This PDF file contains the front matter associated with SPIE Proceedings Volume 11662, including the Title Page, Copyright information, and Table of Contents.

Introduction to SPIE Photonics West BiOS conference 11662: Frontiers in Biological Detection: From Nanosensors to Systems XIII

The hour-glass type nanostructures are fabricated by using the conventional Si processes. When beaming though these structures, we observed that light is collected by the micro scale pyramidal cavity, funneled through the nano-aperture by plasmonic resonance and collimated with enhanced transmission by the surrounding horn-like mirrors (optical horn-effect). Optical transmissions through pyramidal probes with various nano-aperture diameters were measured to be dependent upon the aperture area. For a diameter less than ~ 50 nm or less than area with ~10,000 nm², the transmitted optical intensities are increasing due to the spp-mediated intra-band emission. For the aperture diameter greater than 100 nm, the strong spp-coupled emission is shown. In addition, for the Au (7×7) slit aperture array platform with the slit aperture for a ~ 10 nm width, the broad emission spectra ranging from 600 nm to 860 nm are observed possibly due to nearfield coupling with localized surface plasmon polariton (LSPP).

The programmable nature of sequence-specific targeting by CRISPR-Cas nucleases has revolutionized a wide range of genomic applications and is now emerging as a new method for nucleic acid detection. This talk explores the diversity of CRISPR systems and how their fundamental mechanisms have enabled novel methods for target recognition and readout, highlighting the intersection of biology and engineering. We further discuss the advances and potential for CRISPR-based detection to have an impact across a continuum of diagnostic applications, particularly as it relates to the COVID-19 pandemic.

Micro-ring resonators have emerged as a powerful platform for analyzing and detecting biomolecules at low concentrations. Here we demonstrate a high contrast cleavage detection (HCCD) assay on a micro-ring resonator to sense the cleavage of DNA reporterslinked to high-contrast nanoparticles (NPs), leading to dramatic optical signal amplification. The HCCD mechanism is coupled with a CRISPR-Cas12a assay for rapid and sensitive on-chip nucleic acid detection. Leveraging high-contrast gold nanoparticle (AuNP) reporters, an ~8 nm resonance shift is observed by using a 1 nM of complementary DNA (cDNA) target, matching part of the SARS-CoV-2 sequence. In addition, we show that a micro-ring resonator can not only record the entire surface functionalization process, as has been show previously, but also monitor CRISPR reactions in-situ. This work is the first step toward novel nucleic acid amplification-free detection via a combination of integrated photonics and CRISPR-Cas collateral cleavage assays.

The ongoing COVID-19 pandemic highlights the need for simple and rapid testing for respiratory infections at the point-of-care. With its high sensitivity and specificity, RT-PCR is the gold standard for the molecular diagnosis and differentiation among respiratory pathogens, but it requires complex instrumentation and methods that are not suitable for point-of-care settings. Our simplified Adaptive PCR technology and workflow yields high analytic performance without the complexities of traditional PCR by incorporating mirror-image L-DNA enantiomers—identical in sequence to PCR primers and targets—that are optically monitored to adapt cycling conditions to match the biochemical contents of the sample in real time. This enables rapid, single-tube analyses directly from COVID-19 swab specimens without RNA extraction.

Biological microlasers, which utilize lasing emission as a sensing signal, has recently emerged as a promising approach in biotechnology. As such, biolasers with functionality are of great significance for the detection of tiny molecular interactions in biological systems. Despite considerable progress achieved in biomaterial-based microlasers, the ability to manipulate nanoscaled biostructures and functionalize molecules in microcavity represents a grand challenge. Herein we report the development of hydrogel microlasers by exploiting the versatility and controllability of hydrogels, where whispering-gallery-mode lasing was achieved by printing hydrogel droplets on a mirror. Lasing behaviors and fundamental characteristics of hydrogel lasers were explored under various water-monomer ratios and crosslinking degrees. Furthermore, hydrogel lasing microarray was developed, providing a novel approach to study molecular interactions within the 3D hydrogel network structure. To demonstrate the potential application and functionality, FRET peptide lasing was exploited for molecular analysis. Single-mode FRET laser emission was achieved by tuning the Forster distance in hydrogel droplets. Finally, different types of biomolecules were encapsulated to form biolasing. These findings not only highlight the ability of hydrogel biolasers for high-throughput biomolecular analysis but also provides deep insights into the relationship between biostructure and laser physics.

