The evaluation of large experimental datasets is a fundamental aspect of research in every scientific field. Streamlining this process can improve the reliability of results while making data analysis more efficient and faster to execute. In biomedical research it is often very important to determine the type of cell death after various treatments. Thus, differentiating between viable, apoptotic, and necrotic cells provide critical insights into the treatment efficacy, a key aspect in the field of drug development. Fluorescent microscopy is perceived as a widely used technique for cell metabolism assessment and can therefore be used to investigate treatment outcomes after staining samples with cell death detection kit. However, accurate evaluation of therapeutic results requires quantitative analysis, often necessitating extensive postprocessing of imaging data. In this study, we introduce a complementary tool designed as a macro for the Fiji platform, enabling the automated postprocessing of fluorescent microscopy images to accurately distinguish and quantify viable, apoptotic, and necrotic cells.

• MeSH
• apoptóza MeSH
• buněčná smrt MeSH
• fluorescenční mikroskopie * metody   MeSH
• lidé MeSH
• nekróza MeSH
• počítačové zpracování obrazu * metody   MeSH
• software MeSH
• viabilita buněk MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Quantitative genomic mapping of DNA damage may provide insights into the underlying mechanisms of damage and repair. Sequencing based approaches are bound to the limitations of PCR amplification bias and read length which hamper both the accurate quantitation of damage events and the ability to map them to structurally complex genomic regions. Optical Genome mapping in arrays of parallel nanochannels allows physical extension and genetic profiling of millions of long genomic DNA fragments, and has matured to clinical utility for characterization of complex structural aberrations in cancer genomes. Here we present a new mapping modality, Repair-Assisted Damage Detection - Optical Genome Mapping (RADD-OGM), a method for single-molecule level mapping of DNA damage on a genome-wide scale. Leveraging ultra-long reads to assemble the complex structure of a sarcoma cell-line genome, we mapped the genomic distribution of oxidative DNA damage, identifying regions more susceptible to DNA oxidation. We also investigated DNA repair by allowing cells to repair chemically induced DNA damage, pinpointing locations of concentrated repair activity, and highlighting variations in repair efficiency. Our results showcase the potential of the method for toxicogenomic studies, mapping the effect of DNA damaging agents such as drugs and radiation, as well as following specific DNA repair pathways by selective induction of DNA damage. The facile integration with optical genome mapping enables performing such analyses even in highly rearranged genomes such as those common in many cancers, a challenging task for sequencing-based approaches.

• MeSH
• bromičnany toxicita   MeSH
• lidé MeSH
• mapování chromozomů * přístrojové vybavení   metody   MeSH
• mikrofluidní analytické techniky * přístrojové vybavení   metody   MeSH
• nádorové buněčné linie MeSH
• nanotechnologie * přístrojové vybavení   metody   MeSH
• oprava DNA genetika   MeSH
• oxidační stres účinky léků   genetika   MeSH
• poškození DNA * genetika   MeSH
• regulace genové exprese MeSH
• stanovení celkové genové exprese MeSH
• toxikogenetika * přístrojové vybavení   metody   MeSH
• variabilita počtu kopií segmentů DNA MeSH
• zobrazení jednotlivé molekuly * přístrojové vybavení   metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

