The selection of proper reference genes and materials is critical in the design of PCR experiments, especially for differential expression studies. In this study, we propose a method to identify robust endogenous control miRNAs in the visceral adipose tissue of C57BL/6J mice with non-alcoholic fatty liver disease induced by alternating Western and control diets. This study outlines a comprehensive methodology for the analysis of microRNA endogenous controls using microfluidic cards in conjunction with miRNA profiling through small RNA sequencing and subsequent validation by quantitative PCR and the RefFinder algorithm. Criteria included were fold change, p-value, reads per million, and gene stability assessment. A set of six putative endogenous microRNAs was identified (miR-331-3p, let-7a-5p, miR-1839-5p, miR-151a-5p, let-7d-5p, and let-7c-5p). Subsequent validation and analysis using the RefFinder algorithm assessed the stability of the selected genes, and a combination of the three most stable endogenous miRNA controls (miR-331-3p, let-7a- 5p, and miR-1839-5p) exhibiting consistent expression patterns with minimal variability was set. Given the absence of universal endogenous controls, individual evaluation of normalizers for each experiment is imperative for accurate miRNA expression measurements. This approach, which combines multiple techniques and assessments, provides a reliable strategy for identifying and validating endogenous controls in miRNA studies.

• MeSH
• algoritmy MeSH
• mikro RNA * genetika   metabolismus   MeSH
• modely nemocí na zvířatech * MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• nealkoholová steatóza jater * genetika   metabolismus   patologie   MeSH
• nitrobřišní tuk * metabolismus   MeSH
• regulace genové exprese MeSH
• stanovení celkové genové exprese metody   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• zvířata 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

Proteomics provides an understanding of biological systems by enabling the detailed study of protein expression profiles, which is crucial for early disease diagnosis. Microfluidic-based proteomics enhances this field by integrating complex proteome analysis into compact and efficient systems. This review focuses on developing microfluidic chip structures for proteomics, covering on-chip sample pretreatment, protein extraction, purification, and identification in recent years. Furthermore, our work aims to inspire researchers to select proper methodologies in designing novel, efficient assays for proteomics applications by analyzing trends and innovations in this field.

• MeSH
• biosenzitivní techniky přístrojové vybavení   metody   MeSH
• design vybavení MeSH
• laboratoř na čipu * MeSH
• lidé MeSH
• mikrofluidika metody   MeSH
• mikrofluidní analytické techniky přístrojové vybavení   MeSH
• proteiny analýza   izolace a purifikace   MeSH
• proteom analýza   izolace a purifikace   chemie   MeSH
• proteomika * metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

This study investigates various microfluidic chip fabrication techniques, highlighting their applicability and limitations in the context of urgent diagnostic needs showcased by the COVID-19 pandemic. Through a detailed examination of methods such as computer numerical control milling of a polymethyl methacrylate, soft lithography for polydimethylsiloxane-based devices, xurography for glass-glass chips, and micromachining-based silicon-glass chips, we analyze each technique's strengths and trade-offs. Hence, we discuss the fabrication complexity and chip thermal properties, such as heating and cooling rates, which are essential features of chip utilization for a polymerase chain reaction. Our comparative analysis reveals critical insights into material challenges, design flexibility, and cost-efficiency, aiming to guide the development of robust and reliable microfluidic devices for healthcare and research. This work underscores the importance of selecting appropriate fabrication methods to optimize device functionality, durability, and production efficiency.

• MeSH
• COVID-19 * virologie   MeSH
• design vybavení MeSH
• dimethylpolysiloxany chemie   MeSH
• laboratoř na čipu * MeSH
• lidé MeSH
• mikrofluidika metody   přístrojové vybavení   MeSH
• mikrofluidní analytické techniky přístrojové vybavení   metody   MeSH
• polymethylmethakrylát chemie   MeSH
• SARS-CoV-2 izolace a purifikace   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH

Distance-based detection (DbD) on paper-based microfluidic analytical devices (μPADs) has emerged as a promising, cost-effective, simple, and instrumentation-free assay method. Broadening the applicability of a new way of immobilization of reagent for DbD on μPADs (DμPADs) is presented, employing an ion exchange (IE) interaction of an anionic metallochromic reagent, 2-(5-bromo-2-pyridylazo)-5-[N-n-propyl-N-(3-sulfopropyl)amino]phenol (5-Br-PAPS), on the anion-exchange filter paper. The IE DμPADs demonstrate superiority over standard cellulose filter paper in terms of the degree of reagent immobilization, detection sensitivity, and clear detection endpoints due to the strong retention of 5-Br-PAPS. The study investigated various parameters influencing DbD, including 5-Br-PAPS concentrations (0.25-1 mM), buffer types (acetic acid-Tris, MES), buffer concentrations (20-500 mM), and auxiliary complexing agents (acetic, formic, and glycolic acids). Subsequently, the performance of 17 metals (Ag+, Cd2+, Co2+, Cr3+, Cu2+, Fe2+, Hg2+, La2+, Mn2+, Ni2+, Pb2+, Ti2+, Zn2+, Al3+, As3+, Fe3+, and V4+) was evaluated, with color formation observed for 12 metals. Additionally, the paper surface was examined using SEM and SEM-EDX to verify the suitability of certain areas in the detection channel for reagent immobilization and metal binding. This method demonstrates quantitation limits of metals in the low μg mL-1 range, showing great potential for the rapid screening of toxic metals commonly found in herbal supplements and cosmetics regulated by the Food and Drug Administration (FDA). Thus, it holds promise for enhancing safety and regulatory compliance in product quality assessment. Furthermore, this method offers a cost-effective, environmentally sustainable, and user-friendly approach for the rapid visual quantification of heavy metals for in-field analysis, eliminating the need for complex instrumentation.

• Publikační typ
• časopisecké články MeSH

The review focuses on the design of detection cells, the use of microcontrollers for processing and evaluation of the detection signal, and the development of multi-detection systems for electromigration, liquid chromatography, flow-through and microfluidic techniques. A separate section is the introduction of modern 3D printing techniques and the use of new printing materials for the design of multidetection systems. In addition to traditional utilisation in separation techniques, new versions of contactless conductivity detectors are finding applications in FIA, SIA, portable and paper based analytical systems or as independent sensors. Applicationwise, C4Ds find new use in gas detection, segmented flow monitoring, as part of point of care devices, and in many other biomedical, environmental, agricultural and industrial applications.

• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

As organoids and organ-on-chip (OoC) systems move toward preclinical and clinical applications, there is an increased need for method validation. Using a liquid chromatography-mass spectrometry (LC-MS)-based approach, we developed a method for measuring small-molecule drugs and metabolites in the cell medium directly sampled from liver organoids/OoC systems. The LC-MS setup was coupled to an automatic filtration and filter flush system with online solid-phase extraction (SPE), allowing for robust and automated sample cleanup/analysis. For the matrix, rich in, e.g., protein, salts, and amino acids, no preinjection sample preparation steps (protein precipitation, SPE, etc.) were necessary. The approach was demonstrated with tolbutamide and its liver metabolite, 4-hydroxytolbutamide (4HT). The method was validated for analysis of cell media of human stem cell-derived liver organoids cultured in static conditions and on a microfluidic platform according to Food and Drug Administration (FDA) guidelines with regards to selectivity, matrix effects, accuracy, precision, etc. The system allows for hundreds of injections without replacing chromatography hardware. In summary, drug/metabolite analysis of organoids/OoCs can be performed robustly with minimal sample preparation.

