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Circulating extracellular DNA (ecDNA) is known to worsen the outcome of many diseases. ecDNA released from neutrophils during infection or inflammation is present in the form of neutrophil extracellular traps (NETs). It has been shown that higher ecDNA concentration occurs in a number of inflammatory diseases including inflammatory bowel disease (IBD). Enzymes such as peptidyl arginine deiminases (PADs) are crucial for NET formation. We sought to describe the dynamics of ecDNA concentrations and fragmentation, along with NETosis during a mouse model of chemically induced colitis. Plasma ecDNA concentration was highest on day seven of dextran sulfate sodium (DSS) intake and the increase was time-dependent. This increase correlated with the percentage of cells undergoing NETosis and other markers of disease activity. Relative proportion of nuclear ecDNA increased towards more severe colitis; however, absolute amount decreased. In colon explant medium, the highest concentration of ecDNA was on day three of DSS consumption. Early administration of PAD4 inhibitors did not alleviate disease activity, but lowered the ecDNA concentration. These results uncover the biological characteristics of ecDNA in IBD and support the role of ecDNA in intestinal inflammation. The therapeutic intervention aimed at NETs and/or nuclear ecDNA has yet to be fully investigated.

ABSTRACT Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. This study deals with different kinds of techniques applied to monitor two distinct practices of vinification; spontaneous fermentation using native yeasts and fermentation using commercial yeasts as a starter culture.

Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centers with inconsistent versions of installed libraries and bioinformatics tools. Results: We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, metagenomics, and methylation analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. Conclusion: SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. Keywords: Computational pipeline, framework, massively parallel sequencing, reproducibility, virtual environment

Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis , which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).

Glioblastoma, isocitrate dehydrogenase (IDH1/2) wild-type (IDH-wildtype), is one of the most aggressive and malignant tumors of the central nervous system, characterized by rapid growth, pronounced cellular heterogeneity, and an exceptionally poor prognosis. The median survival time for patients with glioblastoma, IDH-wildtype, is approximately 15 months after diagnosis, and current multimodal treatment strategies remain largely ineffective. This review focuses on contemporary pharmacotherapeutic approaches used in the management of glioblastoma, IDH-wildtype, including temozolomide-based chemotherapy, corticosteroids for edema control, and antiangiogenic therapy in recurrent disease, with particular emphasis on their clinical efficacy and limitations. In addition, the review discusses emerging targeted therapeutic strategies developed for IDH-mutant diffuse gliomas, which represent a biologically distinct disease entity. Particular attention is given to ivosidenib, a selective inhibitor of mutant IDH1, currently evaluated for the treatment of astrocytoma, IDH-mutant, grade 4. Its epigenetic mechanism of action, involving inhibition of the oncometabolite 2-hydroxyglutarate (2-HG), is outlined, along with preliminary clinical evidence suggesting potential to delay disease progression. Finally, innovative drug-delivery technologies designed to overcome the blood–brain barrier are briefly discussed as complementary strategies that may enhance the efficacy of both conventional and targeted therapies. Overall, future advances in the treatment of diffuse gliomas will likely depend on the integration of molecularly targeted agents, predictive biomarkers, and advanced delivery platforms aimed at improving patient survival and quality of life.

Drug discovery is a complex and multi-stage process that requires advanced analytical technologies capable of accelerating preclinical evaluation and improving the precision of therapeutic design. The combination of fluorescence and magnetic resonance imaging (MRI) within multimodal imaging plays an increasingly important role in modern pharmacokinetics, integrating the high molecular sensitivity of fluorescence with the non-invasive anatomical visualization offered by MRI. Fluorescence enables real-time monitoring of cellular processes, including drug–target interactions and molecular dynamics, whereas MRI provides detailed structural information on tissues without exposure to ionizing radiation. Hybrid probes—such as superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with near-infrared (NIR) fluorophores or gadolinium-based complexes linked to optical dyes—enable simultaneous acquisition of molecular and anatomical data in a single examination. These multimodal systems are being explored in oncology, neurology, and cardiology, where they support improved visualization of tumor biology, amyloid pathology, and inflammatory processes in vascular disease. Although multimodal imaging shows great promise for enhancing pharmacokinetic and pharmacodynamic studies, several challenges remain, including the potential toxicity of heavy-metal-based contrast agents, limited tissue penetration of fluorescence signals, probe stability in vivo, and the complexity and cost of synthesis. Advances in nanotechnology, particularly biodegradable carriers and manganese-based MRI contrasts, together with the integration of artificial intelligence algorithms, are helping to address these limitations. In the future, fluorescence–MRI hybrid imaging may become an important tool in personalized medicine, supporting more precise therapy planning and reducing the likelihood of clinical failure.

Cetuximab and panitumumab are anti-EGFR monoclonal antibodies widely used for the treatment of colorectal cancers. However, due to various mechanisms of resistance to these targeted therapies, the patients’ responses vary. These resistances remain a major obstacle in treatment and overcoming them has become a key emphasis of current therapeutic strategies. Intrinsic and acquired resistance often lead to reactivation of downstream signaling pathways, mainly the RAS-RAF-MEK-ERK (MAPK pathway) and PI3K-AKT axes. Prior existing mutations in KRAS, NRAS, and BRAF result in primary resistance by constantly activating the signals, irrespective of EGFR inhibition. That said, acquired resistance manifests under therapeutic burden through the process of clonal evolution via KRAS and BRAF alterations, restoring MAPK pathway activity despite EGFR inhibition. In addition to those mutations, tumor cells exploit mechanisms independent of EGFR, such as the pathway bypass, which includes amplification of ERBB family receptors like HER2 (ERBB2) and activation of MET signaling. To overcome these resistances, novel strategies have emerged, which target multiple nodes within the oncogenic networks. Such methods include vertical pathway inhibition, multi-kinase inhibition, liquid-biopsy-guided therapy, and anti-EGFR rechallenge. Reactivation driven by secondary mutation can be prevented by targeting multiple nodes within the MAPK cascade simultaneously, which is referred to as the vertical pathway inhibition. Overall, this review underscores that overcoming therapeutic resistance requires a multidimensional approach that integrates molecular profiling, rational combination therapies, and adaptive treatment. Finally, these advances underscore the shift toward precision oncology, where therapy is tailored to tumor evolution, leading to improved response and patient outcome.

Magnetic resonance techniques have evolved beyond conventional proton-based imaging, enabling access to a broader range of nuclei that provide complementary structural, functional, and molecular information. This review presents a comprehensive overview of multinuclear NMR and MRI in solid and soft materials as well as in biomedical applications, with particular emphasis on 1H, 13C, 31P, 23Na, and 19F nuclei. Proton-based methods remain the foundation of magnetic resonance due to their high sensitivity and widespread applicability, offering insights into molecular mobility, hydration, and microstructural heterogeneity. In contrast, heteronuclear approaches enable more specific characterization of chemical structure (13C), phosphorus-containing functional groups and membranes (31P), ionic homeostasis and transport (23Na), and exogenous tracers with negligible biological background (19F). Together, these techniques extend magnetic resonance from primarily anatomical imaging toward functional, metabolic, and molecular-level analysis. The review further discusses key hardware aspects, including magnetic field strength and radiofrequency coil design, highlighting the trade-offs between low- and high-field systems and the growing importance of multinuclear coil architectures. For example, because 1H, 23Na, 31P, and 19F resonate at different Larmor frequencies, multinuclear experiments require dedicated or multi-tuned RF coils that balance sensitivity, field homogeneity, and decoupling between channels. Mechanisms of contrast generation are examined in detail, distinguishing between endogenous sources—such as water, ions, and metabolites—and exogenous contrast agents, including gadolinium-, manganese-, and fluorine-based compounds, as well as targeted and theranostic platforms. A comparative framework of endogenous and exogenous signals is presented, emphasizing their complementary roles in balancing safety, specificity, and sensitivity. Finally, the opportunities and challenges of multinuclear magnetic resonance are critically evaluated, including limitations in sensitivity, signal-to-noise ratio, data interpretation in heterogeneous systems, and technical complexity. Emerging directions such as ultrahigh-field imaging, advanced RF technologies, hyperpolarization, and artificial intelligence-assisted reconstruction are discussed as key drivers for future development. Overall, multinuclear NMR and MRI represent a powerful and expanding toolbox for probing complex material and biological systems, with the potential to significantly enhance diagnostic capabilities and deepen our understanding of structure–function relationships across multiple scales.

Background/Objectives: Bladder cancer remains one of the most frequently diagnosed malignancies worldwide and is characterized by high recurrence rates requiring long-term surveillance. Conventional white-light cystoscopy (WLC) remains the standard diagnostic method; however, it may fail to detect flat lesions such as carcinoma in situ or small papillary tumors. In recent years, enhanced imaging techniques, including fluorescence cystoscopy and autofluorescence-based systems, have been introduced to improve diagnostic accuracy. The aim of this study is to evaluate the usefulness of fluorescence-based diagnostic techniques and autofluorescence imaging supported by numerical color value (NCV) analysis in the detection and assessment of bladder lesions. Methods: The study was conducted at the Center of Photodynamic Diagnostics and Therapy, Department of Internal Medicine, Angiology and Physical Medicine, Medical University of Silesia in Bytom. Bladder mucosa was assessed using the Onco-LIFE optical imaging system, which enables visualization under both white-light and autofluorescence conditions. The study included 30 patients diagnosed with non-muscle-invasive bladder cancer or suspected bladder lesions, who underwent cystoscopic evaluation using white-light cystoscopy and autofluorescence imaging. From this cohort, three representative cases were selected for detailed qualitative presentation to illustrate different pathological conditions of the bladder mucosa. In selected cases, photodynamic diagnosis (PDD) using intravesical administration of 5-aminolevulinic acid (ALA) was performed prior to cystoscopic examination. Autofluorescence signals were analyzed using red and green fluorescence channels, and tissue characteristics were evaluated using the numerical color value parameter. Results: Representative cases of non-muscle-invasive bladder lesions were analyzed and compared using conventional white-light cystoscopy and autofluorescence imaging. The use of fluorescence-based imaging enabled improved visualization of suspicious mucosal changes compared with standard WLC. Differences in fluorescence patterns were observed between malignant lesions, inflammatory changes, and carcinoma in situ. NCV analysis allowed quantitative assessment of fluorescence signals and supported differentiation of pathological tissue from normal bladder mucosa. Conclusions: Fluorescence cystoscopy and autofluorescence-based imaging systems represent valuable tools for improving the detection of bladder lesions during endoscopic examination. The integration of enhanced optical imaging techniques with quantitative fluorescence analysis may increase diagnostic sensitivity and support targeted biopsy and tumor resection. Continued technological development and clinical experience may further expand the role of fluorescence diagnostics in the early detection and management of bladder cancer.

To evaluate the utility of tumor necrosis factor–related apoptosis–inducing ligand (TRAIL) as a cancer therapeutic, we created leucine zipper (LZ) forms of human (hu) and murine (mu) TRAIL to promote and stabilize the formation of trimers. Both were biologically active, inducing apoptosis of both human and murine target cells in vitro with similar specific activities. In contrast to the fulminant hepatotoxicity of LZ–huCD95L in vivo , administration of either LZ–huTRAIL or LZ–muTRAIL did not seem toxic to normal tissues of mice. Finally, repeated treatments with LZ–huTRAIL actively suppressed growth of the TRAIL–sensitive human mammary adenocarcinoma cell line MDA–231 in CB.17 (SCID) mice, and histologic examination of tumors from SCID mice treated with LZ–huTRAIL demonstrated clear areas of apoptotic necrosis within 9–12 hours of injection.