This study aimed to establish a rat model of chronic wounds to observe the effects of hyperbaric oxygen (HBO) on chronic wound repair and pyroptosis and explore the potential role of pyroptosis in the pathogenesis of chronic wounds. Sprague-Dawley (SD) rats were randomly divided into acute wound group (control group), chronic wound group (model group), chronic wound + HBO treatment group (HBO group), and chronic wound + VX-765 (IL-converting enzyme/Caspase-1 inhibitor) treatment group (VX-765 group). After 7 days of respective interventions, the wound healing status was observed, and wound tissue specimens were collected. Hematoxylin and eosin (HE) staining was used to observe the pathological changes in wound tissues. Transmission electron microscopy was used to observe the changes in cellular ultrastructure. Immunofluorescence was used to observe the expression and localization of vascular endothelial growth factor A (VEGF-A) and the N-terminal domain of gasdermin D (GSDMD-N). Western blot was conducted to detect the expression of nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3), cysteine-requiring aspartate protease-1 (Caspase-1), VEGF-A, and GSDMD-N proteins in wound tissues. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the expression of NLRP3, Caspase-1, and GSDMD genes. Enzyme-linked immunosorbent assay (ELISA) was performed to observe the expression of the inflammatory cytokines interleukin-1 beta (IL-1beta) and IL-18. The results showed that the HBO group had a faster wound healing rate and better pathology improvement compared to the model group. The expression level of VEGF-A was higher in the HBO group compared to the model group, while the expression levels of NLRP3, Caspase-1, GSDMD, IL-1beta, and IL-18 were lower than those in the model group. HBO can effectively promote the healing of chronic wounds, and the regulation of pyroptosis may be one of its mechanisms of action. Keywords: Hyperbaric oxygen, Pyroptosis, Chronic wounds, Inflammatory.

• MeSH
• chronická nemoc MeSH
• gasderminy MeSH
• hojení ran * fyziologie   MeSH
• hyperbarická oxygenace * metody   MeSH
• krysa rodu rattus MeSH
• potkani Sprague-Dawley * MeSH
• protein NLRP3 metabolismus   MeSH
• proteiny vázající fosfáty metabolismus   MeSH
• pyroptóza * fyziologie   MeSH
• vaskulární endoteliální růstový faktor A metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Activation of nuclear factor-kappa B (NF-κB) signalling is key in the pathogenesis of chronic kidney disease (CKD). However, a certain level of NF-κB activity is necessary to enable tissue repair. METHODS: The relationship between activated and inactivated NF-κB signaling and the pathogenesis of CKD was investigated using mouse models of NF-κB partial inactivation (mutating cysteine at position 59 of the sixth exon on the NF-κB gene into alanine) and activation (mutating cysteine at position 59 of the sixth exon on the NF-κB gene into serine). RESULTS: The density of CD3, CD8, CD68 positive cells, as well as the expression of interleukin 6, Tumor necrosis factor receptor associated factor 1 and Nef-associated factor 1 in the kidney tissues of NF-κBC59A mice were reduced, whereas an opposing pattern was observed in the NF-κBC59S mice. Blood pressure, kidney fibrosis (analyzed by periodic acid-Schiff, Masson trichrome and Sirius Red staining, as well as α-SMA immunofluorescence), serum creatinine and urinary albumin-to-creatinine ratio are markedly increased in NF-κB-activated and -inactivated mice compared with controls. Transmission electron microscopy indicated that the glomerular basement membrane was thicker in both NF-κBC59A and NF-κBC59S mice compared with wild-type mice. CONCLUSIONS: Using mice models with partially activated and inactivated NF-κB pathways suggests that there is an apparently U-shaped relationship between blood pressure, kidney function as well as morphology and the activation of the NF-κB pathway. A certain optimal activity of the NF-κB pathway seems to be important to maintain optimal kidney function and morphology.

• MeSH
• chronická renální insuficience metabolismus   patologie   etiologie   MeSH
• fibróza MeSH
• hypertenze * metabolismus   etiologie   MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• modely nemocí na zvířatech MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• NF-kappa B * metabolismus   MeSH
• signální transdukce * MeSH
• western blotting MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

The application of pulsed electric fields (PEFs) is becoming a promising tool for application in biotechnology, and the food industry. However, real-time monitoring of the efficiency of PEF treatment conditions is challenging, especially at the industrial scale and in continuous production conditions. To overcome this challenge, we have developed a straightforward setup capable of real-time detection of yeast biological autoluminescence (BAL) during pulsing. Saccharomyces cerevisiae culture was exposed to 8 pulses of 100 μs width with electric field strength magnitude 2-7 kV cm-1. To assess the sensitivity of our method in detecting yeast electroporation, we conducted a comparison with established methods including impedance measurements, propidium iodide uptake, cell growth assay, and fluorescence microscopy. Our results demonstrate that yeast electroporation can be instantaneously monitored during pulsing, making it highly suitable for industrial applications. Furthermore, the simplicity of our setup facilitates its integration into continuous liquid flow systems. Additionally, we have established quantitative indicators based on a thorough statistical analysis of the data that can be implemented through a dedicated machine interface, providing efficiency indicators for analysis.

• MeSH
• elektroporace * metody   MeSH
• Saccharomyces cerevisiae * růst a vývoj   MeSH
• Publikační typ
• časopisecké články MeSH

Remodeling of a microvascular network is common part of pathological changes associated with wide spectrum of diseases. Quantitative analysis of these alterations relies often on analysis of a point-pattern on the histological slide, i.e. on sections through the microvascular network only. Common techniques are based on the estimation of the average density of points representing section through microvessels on the histological image. This approach inherently omits the information about the regularity of the pattern. Thus, we used approach based on the Voronoi segmentation and chose the best statistical model of areas of Voronoi cells surrounding microvessels on 20 samples of human myocardium. The best model is based on the log-normal distribution. Parameters of the model for given data can be estimated as a mean and a standard deviation of logarithms of areas of Voronoi cells. Moreover, these parameters can be transformed to the widely used measure called the microvascular density.

• MeSH
• histologické techniky MeSH
• kardiovaskulární nemoci MeSH
• lidé MeSH
• mikrocévy anatomie a histologie   MeSH
• mikroskopie metody   MeSH
• myokard * ultrastruktura   MeSH
• počítačové zpracování obrazu metody   MeSH
• remodelace cév MeSH
• rozpoznávání automatizované MeSH
• Check Tag
• lidé MeSH

We present two cases from the neonatal department with cerebrospinal fluid examination. We revealed a striking discrepancy in polymorphonuclear (PMN) and mononuclear (MN) cell counts using conventional light microscopy in comparison with automated analyzer Sysmex XN-1000 (PMNs - 13 vs. 173x106/L, MNs - 200 vs. 67x106/L in case 1 and PMNs - 13 vs. 372x106/L, MNs - 411 vs. 179x106/L in case 2). We revealed the dominant presence of hemosiderophages in both cases in cytospin slide. Even though Sysmex XN-1000 offers fast examination with a low sample volume, there is possibility of misdiagnosis, with negative impact on the patient.

• MeSH
• leukocyty mononukleární patologie   cytologie   MeSH
• lidé MeSH
• mikroskopie * metody   MeSH
• mozkomíšní mok cytologie   MeSH
• neutrofily cytologie   patologie   MeSH
• novorozenec MeSH
• počet leukocytů MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• kazuistiky MeSH
• srovnávací studie MeSH

Biofilm formation by the pathogenic bacteria generates a serious threat to the public health as it can increase the virulence potential, resistance to drugs, and escape from the host immune response mechanisms. Among the environmental factors that influence the biofilm formation, there are only limited reports available on the role of antimicrobial agents. During the antimicrobial drug administration or application for any purpose, the microbial population can expect to get exposed to the sub-minimum inhibitory concentration (sub-MIC) of the drug which will have an unprecedented impact on microbial responses. Hence, the study has been conducted to investigate the effects of sub-MIC levels of zinc oxide nanoparticles (ZnO NPs) on the biofilm formation of Klebsiella pneumoniae and Staphylococcus aureus. Here, the selected bacteria were primarily screened for the biofilm formation by using the Congo red agar method, and their susceptibility to ZnO NPs was also evaluated. Quantitative difference in biofilm formation by the selected organisms in the presence of ZnO NPs at the sub-MIC level was further carried out by using the microtiter plate-crystal violet assay. Further, the samples were subjected to atomic force microscopy (AFM) analysis to evaluate the properties and pattern of the biofilm modulated under the experimental conditions used. From these, the organisms treated with sub-MIC levels of ZnO NPs were found to have enhanced biofilm formation when compared with the untreated sample. Also, no microbial growth could be observed for the samples treated with the minimum inhibitory concentration (MIC) of ZnO NPs. The results observed in the study provide key insights into the impact of nanomaterials on clinically important microorganisms which demands critical thinking on the antimicrobial use of nanomaterials.

