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
- Bromates toxicity MeSH
- Humans MeSH
- Chromosome Mapping * instrumentation methods MeSH
- Microfluidic Analytical Techniques * instrumentation methods MeSH
- Cell Line, Tumor MeSH
- Nanotechnology * instrumentation methods MeSH
- DNA Repair genetics MeSH
- Oxidative Stress drug effects genetics MeSH
- DNA Damage * genetics MeSH
- Gene Expression Regulation MeSH
- Gene Expression Profiling MeSH
- Toxicogenetics * instrumentation methods MeSH
- DNA Copy Number Variations MeSH
- Single Molecule Imaging * instrumentation methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article 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
- Biosensing Techniques instrumentation methods MeSH
- Equipment Design MeSH
- Lab-On-A-Chip Devices * MeSH
- Humans MeSH
- Microfluidics methods MeSH
- Microfluidic Analytical Techniques instrumentation MeSH
- Proteins analysis isolation & purification MeSH
- Proteome analysis isolation & purification chemistry MeSH
- Proteomics * methods MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Review 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 * virology MeSH
- Equipment Design MeSH
- Dimethylpolysiloxanes chemistry MeSH
- Lab-On-A-Chip Devices * MeSH
- Humans MeSH
- Microfluidics methods instrumentation MeSH
- Microfluidic Analytical Techniques instrumentation methods MeSH
- Polymethyl Methacrylate chemistry MeSH
- SARS-CoV-2 isolation & purification MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Comparative Study 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
- Immunoassay instrumentation methods MeSH
- Humans MeSH
- Limit of Detection MeSH
- Microfluidic Analytical Techniques instrumentation MeSH
- Prostatic Neoplasms diagnosis blood MeSH
- Nanoparticles chemistry MeSH
- Prostate-Specific Antigen * analysis blood MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Mikrofluidika je inovativní obor, který se zabývá zpracováním malého množství kapaliny v mikrokanálech. V kombinaci s pokročilými analytickými technikami, jako je např. mikrofluidní PCR, nabízí významné výhody nejen pro analýzu genové exprese. Tato metoda využívá mikrokanály a mikroventily k přesnému dávkování a míchání činidel, čímž se minimalizuje spotřeba vzorku a činidla a také čas stráve‐ ný pipetováním. Tyto vlastnosti činí mikrofluidní PCR ideální pro analýzu genové exprese, kde je vyžadováno podrobné monitorování a kvantifikace mRNA. Jedním z přístrojů umožňujícím mikrofluidní PCR je Biomark X. Díky své schopnosti multiplexování a také díky své‐ mu mikrofluidnímu designu umožňuje analýzu mnoha vzorků současně. Tato pokročilá technologie má široké uplatnění v biologickém výzkumu, diagnostice a personalizované medicíně a nabízí nové příležitosti k objevování a pochopení genetických procesů.
Microfluidics is an innovative science that deals with the manipulation of small volumes of fluid in microchannels. In combination with advanced analytical techniques such as microfluidic PCR, it offers significant advantages not only for gene expression analysis. Microflui‐ dic PCR enables PCR reactions to be performed using very small sample volumes, as it utilizes microchannels and microvalves for precise reagent dispensing and mixing. This fact increases both sensitivity and accuracy of the analysis. The Biomark X instrument utilizes micro‐ fluidic PCR for gene expression analysis, as it is ideal for mRNA quantification. With its multiplexing capability and microfluidic design, it enables the analysis of multiple samples simultaneously. This advanced technology finds broad applications in biological research, diagnostics, and provides new opportunities for the discovery and understanding of genetic processes.
There is a constant need for the development of easy-to-operate systems for the rapid and unambiguous identification of bacterial pathogens in drinking water without the requirement for time-consuming culture processes. In this study, we present a disposable and low-cost lab-on-a-chip device utilizing a nanoporous membrane, which connects two stacked perpendicular microfluidic channels. Whereas one of the channels supplies the sample, the second one attracts it by potential-driven forces. Surface-enhanced Raman spectrometry (SERS) is employed as a reliable detection method for bacteria identification. To gain the effect of surface enhancement, silver nanoparticles were added to the sample. The pores of the membrane act as a filter trapping the bodies of microorganisms as well as clusters of nanoparticles creating suitable conditions for sensitive SERS detection. Therein, we focused on the construction and characterization of the device performance. To demonstrate the functionality of the microfluidic chip, we analyzed common pathogens (Escherichia coli DH5α and Pseudomonas taiwanensis VLB120) from spiked tap water using the optimized experimental parameters. The obtained results confirmed our system to be promising for the construction of a disposable optical platform for reliable and rapid pathogen detection which couples their electrokinetic concentration on the integrated nanoporous membrane with SERS detection.