• MeSH
• chromatografie kapalinová metody   MeSH
• extrakce na pevné fázi MeSH
• hmotnostní spektrometrie metody   MeSH
• játra * metabolismus   MeSH
• kapalinová chromatografie-hmotnostní spektrometrie MeSH
• knihovny malých molekul analýza   metabolismus   chemie   MeSH
• laboratoř na čipu MeSH
• léčivé přípravky metabolismus   analýza   MeSH
• lidé MeSH
• organoidy * metabolismus   cytologie   MeSH
• tolbutamid metabolismus   analýza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH

Early-stage diagnosis of prostatic carcinoma is essential for successful treatment and, thus, significant prognosis improvement. In laboratory practice, the standard non-invasive diagnostic approach is the immunochemical detection of the associated biomarker, prostate-specific antigen (PSA). Ultrasensitive detection of PSA is essential for both diagnostic and recurrence monitoring purposes. To achieve exceptional sensitivity, we have developed a microfluidic device with a flow-through cell for single-molecule analysis using photon-upconversion nanoparticles (UCNPs) as a detection label. For this purpose, magnetic microparticles (MBs) were first optimized for the capture and preconcentration of PSA and then used to implement a bead-based upconversion-linked immunoassay (ULISA) in the microfluidic device. The digital readout based on counting single nanoparticle-labeled PSA molecules on MBs enabled a detection limit of 1.04 pg mL-1 (36 fM) in 50% fetal bovine serum, which is an 11-fold improvement over the respective analog MB-based ULISA. The microfluidic technique conferred several other advantages, such as easy implementation and the potential for achieving high-throughput analysis. Finally, it was proven that the microfluidic setup is suitable for clinical sample analysis, showing a good correlation with a reference electrochemiluminescence assay (recovery rates between 97% and 105%).

• MeSH
• imunoanalýza přístrojové vybavení   metody   MeSH
• lidé MeSH
• limita detekce MeSH
• mikrofluidní analytické techniky přístrojové vybavení   MeSH
• nádory prostaty diagnóza   krev   MeSH
• nanočástice chemie   MeSH
• prostatický specifický antigen * analýza   krev   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Despite the significant health risks associated with Dermanyssus gallinae infestations in humans, they are often overlooked. This study investigated a household case of D. gallinae infestation and explored the resulting clinical manifestations and risk of infection in family members. Microfluidic PCR was employed for high-throughput screening of pathogens in collected mites and blood samples from both chickens and family members. Morphological and molecular examinations confirmed the identity of the mites as D. gallinae sensu stricto (s.s.), with evidence indicating recent blood feeding. Results indicated that the mites exclusively harbored various pathogens, including Bartonella spp., Ehrlichia spp., Apicomplexa, and Theileria spp. Blood samples from family members and poultry tested negative for these pathogens, suggesting a potential reservoir role for D. gallinae. The study further identified haplotypes of D. gallinae, classifying them into D. gallinae s.s., cosmopolitan haplogroup A. Serological analysis revealed elevated IgE seroreactivity against mite proteins in the family member with bite lesions. Antibodies against Bartonella spp. were detected in this individual, indicating exposure to the pathogen. In summary, this study sheds light on the clinical manifestations, pathogen detection, and genetic characterization of D. gallinae infestations, underscoring the necessity of adopting comprehensive approaches to manage such infestations effectively.

• Publikační typ
• časopisecké články MeSH

Persistent infection with high-risk types of human papillomaviruses (HPV) is a major cause of cervical cancer, and an important factor in other malignancies, for example, head and neck cancer. Despite recent progress in screening and vaccination, the incidence and mortality are still relatively high, especially in low-income countries. The mortality and financial burden associated with the treatment could be decreased if a simple, rapid, and inexpensive technology for HPV testing becomes available, targeting individuals for further monitoring with increased risk of developing cancer. Commercial HPV tests available in the market are often relatively expensive, time-consuming, and require sophisticated instrumentation, which limits their more widespread utilization. To address these challenges, novel technologies are being implemented also for HPV diagnostics that include for example, isothermal amplification techniques, lateral flow assays, CRISPR-Cas-based systems, as well as microfluidics, paperfluidics and lab-on-a-chip devices, ideal for point-of-care testing in decentralized settings. In this review, we first evaluate current commercial HPV tests, followed by a description of advanced technologies, explanation of their principles, critical evaluation of their strengths and weaknesses, and suggestions for their possible implementation into medical diagnostics.

• MeSH
• infekce papilomavirem * komplikace   MeSH
• lidé MeSH
• lidské papilomaviry MeSH
• nádory děložního čípku * MeSH
• Papillomaviridae genetika   MeSH
• technologie MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH