Biology and Life Sciences

Abstract: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is widely employed in pesticide residue analysis. Machine learning methods for automated spectral interpretation depend on large, well-curated training datasets; however, publicly available pesticide mass spectrometry data are fragmented across heterogeneous repositories, lack standardized preprocessing, and suffer from incomplete metadata. We introduce PAID (Pesticide AI-ready Dataset), comprising two curated LC-MS/MS spectral collections derived from 15 public sources (GNPS, MassIVE, MoNA, MassBank). Starting from 91,420 raw spectra, after initial pesticide-directed screening, a seven-step reproducible pipeline—spanning multi-source integration, spectral cleaning, deduplication, metadata standardization, quality scoring, stratified splitting, and feature engineering—yields PAID-Strict (7,527 spectra; 3,197 compounds) and PAID-Extended (21,292 spectra; 3,224 compounds). Both versions cover eight pesticide categories across QTOF and Orbitrap platforms, with core metadata fields (SMILES, InChIKey, molecular formula) exceeding 98% completeness. A feature suite of 32 chemoinformatic descriptors, 2,214 molecular fingerprints, and 30 spectral features is provided alongside the spectra. Benchmark classification of the eight pesticide categories using XGBoost and LightGBM achieved 81.5% accuracy. The dataset, code, and pre-computed features are publicly available under CC BY 4.0 and MIT licenses (DOI: 10.57760/sciencedb.35414).

Abstract: Chickpea (Cicer arietinum) is an economically important pulse crop around the world, including Pakistan. However, its productivity per hectare is limited due to Fusarium wilt, which is caused by Fusarium oxysporum f. sp. ciceris (Foc) and poor farming practices. This study examined the ability of two Trichoderma spp. and one bacterial strain, Bacillus subtilis, to combat Foc and their effects on disease control and chickpea growth. The antagonistic activity was examined using a dual culture assay. Pot and field experiments were conducted to study disease severity, growth characteristics, and yield performance. Confocal laser scanning microscopy and rhizoscanning were carried to study root colonization and morphology. Dual culture assay showed 69% growth inhibition of Foc by both Trichoderma spp. The pot experiments revealed significant growth improvements and defense-related enzymes. Microscopy confirmed effective root colonization and suppression of pathogen structures along chickpea roots. Rhizoscanning revealed better root morphological characteristics. In field experiments involving susceptible (Bittle 98) and resistant (Pb2008) chickpea cultivars in both wilt sick and healthy soils, 90% reduction in disease incidence and an increase in grain yield was observed. Overall, Trichoderma species showed more effective performance than the bacterial treatment for managing Fusarium wilt. These fungal biocontrol agents could be applied in Pakistan for sustainably improving chickpea growth and yield.

Abstract: Colorectal cancer represents a global health burden, being the third most fre-quently diagnosed cancer worldwide, counting about 1.9 million new cases annually, and the second leading cause of cancer-related deaths, counting over 900,000 deaths per year. These figures highlight the urgent need for innovative and non-invasive methods for early detection to improve current diagnostic approaches. In this study, two nanostructured chemoresistive gas sensors based on tin oxide–titanium oxide compo-sites were selected to detect the metabolic patterns associated with human healthy and colorectal cancer tissues. As an additional validation of the biopsy-derived results, the sensors were tested on two colorectal cancer-derived cell lines, namely Caco-2 and RKO. Both sensors demonstrated a clear ability to discriminate between healthy and cancerous samples, with discrimination powers of 11% and 8%, respectively. These results were further confirmed by principal component analysis (PCA), which showed a reasonable separation between healthy and cancerous samples in both the PC1–PC2 and PC1–PC3 score plots and a hierarchical clustering approach for cell samples. While these sensors cannot identify the specific metabolites associated with cancerous tissue, they outlined a characteristic volatile fingerprint of the samples, enabling reliable dis-crimination between healthy and tumor samples.

