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Accounts of Chemical Research May 2023There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular...
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
Topics: Nucleic Acids; Proteins; Coloring Agents; Microfluidics; Biomarkers
PubMed: 37068158
DOI: 10.1021/acs.accounts.3c00030 -
The Analyst Oct 2021Surface enhanced Raman scattering (SERS) is a technique that demonstrates a number of advantages for the rapid, specific and sensitive detection of pathogenic... (Review)
Review
Surface enhanced Raman scattering (SERS) is a technique that demonstrates a number of advantages for the rapid, specific and sensitive detection of pathogenic microorganisms. In this review, an overview of label-free and label-based SERS approaches, including microfluidics, nucleic acid detection and immunoassays, for the multiplexed detection of pathogenic bacteria and viruses from the last decade will be discussed, as well as their transition into promising point-of-use detection technologies in industrial and medical settings.
Topics: Bacteria; Immunoassay; Microfluidics; Spectrum Analysis, Raman
PubMed: 34492668
DOI: 10.1039/d1an00865j -
Integrative Biology : Quantitative... Apr 2023Sensory pathways first elucidated in Caenorhabditis elegans are conserved across free-living and parasitic nematodes, even though each species responds to a diverse...
Sensory pathways first elucidated in Caenorhabditis elegans are conserved across free-living and parasitic nematodes, even though each species responds to a diverse array of compounds. Most nematode sensory assays are performed by tallying observations of worm behavior on two-dimensional planes using agarose plates. These assays have been successful in the study of volatile sensation but are poorly suited for investigation of water-soluble gustation or parasitic nematodes without a free-living stage. In contrast, gustatory assays tend to be tedious, often limited to the manipulation of a single individual at a time. We have designed a nematode sensory assay using a microfluidics device that allows for the study of gustation in a 96-well, three-dimensional environment. This device is suited for free-living worms and parasitic worms that spend their lives in an aqueous environment, and we have used it to show that ivermectin inhibits the gustatory ability of vector-borne parasitic nematodes. Insight box Nematodes are powerful model organisms for understanding the sensory biology of multicellular eukaryotes, and many parasitic species cause disease in humans. Simple sensory assays performed on agarose plates have been the bedrock for establishing the neuronal, genetic, and developmental foundations for many sensory modalities in nematodes. However, these classical assays are poorly suited for translational movement of many parasitic nematodes and the sensation of water-soluble molecules (gustation). We have designed a device for high-throughput nematode sensory assays in a gel matrix. This 'gustatory microplate' is amenable to several species and reveals novel responses by free-living and parasitic nematodes to cues and drugs.
Topics: Caenorhabditis elegans; High-Throughput Screening Assays; Animals; Microfluidics; Behavior, Animal; Brugia pahangi; Dirofilaria immitis
PubMed: 37555835
DOI: 10.1093/intbio/zyad010 -
Biosensors Jun 2022Single-cell RNA sequencing (scRNA-seq) technology provides a powerful tool for understanding complex biosystems at the single-cell and single-molecule level. The past... (Review)
Review
Single-cell RNA sequencing (scRNA-seq) technology provides a powerful tool for understanding complex biosystems at the single-cell and single-molecule level. The past decade has been a golden period for the development of single-cell sequencing, with scRNA-seq undergoing a tremendous leap in sensitivity and throughput. The application of droplet- and microwell-based microfluidics in scRNA-seq has contributed greatly to improving sequencing throughput. This review introduces the history of development and important technical factors of scRNA-seq. We mainly focus on the role of microfluidics in facilitating the development of scRNA-seq technology. To end, we discuss the future directions for scRNA-seq.
Topics: High-Throughput Nucleotide Sequencing; Microfluidics; Sequence Analysis, RNA; Single-Cell Analysis
PubMed: 35884253
DOI: 10.3390/bios12070450 -
Proceedings of the National Academy of... Jan 2020Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and...
Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 10 EID/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.
Topics: Humans; Influenza A virus; Microbiological Techniques; Microtechnology; Nanotubes, Carbon; Respiratory Tract Infections; Respirovirus; Rhinovirus; Sensitivity and Specificity; Silicon Dioxide; Spectrum Analysis, Raman; Staining and Labeling; Virion; Virology; Virus Diseases; Viruses
PubMed: 31882450
DOI: 10.1073/pnas.1910113117 -
Advanced Drug Delivery Reviews 2020Microneedles (MNs) have been used to deliver drugs for over two decades. These platforms have been proven to increase transdermal drug delivery efficiency dramatically...
Microneedles (MNs) have been used to deliver drugs for over two decades. These platforms have been proven to increase transdermal drug delivery efficiency dramatically by penetrating restrictive tissue barriers in a minimally invasive manner. While much of the early development of MNs focused on transdermal drug delivery, this technology can be applied to a variety of other non-transdermal biomedical applications. Several variations, such as multi-layer or hollow MNs, have been developed to cater to the needs of specific applications. The heterogeneity in the design of MNs has demanded similar variety in their fabrication methods; the most common methods include micromolding and drawing lithography. Numerous materials have been explored for MN fabrication which range from biocompatible ceramics and metals to natural and synthetic biodegradable polymers. Recent advances in MN engineering have diversified MNs to include unique shapes, materials, and mechanical properties that can be tailored for organ-specific applications. In this review, we discuss the design and creation of modern MNs that aim to surpass the biological barriers of non-transdermal drug delivery in ocular, vascular, oral, and mucosal tissue.