• MeSH
• antibakteriální látky * farmakologie   MeSH
• biofilmy * účinky léků   růst a vývoj   MeSH
• Klebsiella pneumoniae * účinky léků   fyziologie   růst a vývoj   MeSH
• kovové nanočástice chemie   MeSH
• mikrobiální testy citlivosti * MeSH
• mikroskopie atomárních sil MeSH
• nanočástice chemie   MeSH
• oxid zinečnatý * farmakologie   chemie   MeSH
• Staphylococcus aureus * účinky léků   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH

The unicellular parasite Leishmania has a precisely defined cell architecture that is inherited by each subsequent generation, requiring a highly coordinated pattern of duplication and segregation of organelles and cytoskeletal structures. A framework of nuclear division and morphological changes is known from light microscopy, yet this has limited resolution and the intrinsic organisation of organelles within the cell body and their manner of duplication and inheritance is unknown. Using volume electron microscopy approaches, we have produced three-dimensional reconstructions of different promastigote cell cycle stages to give a spatial and quantitative overview of organelle positioning, division and inheritance. The first morphological indications seen in our dataset that a new cell cycle had begun were the assembly of a new flagellum, the duplication of the contractile vacuole and the increase in volume of the nucleus and kinetoplast. We showed that the progression of the cytokinesis furrow created a specific pattern of membrane indentations, while our analysis of sub-pellicular microtubule organisation indicated that there is likely a preferred site of new microtubule insertion. The daughter cells retained these indentations in their cell body for a period post-abscission. By comparing cultured and sand fly derived promastigotes, we found an increase in the number and overall volume of lipid droplets in the promastigotes from the sand fly, reflecting a change in their metabolism to ensure transmissibility to the mammalian host. Our insights into the cell cycle mechanics of Leishmania will support future molecular cell biology analyses of these parasites.

• MeSH
• buněčné dělení MeSH
• buněčný cyklus MeSH
• Leishmania mexicana * genetika   MeSH
• Leishmania * MeSH
• paraziti * MeSH
• Psychodidae * parazitologie   MeSH
• savci MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Testing the hemocompatibility of medical devices after their interaction with blood entails the need to evaluate the activation of blood elements and the degree of their coagulation and adhesion to the device surface. One possible way to achieve this is to use scanning electron microscopy (SEM). The aim was to develop a novel SEM-based method to assess the thrombogenic potential of medical devices and their adhesiveness to blood cells. As a part of this task, also find a convenient procedure of efficient and non-destructive sample fixation for SEM while reducing the use of highly toxic substances and shortening the fixation time. A polymeric surgical mesh was exposed to blood so that blood elements adhered to its surface. Such prepared samples were then chemically fixed for a subsequent SEM measurement; a number of fixation procedures were tested to find the optimal one. The fixation results were evaluated from SEM images, and the degree of blood elements' adhesion was determined from the images using ImageJ software. The best fixation was achieved with the May-Grünwald solution, which is less toxic than chemicals traditionally used. Moreover, manipulation with highly toxic osmium tetroxide can be avoided in the proposed procedure. A convenient methodology for SEM image analysis has been developed too, enabling to quantitatively evaluate the interaction of blood with the surfaces of various medical devices. Our method replaces the subjective assessment of surface coverage with a better-defined procedure, thus offering more precise and reliable results.

• MeSH
• histologické techniky * MeSH
• mikroskopie elektronová rastrovací MeSH
• oxid osmičelý * MeSH
• Publikační typ
• časopisecké články MeSH