Abstract: Amanita muscaria is one of the most recognizable toxic mushrooms, yet its chemical and toxicological variability remains insufficiently understood. Its principal neuroactive isoxazole compounds, ibotenic acid and muscimol, differ substantially in pharmacological profile: ibotenic acid is associated mainly with glutamatergic excitatory activity, whereas muscimol is a potent GABAergic compound. Because ibotenic acid can be converted to muscimol through decarboxylation, the ibotenic acid–muscimol ratio may represent a dynamic marker of chemical phenotype rather than a fixed species-level trait. This review proposes a neuroecological model in which environmental and post-harvest stressors influence the biosynthesis, stability, and transformation of ibotenic acid and muscimol in A. muscaria. Abiotic factors such as temperature, drought, soil chemistry, nitrogen availability, and xenochemical exposure, as well as biotic factors including microbial interactions, host-tree physiology, developmental stage, and fungivory, may contribute to variation in fungal secondary metabolism. Post-harvest conditions such as drying, heating, cooking, extraction, and storage may further modify the ibotenic acid–muscimol ratio. This chemical variability may influence neurotoxicological outcome by shifting the balance between excitatory and inhibitory effects after human or animal exposure. The review integrates fungal stress biology, analytical toxicology, neuropharmacology, clinical toxicology, veterinary exposure, and public health concerns related to emerging A. muscaria products. Current evidence supports developmental variability, pro-cessing-related chemical transformation, and the need for standardized analytical quantification, but direct controlled studies linking specific environmental stressors to ibotenic acid biosynthesis remain limited. The proposed model identifies the ibotenic acid–muscimol ratio as a testable mechanistic marker connecting environmental stress in A. muscaria with variable neurotoxicological risk.

Abstract: Circular RNAs (circRNAs) have recently emerged as a class of abundant and remarkably stable non-coding RNAs preferentially enriched in the nervous system. In neurons, the fine-tuned spatial regulation of gene expression is critical for proper synaptic function; accordingly, several studies have demonstrated that circRNAs exhibit highly compartmentalized localization, specifically within dendrites, axons, and synapses. These spatial localization properties imply the presence of active transport mechanisms which control the intracellular trafficking of circRNAs. This review highlights current understanding of circRNA transport in neurons, focusing on molecular machinery driving synaptic enrichment. We specifically address the role of Ribonucleoprotein-based transport as a primary mechanism driving circRNA localization and examine how this spatial distribution influences synaptic plasticity and post-transcriptional gene regulation. Finally, we discuss the clinical implications of these processes, exploring the link between dysregulated RNA transport and the development of neuronal abnormalities.

Abstract: Commercial manufacturing of prebiotics relies on diverse processing steps tailored to the raw material and finished product. Commercial manufacturing operations are distinct from processes suggested in the research literature, accounting for scalability, cost and environmental metrics, and process reproducibility. Common prebiotic production processes involve extraction, hydrolysis using enzymes, acids or hot water, synthesis, condensation polymerization and precision fermentation. Crude extracts are purified using ion exchange, activated carbon, and membrane separation processes to remove impurities and produce prebiotic oligosaccharides with the targeted composition and degree of polymerization. Purified extracts are often concentrated using evaporation systems and may be dried or crystallized to produce a dry finished product. Though not an all encompassing list of prebiotics, detailed descriptions of processes for the production of some of the more common prebiotics, including acacia, fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), human milk oligosaccharides (HMOs), inulin, mannan-oligosaccharides (MOS), certain types of resistant starch (RS), xylo-oligosaccharides (XOS), and arabinoxylan oligosaccharides (AXOS) are provided in this manuscript, along with descriptions of commercial scale unit operations that may be applied more generally to newer compounds being investigated for their prebiotic properties. The unique attributes of each type of prebiotic and prebiotic formulation, particularly the degree of polymerization and chemical structure, are strongly controlled by the processes employed in their manufacture. Strategic selection of enzymes (or hydrolysis processes in general), fermentation systems, and extraction systems/solvents will influence the product composition and degree of polymerization, leading to a diverse array of products. Regulatory requirements and quality control systems employed during manufacturing of prebiotics ensure that finished products are safe and effective for consumers, delivering the expected health and physiological benefits.

Abstract: Medical implants are artificial devices or prostheses surgically inserted into the human body to treat/monitor health conditions, support, augment, or replace biological structures to restore normal bodily functions. Despite their significant contributions to healthcare advancement and quality of life improvement, medical implants encounter substantial challenges and limitations. Chief among these is microbial colonization, proliferation, and subsequent biofilm formation; which can precipitate into medical implant-associated infections (MIAIs) and implant failure, ultimately leading to serious inevitable complications and compromised patient health. Initially, MIAIs were attributed to only limited types of bacterial species (predominantly Staphylococcus spp., Streptococcus spp., P. aeruginosa, and E. coli), however, recent investigations have unveiled a broad spectrum of microbial involvement, extending from a multitude of other bacterial groups to numerous cross-kingdom species, including fungi (such as Candida spp., Aspergillus spp., Cryptococcus spp., and Penicillium spp.), along with few archean species. This review extensively categorizes the whole diversity of biofilm-mediating microbes (including bacteria, fungi & archaeal) that have been identified and implicated with the contamination and infections of various types of medical implants so far. Furthermore, it also presents the latest innovative novel approaches to combat these microbial biofilms in a revolutionary way because the traditional method of utilizing antibiotics for the treatment of microbial biofilms on medical implants faces several limitations; notably antibiotic resistance, cytotoxicity of normal host cells, and versatile morphology of cross-kingdom microbes.

