Biology subjects

Waitkus, J.

Publications and source records attributed to Waitkus, J..

4 recordsLinked to original sources

bioRxiv2025

Silicon Micropillar-Enhanced CRISPR Biosensor for Rapid and Sensitive Detection of Drug-Resistant Bacteria

1The growing threat of antibiotic-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), underscores the urgent need for rapid, sensitive, and field-deployable diagnostic technologies. Here, we present a silicon micropillar-enhanced CRISPR biosensor that integrates high-aspect-ratio microstructures with a one-pot RPA/CRISPR-Cas12a assay for ultrasensitive and specific detection of MRSA. Micropillar arrays with fixed diameters and varying heights (100 {micro}m, 300 {micro}m, and 500 {micro}m) were fabricated via deep reactive ion etching and functionalized for surface probe immobilization. Suboptimal crRNA design was employed to modify Cas12a activation kinetics, enabling declined trans-cleavage and enhanced end-point signal accumulation. The 500 {micro}m micropillar configuration demonstrated a tenfold improvement in sensitivity compared to the 100 {micro}m array, with a limit of detection reaching 103 CFU mL-1. The platform also showed high specificity against non-target bacterial strains. These findings highlight the potential of combining microstructured chips with one-pot CRISPR diagnostics to advance next-generation point-of-care tools for infectious disease monitoring. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/694528v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@5f5f7corg.highwire.dtl.DTLVardef@175cb35org.highwire.dtl.DTLVardef@7043e5org.highwire.dtl.DTLVardef@79aa15_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Multi-Channel Funnel Adapted Sensing Tube (MFAST) for the Simple and Duplex Detection of Parasites

Leishmaniasis poses a significant global health threat, infecting millions of people annually, particularly in tropical and subtropical regions. Timely and accurate detection of Leishmania species is crucial for effective treatment and control of this debilitating disease. This study introduces the Multi-channel Funnel Adapted Sensing Tube (MFAST) chip, an innovative diagnostic tool designed for the rapid detection of Leishmania panamensis. MFAST is fabricated through 3D printing and sacrificial molding of acrylonitrile butadiene styrene (ABS) and the reagents are transported between the reservoirs by gravity. We combine experiments and finite element analysis to reduce the leaking issues and facilitate smoother fluid flow, improving the overall performance of the device. Highly sensitive and specific RPA-CRISPR/Cas12a assay is utilized in the chip, achieving a detection limit as low as 1,000 parasites/mL (detecting as few as 5 parasites per reaction). The multi-channel design enables duplex detection, allowing for simultaneous identification of both L. braziliensis and L. panamensis through distinct channels. Furthermore, stability tests indicate that lyophilized reagents retain functionality for up to 15 days when stored at 4 {degrees}C, underscoring the potential of this chip for practical diagnostic applications in low-resource settings.

bioengineering↗

bioRxiv2024

Antibiotic-Mediated Plasmonic Resonance on a Novel Nanopillar Metasurface Array

This study demonstrates a silicon nanopillar metasurface coupled with localized surface plasmon resonance (LSPR) mediated by the presence of cephalexin antibiotics in solution for biosensing applications. A facile fabrication process was developed to create the metasurface on silicon wafers with a unique resonance signature. The resulting metasurface consists of periodic nanopillars approximately 180 nm in diameter, 210 nm deep, and with a controlled edge-to-edge separation of 200 nm. These dimensions were chosen based on a finite element method simulation that was used to investigate the ideal parameters to produce the desired resonance effect in the metasurface reflection spectra. Optimization of the nanopillar surface properties and the sidewall angle allowed for replication of the simulations. This metasurface was coupled with BSA-coated gold nanospheres (BSANS) to mediate the redshift of peak resonance wavelength values, occurring only in the presence of the antibiotic linker. The device fabricated herein exhibits a significant 22 nm wavelength shift resulting from changes to the local refractive index in the presence of the BSANS-antibiotic coupling. Further enhancement of the binding events is promoted by the LSPR hot spots formed between the nanoparticles and the metasurface allowing for sensitive and real-time detection.

bioengineering↗

bioRxiv2022

On-Demand Fully-Enclosed Superhydrophobic-Optofluidic Device Enabled by High Precision Microstereolithography

Superhydrophobic surface-based optofluidics have been introduced to biosensors and unconventional optics with unique advantages such as low light loss and power consumption. However, most of these platforms were made with planar-like micro- and nano-structures, which may cause bonding issues and resulting in significant waveguide loss. Here, we introduce a fully-enclosed superhydrophobic-based optofluidics system, enabled by a one-step high precision microstereolithography procedure. Various micro-structured cladding designs with a feature size down to 100 m were studied and a "T-type" overhang design exhibits the lowest optical loss, regardless of the excitation wavelength. Surprisingly, the optical loss of superhydrophobic-based optofluidics is not solely decided by the solid area fraction at the solid/water/air interface, but also the cross-section shape and the effective cladding layer composition. We show that this fully-enclosed optofluidic system can be used for CRISPR-labeled quantum dot quantification, intended for in vitro and in vivo CRISPR therapeutics.

bioengineering↗