widely in clinical tasks, endpoints, preprocessing, and validation, limiting direct comparability. Conclusions: The mapped evidence indicates growing methodological activity in radiopathomics and cross-scale association modeling, while tri-modal pipelines and clinically deployable multimodal workflows remain underdeveloped. Surgomics is presented as a conceptual, staged roadmap informed by these gaps rather than a current clinical capability. Full article

Background. Eriobotrya seguinii (Lév.) Cardot ex Guillaumin (Rosaceae, Maleae) is native to China and inhabits various altitudes within the subtropical biome of the Yunnan-Guizhou Plateau. The complexity of the plant mitogenome has impeded a systematic description of this species, leading to a limited understanding of its evolutionary position. Methods. In this study, we constructed, annotated, characterized, and compared the complete E. seguinii mitogenome with previously reported Eriobotrya japonica. Results. The E. seguinii mitogenome exhibited a typical circular architecture, spanning 372,899 bp in length, with a GC content of 46%, making it the smallest and highest GC content of any known Eriobotrya species. It encodes 71 unique genes, comprising 47 protein-coding genes, 20 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The genome contains rich repetitive sequences, with mononucleotides, A/T bias, and forward and palindromic repeats being the most prevalent. The predominant codons were GCU (Ala) and UAU (Tyr), with frequencies of 1.54 and 1.53, respectively. Thirteen genes (atp9, atp6, atp1, rps14, sdh4, sdh3, rps12, rnaseH, nad1, nad6, nad7, rpl16, and mttB) demonstrated high Pi values, ranging from 0.84 to 1. The evolutionary lineage of E. seguinii was explored using mitogenome data from 19 genera within the Rosaceae family, revealing that Eriobotrya species are monophyletic and closely related to E. japonica (MN481990). Conclusions. Understanding the mitogenome characteristics of E. seguinii enhances our understanding of its genesis and classification based on mitochondrial genome data. This study provides additional evidence for future research on the evolutionary relationships among species in the Rosaceae family. Full article

Sphaerodactylidae play a crucial role in ecosystems, possessing significant ecological, scientific, and conservation value. They contribute to pest control and the maintenance of ecological balance, and also provide abundant materials for research in evolutionary biology and biodiversity. To refine the phylogenetic position of Teratoscincus scincus within the Sphaerodactylidae using mitogenomic data, this study sequenced the complete mitochondrial genome of T. scincus using the Illumina NovaSeq Xplus platform, and subsequently performed assembly, annotation, and analysis. The phylogenetic relationships of T. scincus within the Sphaerodactylidae were analyzed using 13 protein-coding genes (PCGs) from the mitochondrial genome via Bayesian inference (BI) and maximum likelihood (ML) methods. The complete mitochondrial genome of T. scincus is 16,943 bp in length and consists of 13 PCGs, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The base composition shows a distinct AT preference, with the highest A + T content (56.3%) found in the PCGs region. A phylogenetic tree was constructed based on the amino acid sequences of 13 PCGs from the mitochondrial genomes of nine Sphaerodactylidae species retrieved from GenBank and the newly sequenced T. scincus generated in this study. The results confirm that T. scincus belongs to the genus Teratoscincus within the family Sphaerodactylidae. Phylogenetic analysis reveals that T. scincus and Teratoscincus keyserlingii cluster into a monophyletic group, suggesting a close phylogenetic relationship. Additionally, the phylogenetic tree provides new molecular evidence for understanding the formation mechanism of Sphaerodactylidae diversity. This study not only enriches the mitochondrial genome database of Sphaerodactylidae but also lays an important foundation for subsequent research on the adaptive evolution and conservation biology of T. scincus. Full article

Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism. Full article

(1) Background: Listeria monocytogenes (Lm) is recognized by the World Health Organization (WHO) as one of the four principal foodborne pathogens. This study aimed to investigate the molecular characteristics of Lm isolates from Jiaxing, China, using whole-genome sequencing (WGS) to enhance our understanding of their molecular epidemiology. (2) Methods: A total of 39 foodborne Lm isolates and 7 clinical Lm isolates were analyzed via WGS to identify resistance genes, virulence factors, lineage, sequence type (ST), and clonal complex (CC). Antibiotic susceptibility was assessed using Minimum Inhibitory Concentration (MIC) testing, and serotypes were confirmed via multiplex PCR. (3) Results: We found that 39 food isolates were mainly lineage II (66.67%), with 13 STs; ST8 was the dominant ST, and 2 new types, ST3210 and ST3405, were found. Among the seven clinical isolates, lineage I was dominant (57.14%), and ST87 was the dominant ST. Serotype 1/2a was dominant, accounting for 54.35%, followed by 1/2b, which accounted for 36.96%. The overall antimicrobial resistance rate was 13.04%, with a multidrug resistance rate of 2.17%. All strains harbored LIPI-1 and LIPI-2, and five strains carried LIPI-3 genes: one strain belonged to ST619 of lineage I, two strains belonged to ST224 of lineage I, and two strains belonged to ST11 of lineage II. (4) Conclusions: This study clarified the genotype and serotype characteristics of Listeria monocytogenes in Jiaxing, as well as their molecular characteristics relating to drug resistance and virulence, thus providing a technical basis for improving exposure risk assessment of Listeria monocytogenes. Continuous monitoring, prevention, and control are recommended to further improve regional public health and safety. Full article

Genome-wide association studies (GWAS) are essential for identifying genomic regions associated with agronomic traits, but Linear Mixed Model (LMM)-based GWAS face challenges in capturing complex gene interactions. This study explores the potential of machine learning (ML) methodologies to enhance marker identification and association modeling in plant breeding. Unlike LMM-based GWAS, ML approaches do not require prior assumptions about marker–phenotype relationships, enabling the detection of epistatic effects and non-linear interactions. The research sought to assess and contrast approaches utilizing ML (Decision Tree—DT; Bagging—BA; Random Forest—RF; Boosting—BO; and Multivariate Adaptive Regression Splines—MARS) and LMM-based GWAS. A simulated F₂ population comprising 1000 individuals was analyzed using 4010 SNP markers and ten traits modeled with epistatic interactions. The simulation included quantitative trait loci (QTL) counts varying between 8 and 240, with heritability levels set at 0.5 and 0.8. These characteristics simulate traits of candidate crops that represent a diverse range of agronomic species, including major cereal crops (e.g., maize and wheat) as well as leguminous crops (e.g., soybean), such as yield, with moderate heritability and a high number of QTLs, and plant height, with high heritability and an average number of QTLs, among others. To validate the simulation findings, the methodologies were further applied to a real Coffea arabica population (n = 195) to identify genomic regions associated with yield, a complex polygenic trait. Results demonstrated a fundamental trade-off between sensitivity and precision. Specifically, for the most complex trait evaluated (240 QTLs under epistatic control), Ensemble methods (Bagging and Random Forest) maintained a Detection Power (DP) exceeding 90%, significantly outperforming state-of-the-art GWAS methods (FarmCPU), which dropped to approximately 30%, and traditional Linear Mixed Models, which failed to detect signals (0%). However, this sensitivity resulted in lower precision for ensembles. In contrast, MARS (Degree 1) and BLINK achieved exceptional Specificity (>99%) and Precision (>90%), effectively minimizing false positives. The real data analysis corroborated these trends: while standard GWAS models failed to detect significant associations, the ML framework successfully prioritized consensus genomic regions harboring functional candidates, such as SWEET sugar transporters and NAC transcription factors. In conclusion, ML Ensembles are recommended for broad exploratory screening to recover missing heritability, while MARS and BLINK are the most effective methods for precise candidate gene validation. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of public health concern, requiring a One Health approach to clarify its transmission and distribution. However, its prevalence and genomic characteristics in livestock and companion animals remain underexplored in low-income countries. We investigated prevalence and genomic features of STEC in animals in western Ghana, representing the first genomic report of STEC in Ghana. Fecal samples (97) were collected from goats (n = 33), sheep (n = 33), dogs (n = 30), and a cat (n = 1), with STEC detected in 12.1% of goats and sheep samples. Whole-genome sequencing identified serotypes O38:H26, O43:H2, and O157:H7. stx1c and stx2b genes were detected in O38:H26 and O43:H2, whereas stx2c and key virulence genes (chuA, eae, esp, nle, tir, and toxB) were exclusively found in O157:H7. Phylogenetic analysis revealed that O38:H26 isolates form a cluster closely related to clinical strains from the UK. O43:H2 isolates exhibited diverse stx profiles, linking animal, environmental, and clinical strains from North America and the UK. O157:H7 isolates were genetically similar to European clinical and food-derived strains, suggesting that goats and sheep are important STEC reservoirs in Ghana, offering data for public health risk assessment and effective One Health-based control strategies. Full article