Abstract: Floral yeasts are generally recognized to exhibit high metabolic activities. We isolated 437 yeast strains from 45 flower samples collected from the Beijing Olympic Forest Park, a unique urban ecosystem harbouring diverse plants, which facilitated a thorough survey of floral yeast diversity. Based on sequence analysis of the D1/D2 domain of the large subunit ribosomal RNA gene (LSU rRNA) and the internal transcribed spacer region (ITS), these strains were assigned to more than 70 species, with Starmerella bombicola, Kwoniella ovata and Aureobasidium pini being the dominant taxa. Ten representative strains were characterized comprehensively and identified as two novel genera and four novel species. Integrating molecular data, genome information and phenotypic/physiological traits, the 10 novel yeast strains were described as six novel yeast taxa, including two novel species of two novel genera, Fanglaniella lipolytica gen. nov. sp. nov., and Polychromogenomyces tardus gen. nov. sp. nov., and four novel species as Pseudotremella jasmini sp. nov., Teunia pruni sp. nov., Kurtzmanomyces yulaniae sp. nov., and Trigonosporomyces otomorphus sp. nov. Furthermore, enzyme activity tests confirmed lipase production in all six novel species, and their corresponding lipase-related genes were identified. Our findings highlight the high diversity and potent lipase activity of floral yeasts, suggesting their great potential for microbial manufacturing.

Abstract: Tomato is a highly perishable climacteric fruit that experiences substantial post-harvest losses under ambient tropical conditions. This study evaluated the effectiveness of garlic (Garlic) and ginger (Ginger) extracts in extending tomato shelf-life during storage. Tomatoes at breaker stage were treated with 10% garlic extract or 10% ginger extract, while untreated fruits served as controls. Treated fruits were stored at 25 ± 2°C and 60 ± 5% relative humidity for 14 days in a completely randomized design with three replicates. Microbial load, physiological weight loss, spoilage incidence, total soluble solids, and titratable acidity were evaluated. Ginger-treated fruits showed the greatest numerical reduction in microbial load (93%), although differences among treatments were not significant (p > 0.05). Garlic-treated tomatoes recorded significantly lower physiological weight loss (3.34%) than control (15.3%) and ginger-treated fruits (23.3%) after 14 days of storage. Spoilage incidence was also lowest in garlic-treated fruits (7.1%). Total soluble solids increased, while titratable acidity decreased across all treatments, indicating normal ripening progression. Overall, garlic extract was more effective in maintaining post-harvest quality and extending shelf life under ambient storage conditions. The findings demonstrate the potential of garlic-based coatings as low-cost and environmentally friendly alternatives for reducing post-harvest tomato losses in resource-limited settings.

Abstract: The global proliferation of microplastics demands sustainable remediation alternatives to energy-intensive conventional methods, shifting research focus toward polymer-degrading microbial communities within the „Plastisphere“. This work elucidates microplastic colonization dynamics, evaluates next-generation biochemical strategies to overcome polyolefin crystallinity, and presents an AI-managed hybrid engineering framework that couples Advanced Oxidation Processes with Membrane Bioreactors. Empirically, the polyolefin-degrading efficacy of a newly isolated strain, Hafnia paralvei UUNT_MP29, was documented over a 16-day biotic exposure period, and a universal four-pillar Biodegradability Index (BI) was developed to standardize tracking of polymer degradation. Microplastic colonization initiated with a „Phase Zero“ conditioning film that modulated Zeta potential to anchor pioneer r-strategists. Biotic exposure to H. paralvei UUNT_MP29 yielded a Carbonyl Index of 0.4594 and a 10.95 °C reduction in thermal stability ΔT_max). Ultimately, the integrated bioprocess configuration successfully accelerates stoichiometric mineralization while mitigating additive-mediated toxicity. This comprehensive framework successfully bridges fundamental microbial ecology and scalable engineering, providing a vital blueprint for transitioning from passive waste containment to a restorative circular bio-economy.