- MeSH
- Equipment Design MeSH
- Metal Nanoparticles chemistry MeSH
- Lab-On-A-Chip Devices * MeSH
- Microfluidic Analytical Techniques instrumentation MeSH
- Drinking Water microbiology MeSH
- Spectrum Analysis, Raman instrumentation MeSH
- Silver chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
A device with four parallel channels was designed and manufactured by 3D printing in titanium. A simple experimental setup allowed splitting of the mobile phase in four parallel streams, such that a single sample could be analysed four times simultaneously. The four capillary channels were filled with a monolithic stationary phase, prepared using a zwitterionic functional monomer in combination with various dimethacrylate cross-linkers. The resulting stationary phases were applicable in both reversed-phase and hydrophilic-interaction retention mechanisms. The mobile-phase composition was optimized by means of a window diagram so as to obtain the highest possible resolution of dopamine precursors and metabolites on all columns. Miniaturized electrochemical detectors with carbon fibres as working electrodes and silver micro-wires as reference electrodes were integrated in the device at the end of each column. Experimental separations were successfully compared with those predicted by a three-parameter retention model. Finally, dopamine was determined in human urine to further confirm applicability of the developed device.
PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.
- MeSH
- Betacoronavirus genetics isolation & purification MeSH
- COVID-19 MeSH
- Equipment Design MeSH
- Clinical Laboratory Techniques instrumentation methods MeSH
- Coronavirus Infections diagnosis virology MeSH
- Humans MeSH
- Microfluidic Analytical Techniques instrumentation methods MeSH
- Pandemics MeSH
- Polymerase Chain Reaction instrumentation methods MeSH
- SARS-CoV-2 MeSH
- COVID-19 Testing MeSH
- Pneumonia, Viral diagnosis virology MeSH
- Point-of-Care Systems MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
A microfluidic device made of polydimethylsiloxane was developed for continuous evaluation of natural migration mobility of many eukaryotic cells in relaxed and deformed state. The device was fabricated by standard photolithography and soft lithography techniques using the SU-8 3010 negative photoresist on a glass wafer as the master mold. The simple flow-free device exploits the chemotactic movement of cells through a set of mechanical barriers in the direction of concentration gradients of attractants. The barriers are formed by arrays of circular cross-section pillars with decreasing spacing 7, 5, and 3 μm. To pass through the obstacles, the cells are deformed and change their cytoskeletal architecture. The instantaneous migration velocities of cells are monitored in a time-lapse setup of the scanning confocal microscope. Thus, the cellular deformability and migratory activity can easily be evaluated. The functionality of the device was tested with model HeLa cells stably transfected with fluorescent Premo FUCCI Cell Cycle Sensor. The designed device has the potential to be implemented for testing the tendency of patients' tumors to metastasis.
- MeSH
- Cell Culture Techniques instrumentation MeSH
- Equipment Design MeSH
- Dimethylpolysiloxanes chemistry MeSH
- HeLa Cells MeSH
- Microscopy, Confocal MeSH
- Humans MeSH
- Microfluidic Analytical Techniques instrumentation MeSH
- Cell Movement physiology MeSH
- Cell Shape physiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
- MeSH
- Biosensing Techniques MeSH
- Equipment Design MeSH
- DNA, Viral analysis MeSH
- Enzyme-Linked Immunosorbent Assay MeSH
- Real-Time Polymerase Chain Reaction MeSH
- Lab-On-A-Chip Devices * MeSH
- Humans MeSH
- Microfluidic Analytical Techniques instrumentation MeSH
- Nucleic Acids analysis MeSH
- Virus Diseases diagnosis MeSH
- Point-of-Care Systems MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