Background: KMT2A partial tandem duplication (PTD) occurs in approximately 5–10% of acute myeloid leukemia (AML) cases and is associated with poor prognosis. While its cytogenetic and molecular features are well described, the immunophenotypic characteristics of AML with KMT2A-PTD remain incompletely defined. Methods: We identified 47 cases of AML with KMT2A-PTD by optical genome mapping. All cases underwent flow cytometric immunophenotypic analysis and next-generation sequencing using an 81-gene panel. Results: The cohort included 32 men and 15 women with a median age of 67 years (range, 19–87). Thirty-eight cases were de novo AML, and nine were secondary to myelodysplastic syndrome and/or myeloproliferative neoplasm. Most cases (93%) demonstrated a normal or non-complex karyotype. The most frequent mutations involved FLT3-ITD (47%), DNMT3A (43%), and RUNX1 (23%). Thirty-one cases (66%) were granulocytic, while 16 (34%) showed granulocytic and/or monocytic differentiation. Blasts uniformly expressed HLA-DR and frequently expressed CD117 (91%) and CD34 (79%). Increased expression of CD123 (74%) and CD117 (43%) and decreased expression of HLA-DR (74%) and CD38 (69%) were common. Aberrant CD25 expression was observed in 51% of cases. Increased CD123 and aberrant CD25 expression were significantly associated with FLT3-ITD mutations (both p < 0.0001) but not with other recurrent mutations. There was no correlation between FLT3-ITD mutation and expression levels of CD117, CD38 or HLA-DR (all p > 0.05). Conclusions: AML with KMT2A-PTD shows distinctive immunophenotypic features with increased CD123 and aberrant CD25 expression, both associated with FLT3-ITD. These markers may have diagnostic and therapeutic relevance in this AML subtype. Full article

Choy sum (Brassica rapa var. parachinensis) is an important vegetable crop in Brassicaceae. However, its mitochondrial genome has not been well studied. In this study, Illumina and Nanopore sequencing technologies were combined to assemble the complete mitochondrial genome of choy sum. The mitochondrial genome is a circular molecule of 219,775 bp, with a GC content of 45.23%. A total of 60 genes were annotated, including 33 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and one pseudogene. A total of 466 RNA editing sites were identified in the PCGs. Codon usage analysis revealed that leucine (leu) was the most frequently used amino acid. Twenty-nine codons showed a relative synonymous codon usage (RSCU) value greater than 1. Most of these preferred codons ended with A or U. A total of 308 repetitive sequences were detected, including 136 dispersed repeats, 17 tandem repeats, and 55 simple sequence repeats (SSRs). Evolutionary analysis indicated that most mitochondrial genes are under negative selection. The highest nucleotide diversity detected in the cox2 gene suggests that this gene could serve as a valuable molecular marker for mitochondrial research in the species. Homology analysis found 22 homologous fragments between the mitochondrial and chloroplast genomes of choy sum. These fragments total 13,325 bp, representing 6.06% of the mitochondrial genome. Phylogenetic analysis showed that choy sum is most closely related to B. rapa var. purpuraria. This study offers a genomic resource for genetic improvement and breeding of choy sum. It also provides molecular insights into the evolution of Brassica species. Full article

Bifidobacterium animalis subsp. lactis is a widely used probiotic, yet its efficacy is highly strain-specific, and growing antibiotic resistance necessitates rigorous safety evaluations. We used whole-genome sequencing and in vitro assays to characterize the safety and probiotic traits of infant feces-sourced strain BD1, which shows preliminary mood-modulating and anti-inflammatory potential. The BD1 genome showed a favorable safety profile. VFDB analysis identified 139 low-similarity homologs, with no major toxins detected. Only four chromosomally encoded antibiotic resistance genes were found; phenotypic testing confirmed resistance solely to tetracycline and mupirocin. Although the tetracycline resistance gene tet(W) was identified in genomic island GI01, the absence of associated mobile genetic elements results in a negligible risk of its mobilization. Functional annotation highlighted a dominant metabolic capacity for carbohydrate and amino acid metabolism. BD1 is rich in CAZymes, enabling superior utilization of diverse substrates (starch, sucrose, galactose). Enrichment in lipid metabolism pathways (glycerolipid, sphingolipid) further suggests potential for enhancing fermented product flavor. In vitro assessment demonstrated moderate gastrointestinal tolerance and strong bile salt tolerance. Surface properties showed pronounced cell surface hydrophobicity and confirmed biofilm-forming potential. In conclusion, BD1 exhibits robust safety, metabolic versatility, and strong probiotic characteristics, supporting its development as a functional probiotic strain. Full article