Topics: Administration, Topical; Biological Transport; Drug Delivery Systems; Equipment Design; Humans; Microinjections; Microtechnology; Polymers; Prostheses and Implants
PubMed: 31837356
DOI: 10.1016/j.addr.2019.11.010 -
International Journal of Molecular... Feb 2023Organ-on-A-chip (OoAC) devices are miniaturized, functional, in vitro constructs that aim to recapitulate the in vivo physiology of an organ using different cell types... (Review)
Review
Organ-on-A-chip (OoAC) devices are miniaturized, functional, in vitro constructs that aim to recapitulate the in vivo physiology of an organ using different cell types and extracellular matrix, while maintaining the chemical and mechanical properties of the surrounding microenvironments. From an end-point perspective, the success of a microfluidic OoAC relies mainly on the type of biomaterial and the fabrication strategy employed. Certain biomaterials, such as PDMS (polydimethylsiloxane), are preferred over others due to their ease of fabrication and proven success in modelling complex organ systems. However, the inherent nature of human microtissues to respond differently to surrounding stimulations has led to the combination of biomaterials ranging from simple PDMS chips to 3D-printed polymers coated with natural and synthetic materials, including hydrogels. In addition, recent advances in 3D printing and bioprinting techniques have led to the powerful combination of utilizing these materials to develop microfluidic OoAC devices. In this narrative review, we evaluate the different materials used to fabricate microfluidic OoAC devices while outlining their pros and cons in different organ systems. A note on combining the advances made in additive manufacturing (AM) techniques for the microfabrication of these complex systems is also discussed.
Topics: Humans; Microfluidics; Biocompatible Materials; Microphysiological Systems; Hydrogels; Microtechnology; Printing, Three-Dimensional
PubMed: 36834645
DOI: 10.3390/ijms24043232 -
The FEBS Journal Nov 2019Crystallography has made a notable contribution to our knowledge of structural biology. For traditional crystallography experiments, the growth of crystals with large... (Review)
Review
Crystallography has made a notable contribution to our knowledge of structural biology. For traditional crystallography experiments, the growth of crystals with large size and high quality is crucial, and it remains one of the bottlenecks. In recent years, the successful application of serial femtosecond crystallography (SFX) provides a new choice when only numerous microcrystals can be obtained. The intense pulsed radiation of X-ray free-electron lasers (XFELs) enables the data collection of small-sized crystals, making the size of crystals no longer a limiting factor. The ultrafast pulses of XFELs can achieve 'diffraction before destruction', which effectively avoids radiation damage and realizes diffraction near physiological temperatures. More recently, the SFX has been expanded to serial crystallography (SX) that can additionally employ synchrotron radiation as the light source. In addition to the traditional ones, these techniques provide complementary opportunities for structural determination. The development of SX experiments strongly relies on the advancement of hardware including the sample delivery system, the X-ray source, and the X-ray detector. Here, in this review, we categorize the existing sample delivery systems, summarize their progress, and propose their future prospectives.
Topics: Crystallography, X-Ray; Lasers; Microfluidics
PubMed: 31618529
DOI: 10.1111/febs.15099 -
Sensors (Basel, Switzerland) Feb 2021Microfabrication and Polydimethylsiloxane (PDMS) soft-lithography techniques became popular for microfluidic prototyping at the lab, but even after protocol... (Review)
Review
Microfabrication and Polydimethylsiloxane (PDMS) soft-lithography techniques became popular for microfluidic prototyping at the lab, but even after protocol optimization, fabrication is yet a long, laborious process and partly user-dependent. Furthermore, the time and money required for the master fabrication process, necessary at any design upgrade, is still elevated. Digital Manufacturing (DM) and Rapid-Prototyping (RP) for microfluidics applications arise as a solution to this and other limitations of photo and soft-lithography fabrication techniques. Particularly for this paper, we will focus on the use of subtractive DM techniques for Organ-on-a-Chip (OoC) applications. Main available thermoplastics for microfluidics are suggested as material choices for device fabrication. The aim of this review is to explore DM and RP technologies for fabrication of an OoC with an embedded membrane after the evaluation of the main limitations of PDMS soft-lithography strategy. Different material options are also reviewed, as well as various bonding strategies. Finally, a new functional OoC device is showed, defining protocols for its fabrication in Cyclic Olefin Polymer (COP) using two different RP technologies. Different cells are seeded in both sides of the membrane as a proof of concept to test the optical and fluidic properties of the device.
Topics: Lab-On-A-Chip Devices; Microfluidics; Microtechnology; Oligonucleotide Array Sequence Analysis; Polymers
PubMed: 33669434
DOI: 10.3390/s21041382 -
Topics in Current Chemistry (Cham) Oct 2016A compact snapshot of the current convergence of novel developments relevant to chemical engineering is given. Process intensification concepts are analysed through the... (Review)
Review
A compact snapshot of the current convergence of novel developments relevant to chemical engineering is given. Process intensification concepts are analysed through the lens of microfluidics and sonochemistry. Economical drivers and their influence on scientific activities are mentioned, including innovation opportunities towards deployment into society. We focus on the control of cavitation as a means to improve the energy efficiency of sonochemical reactors, as well as in the solids handling with ultrasound; both are considered the most difficult hurdles for its adoption in a practical and industrial sense. Particular examples for microfluidic clogging prevention, numbering-up and scaling-up strategies are given. To conclude, an outlook of possible new directions of this active and promising combination of technologies is hinted.
Topics: Crystallization; Durapatite; Microfluidics; Sonication
PubMed: 27654863
DOI: 10.1007/s41061-016-0070-y