Abstract: Background With the advancement of sequencing technologies and increasing quality of assembly and annotation tools, the amount of biological sequence data produced by research grows rapidly. To keep this data accessible for potential re-analysis, it is typically stored in public online databases, such as the European Nucleotide Archive (ENA). However, the increase in data entails an increase in time needed for metadata curation and upload. We propose a tool to simplify and automatize the upload of experimental and metadata to public repositories. Results We developed ENflorA, a set of scripts by which sample, sequence read and (annotated) assembly data can be uploaded to ENA in a simple and standardized manner. Our software allows easy metadata entry via spreadsheets, is suitable for batch upload of data from different sources, and can be fully integrated in bioinformatic workflows. It is platform independent and can be run natively on High Performance Computers, integrates an lftp upload option for big files and a test upload option. Conclusions By easing the ENA submission process, ENflorA contributes to making high-throughput sequencing data findable, accessible, interoperable and reusable.

Abstract: Bioanalytical methods to quantitate conjugated payloads are essential for assessing antibody-drug conjugate (ADC) stability and pharmacokinetics (PK). Dual-payload ADCs present analytical challenges; different linker chemistries can require complex digestion conditions and to perform the cleavage. Developing separate methods for each linker combination can be time and resource demanding. Rat tritosomes—purified lysosomal fractions from Triton-treated rat liver—provide a comprehensive enzymatic mixture that mimics the lysosomal environment. The presented bioanalytical method combines immunoaffinity purification with tritosome-mediated digestion for simultaneous quantitation of dual conjugated payloads. The method was applied to a model dual-payload ADC containing two different cytotoxic payloads, conjugated using different enzymatically cleavable linkers, with not related Dar (drug-to-antibody-ratio). Method validation in mouse plasma demonstrated excellent accuracy (bias ± 20%, LLOQ and ULOQ ± 25%) and precision (coefficient of variation CV% ≤ 20%, LLOQ and ULOQ ± 25%) across all concentration levels (lower to upper limit of quantitation ,LLOQ to ULOQ) for both payloads, with 100% of quality control samples (QCs) meeting acceptance criteria for hybrid LC-MS/MS quantitation methods. This tritosome-based approach provides a unified, efficient platform for multi-payload ADC bioanalysis, eliminates linker-specific method optimization and enables robust support for preclinical studies. The method has been tested for accuracy and precision on 4 different model ADCs and employed to quantify the conjugated payloads in in-vivo samples from a homozygous hFcRn transgenic mouse model (Tg32) PK study, resulting in reliable data in accordance with total antibody measurements.

Abstract: In breast cancer, current knowledge of the associations between clinicopathologic characteristics, genetic changes, and subtype-specific patterns remain unclear. This research investigated how pathological and clinical variables affect the actionability of NGS-based tumor molecular data. Materials and methods: 227 breast cancer patients referred to Genekor’s laboratory for tumor molecular profile analysis were included in the study. Pathology records, available in all cases, were used to assess critical clinicopathological features including HER2, ER, PR, Ki67, grade, metastatic site, and age. A 1021 gene NGS-based multigene panel was utilized to assess tumors’ biology alongside tumor mutational burden (TMB) and microsatellite instability (MSI) Results: Comprehensive genomic profiling revealed that 95.6% of the patients harbored at least one oncogenic or likely oncogenic alteration, highlighting the high diagnostic yield of NGS-based testing. Distinct subtype-specific patterns were observed: HR+/HER2-tumors were enriched for PIK3CA and ESR1 gene alterations, while Triple Negative Breast Cancer (TNBC) was dominated by TP53 alterations. Clinically actionable alterations were most common in HR+/HER2-tumors (~60% on-label), whereas TNBC more often harbored off-label or trial-associated targets. The inclusion of tumor-agnostic biomarkers (TMB/MSI) increased on-label actionability up to 64.5% in ER−/PR+ tumors. primarily driven by TMB-high cases. Median TMB values were low, and age was the only independent predictor. Furthermore, the presence of actionable alterations was significantly higher in metastatic tumors, and TP53 alterations were associated with aggressive tumor characteristics.Conclusions: Comprehensive NGS-based genomic profiling identifies clinically actionable alterations in over half of breast cancer patients, with substantial variability across molecular subtypes. The HR+/HER2-subtype demonstrates the highest prevalence of on-label actionable biomarkers. These findings support the routine implementation of comprehensive genomic profiling, especially in metastatic HER2-negative breast cancer, to guide precision oncology strategies and enable enrollment in biomarker-driven clinical trials.

Abstract: Microorganisms naturally produce many pharmaceutically and industrially relevant secondary metabolites. For this process they usually use biosynthetic units. For example, microbes from the genus Streptomyces possess great ability to produce a variety of natural products in such manner, which is possible due to complicated crosstalk between primary and secondary metabolism. These microbial cell factories produce more than 2/3 of antibiotics used in medicine, and a large variety of other bioactive compounds. Although bacterial producer hosts, including Bacillus spp. and Streptomyces spp., have been studied for decades, the engineering of these bacteria remains challenging, and the genetic potential has not been fully utilized. This is due to limited genetic toolbox, restriction activity and occurrence of silent biosynthetic gene clusters. Recent advancements in genetic manipulation of microorganisms allowed to improve the turnaround time of strain engineering, but still has strain-specific limitations. However, a new perspective offered by synthetic biology to exploit the potential of existing and novel pathways in primary and secondary metabolism allows combining of different biosynthetic steps originating from diverse bacteria using a limited toolbox. Synthetic biology has emerged as a robust strategy to understand, investigate, design, and engineer the biosynthetic capability of bacterial antibiotics machinery, including such in Streptomyces. Innovative synthetic biology and metabolic engineering tools have rapidly accelerated the discovery of new natural products as well as engineering of Streptomyces, e.g. enzymatic modules for secondary metabolite production can be combined in synthetic cells to produce new derivatives of natural products. Furthermore, with the recent advances in molecular biology and genome editing, Synthetic biology has focused at generation of controlled phenotypes from a given input and at other sophisticated approaches. In this review, developments of novel approaches of Synthetic biology for microbial engineering with focus on antibiotics producers like Streptomyces spp. are discussed.

Abstract: Microbial biopolymers produced from low-cost agro-industrial residues represent a promising alternative to persistent petroleum-derived plastics. In this study, the filamentous fungus Acrostalagmus luteoalbus, isolated from the beetle Ulomoides dermestoides, was evaluated for its ability to synthesize extracellular biopolymeric material using waste-derived carbon sources. To the best of our knowledge, no previous reports have described the production of extracellular biopolymers by A. luteoalbus. Biopolymer accumulation at the culture surface was monitored for up to eleven weeks using fruit-derived residues, with sucrose employed as a reference substrate. Substrate-to-product conversion yields showed a strong dependence on carbon source composition, with the highest value obtained using pulp with Crataegus mexicana (tejocote) peel (≈17.10 ± 1.29% at week nine), followed by sucrose-based media. The recovered material was dark brown, brittle, and insoluble in common polar and non-polar solvents, and exhibited a compact, heterogeneous surface morphology under scanning electron microscopy. Elemental (CHNS) analysis indicated a carbon-rich, nitrogen-poor composition, while thermogravimetric and calorimetric analyses revealed multistep thermal degradation with major mass-loss events occurring above 250 °C, consistent with a thermally stable polymeric material. These results demonstrate that A. luteoalbus can convert diverse agro-industrial residues into extracellular biopolymeric material under simple culture conditions. Although the detailed monomeric composition of the material remains to be elucidated, this work provides an initial physicochemical and thermal characterization that expands current knowledge of fungal biopolymer-producing systems and supports further investigation of this species as an alternative microbial platform.

Abstract: Background: Identification of tumor-specific cell surface targets is a critical step in the development of precision oncology therapeutics, including radioligand and antibody-based approaches. However, existing strategies often rely on single-layer analyses and lack systematic integration of proteomic, genomic, and clinical metadata. Methods: We developed a multi-layered proteogenomic filtering framework integrating quantitative proteomics from colorectal cancer (CRC) cohorts with curated metadata on protein localization, normal tissue expression, and drugability. Eleven complementary filtering strategies were applied, followed by manual curation for extracellular accessibility and composite scoring based on protein rank, localization, and clinical relevance. Results: Application of the pipeline to metastatic CRC (mCRC) identified multiple high-confidence candidate targets, including GPRC5A, SLC2A1, CD47, DPEP1 and IFITM1. The average pairwise overlap between filtering strategies was low (0.11), indicating limited redundancy and complementary target identification across approaches. Importantly, candidates detected by multiple strategies were significantly enriched for established biomarkers (FAP, CEACAM5, ITGAV, ITGB4), which were exclusively found among multi-strategy candidates (10.3% vs. 0%; Fisher’s exact test, p = 0.0064), supporting overlap-based prioritization as a marker of biological and translational relevance. Composite scoring further prioritized GPRC5A as a leading candidate. Additional validation layers confirmed tumor-enriched expression, plasma membrane localization, and relevance across multiple cancer indications. Conclusion: This study presents a scalable and generalizable framework for the prioritization of cell surface therapeutic targets in solid tumors. By integrating multiple data layers and incorporating translational criteria early in the discovery process, this approach may facilitate more efficient identification of targets for downstream development, including antibody- and radioligand-based therapies.

Abstract: Shallot (Allium cepa var. aggregatum) is an annual herbaceous plant of the Amaryllidaceae family cultivated worldwide for its gastronomic importance, unique flavor, and nutri-tional properties. In Ecuador, shallot is considered an emerging crop; nevertheless, the lack of effective detection and treatment options for phytoviruses remains a challenge for farmers. These viruses negatively impact crop yield, leading to substantial economic losses and declining crop quality. Simultaneous infections can synergistically exacerbate crop damage. In this study, the molecular detection of the five most common shallot vi-ruses was explored: Shallot latent virus (SLV), Onion yellow dwarf virus (OYDV), Shallot virus X (ShVX), Leek yellow stripe virus (LYSV), and Iris yellow spot virus (IYSV) in shallots from different suppliers of markets in Quito, Ecuador. We identified two viruses using RT-PCR: SLV (latent) and IYSV (responsible for severe disease symptoms). Shoot tip culture produced shallot plants completely free of IYSV, while SLV persisted in the regenerated plants. This study constitutes the first report of IYSV in shallots in the coun-try and shows that shoot tip culture can serve as a partial cleaning method to improve crop quality and support more effective pathogen management and control.

Abstract: Marine pufferfishes are globally distributed and ecologically important organism notable for accumulating tetrodotoxin [TTX], a potent neurotoxin with wide ecological ramifica-tions. Unlike many endogenous defences, TTX in pufferfishes is acquired indirectly via microbial and trophic pathways, linking pufferfish toxicity to the dynamics of marine mi-crobial assemblages and food webs. Anthropogenic climate change principally ocean warming, deoxygenation, and acidification is rapidly reshaping marine environments in ways that are likely to intensify and redistribute TTX exposure. Observational and experimental studies indicate that elevated seawater temperatures favour the proliferation of thermophilic, toxin-producing bacteria [e.g., Vibrio spp.], increase the abundance of toxic prey, and raise TTX burdens in pufferfish tissues seasonally and spatially. Concurrently, warming-driven range shifts have promoted poleward expansions of several tropical and subtropical puffer species, producing novel sympatric assemblages, hybridization events, and “cryptic” toxic phenotypes that complicate species identification and risk assess-ment. These biogeographic rearrangements, together with altered prey communities and microbial composition, reconfigure the trophic pathways by which TTX is transferred and concentrated in higher trophic levels. Early evidence also links multistressor conditions elevated temperature combined with hypoxia or acidification to altered developmental success and changes in toxin allocation during reproduction, suggesting potential popu-lation-level consequences. This review synthesizes current global evidence on cli-mate-linked changes in pufferfish TTX dynamics, integrating microbial ecology, trophic transfer, life-history shifts, and biogeography. We highlight [i] mechanistic pathways by which warming and associated ocean changes increase environmental TTX availability, [ii] how shifting species ranges and hybridization alter toxicity patterns across regions, and [iii] key methodological advances [e.g., high-resolution LC-MS/MS, metagenomics] needed to resolve open questions. We identify critical research gaps long-term field moni-toring, integrated microbial–trophic mapping, and multistressor population studies and recommend synthesis strategies that link environmental monitoring to toxin surveillance. Understanding pufferfish toxification as a climate-sensitive ecological process [not a static species trait] is essential to anticipate how marine toxin landscapes will change in the Anthropocene and to develop timely, science-based monitoring frameworks.

Abstract: Myelodysplastic syndromes are clonal hematopoietic neoplasms in which ineffective hematopoiesis arises within the context of chronic inflammation and immune dysregulation. Growing evidence indicates that aging-associated inflammaging and inflammation-driven remodeling of the bone marrow microenvironment are not secondary phenomena, but active forces that shape clonal selection, lineage commitment, and disease evolution. This narrative review integrates recent insights from translational immunology, stem cell biology, multi-omics analyses, and clinical studies to examine the reciprocal interplay between inflammation and myelodysplastic syndromes pathogenesis. Chronic inflammatory stress imposes selective pressure on hematopoietic stem, favoring the expansion of mutation-bearing clones characteristic of clonal hematopoiesis and overt disease. As inflammation persists, immune dysfunction, together with stromal alterations, progressively reinforce ineffective hematopoiesis and clonal dominance. Genetic lesions, including TP53 and spliceosome mutations, further amplify inflammatory signaling and reshape the marrow niche, conferring clonal fitness and genomic instability. Clinically, readily accessible peripheral blood inflammatory indices reflect these biological processes and correlate with prognosis and therapeutic response. Collectively, these observations position inflammation as a unifying determinant of myelodysplastic syndromes initiation, progression, and treatment sensitivity. Integrating inflammatory signatures with genomic profiling may refine risk stratification and support the development of therapeutic strategies aimed at restoring marrow homeostasis and limiting inflammation-driven clonal evolution.

Abstract: Background: Metabolic syndrome (MeS) is a multifactorial metabolic disorder characterized by obesity, dyslipidemia, insulin resistance, and hypertension, and is strongly associated with an increased risk of cardiovascular diseases (CVDs) and type-2 diabetes mellitus (T2DM)-related complications. Chronic low-grade inflammation and immune dysregulation are increasingly recognized as central contributors to metabolic and cardiovascular pathogenesis. However, the molecular mechanisms linking MeS-related etiologies to coronary artery disease (CAD) remain incompletely understood. The present study aimed to identify shared inflammatory and immuno-metabolic transcriptional signatures associated with MeS and its cardiovascular complications using an integrative bioinformatics approach. Methods: Three publicly available peripheral blood mononuclear cell (PBMC) microarray datasets from the Gene Expression Omnibus (GEO) database, including metabolic syndrome (GSE98895), recent-onset type 1 diabetes (GSE193273), and diabetes mellitus with coronary artery disease (GSE250283), were analyzed using R-based bioinformatics pipelines. Differentially expressed genes (DEGs) were identified using the limma package, followed by Gene Set Enrichment Analysis (GSEA) using MSigDB Gene Ontology Biological Process C5 gene sets. Shared DEGs were subjected to protein-protein interaction (PPI) network construction using STRING and Cytoscape http://www.cytoscape.org/. Hub genes were identified using the CytoHubba MCC algorithm, and associated miRNAs were predicted using miRNet. Functional enrichment analysis of candidate miRNAs was performed using TAM 2.0. Results: GSEA demonstrated prominent enrichment of inflammatory, immune-regulatory, cytokine-mediated, oxidative stress, and metabolic pathways across the datasets. T1D samples exhibited enrichment of interferon-mediated signaling, cytokine responses, and proliferative cellular programs. MeS samples showed activation of adaptive immune responses, leukocyte-mediated immunity, and inflammatory signaling pathways. DMCAD samples demonstrated strong enrichment of inflammatory cytokine production, oxidative phosphorylation, mitochondrial metabolism, reactive oxygen species pathways, and leukocyte activation. Comparative analysis identified 19 shared DEGs between MeS and DMCAD, including CXCL16, CCR1, FPR1, C5AR1, CD86, and TNFRSF21, which formed a significantly interconnected inflammatory interaction network. Functional enrichment analyses revealed enrichment of chemotaxis, complement signaling, immune receptor activity, interferon gamma response, inflammatory response, and IL6-JAK-STAT3 signaling pathways. miRNA interaction analysis identified candidate regulatory miRNAs, including miR-146a-5p, miR-21-5p, miR-155-5p, and members of the miR-17-92 cluster, which were enriched in inflammatory, cardiovascular, and metabolic disease-associated pathways. Conclusions: The present integrative bioinformatics analysis demonstrates that MeS and DMCAD share common inflammatory and immuno-metabolic transcriptional programs characterized by immune activation, cytokine signaling, oxidative stress, and vascular-inflammatory regulatory networks. The identified hub genes and candidate miRNAs may represent potential biomarkers and therapeutic targets associated with inflammation-driven cardiovascular complications in metabolic disorders.