Microfluidic reactors have become increasingly popular for the characterization of reaction parameters. They have found an important role in the synthesis and monitoring of an expansive list of bioreactions. To study protein phosphorylation, a biochemical reaction that is responsible for a broad range of signal transduction roles, we designed microfluidic reactors based on tubular flow for studying in real time reactor kinetic parameters in protein phosphorylation. In order to monitor phosphorylation as it occurs, we probed the environment where the reaction takes place without influencing the reactor kinetics, while collecting molecular information such as structure and conformation of native proteins. We designed and tested polydimethylsiloxane (PDMS) microfluidic reactors compatible with our confocal Raman spectrometer and overcame significant absorption of important Raman bands from the PDMS. We studied the PDMS device interfaces, determined experimentally which interfaces were least absorbing, and redesigned the microfluidic device using 3D rapid prototyping. Using redesigned devices, we measured Raman spectra on aqueous Adenosine triphosphate (ATP) solutions at varying molar concentrations (0.1 M – 1.0 M) at room temperature over the wavenumber range of 50 - 4000 /cm and accurately observed the behavior of phosphate bonds involved in the protein phosphorylation reaction. We also studied the effects of fluid flow in order to account for effects under transient conditions. To do this, we preloaded the reactor and initiated ATP fluid flow and collected spectra. Our modified design proved to overcome significant signal absorption from PDMS and accurately measured concentrations.

Point-of-Care diagnostics are instrumental to patient care and are broadly applied in the clinical setting. The simplest such device is the lateral flow assay, which is used to influence clinical decisions ranging from pregnancy to malarial infection. Lateral flow assays are ubiquitous; however, they are semi-quantitative, require labeled reagents, and are often less sensitive than comparable clinical laboratory technology. We hypothesize that an attractive method to introduce label-free quantification to Point-of-Care diagnostics is to couple them to photonic sensors. Photonic sensors are attractive as biological measurement tools, as they have low size, weight, and power requirements while providing high sensitivity. In this manuscript we describe post-processing of foundry-prepared photonic sensor chips in preparation for integration with a lateral flow format.

We present a methodology for quantitative sensing of the contents of a target material (TM) in a given sample which employs biosensing bioluminescent bacteria. These bacteria are genetically engineered to respond to the presence of a specific TM in their microenvironment by producing bioluminescence. Herein, we extend this methodology to include quantitative sensing of the TM content in the inspected sample by exploiting the dependence of the bioluminescence produced by the bacteria on the content of the TM in the inspected sample. However, employing bacteria as precise measurement devices is inherently problematic, as the signal they produce varies between different batches of bacteria, and changes as the batch ages. Moreover, As the methodology is designed for outdoor operation, the sensitivity of the bacteria response to changes in the environmental conditions needs to be taken into account. These hurdles are overcome in a special optoelectronic sensor which measures in parallel the responses produced by the inspected sample, and a standard sample containing a known quantity of the TM. Both measurements are conducted by identical sensing channels using bacteria from the same batch, and under the same environmental conditions. The “standard ratio” (SR) defined as the ratio between the maximum responses of the inspected sample and the standard sample was found to be independent of the batch and environmental conditions. A calibration curve of the SR vs. the TM concentration in a set of preprepared samples is used to gauge SR at the sensor output to the TM concentration in the inspected sample.

We present a signal processing method capable of significantly lowering the detection limit of thin film optical biosensors. This signal processing method, which we term LAMP, is based on Morlet wavelet filtering and extracting phase information. LAMP drastically reduces noise contributions typically encountered in sensor measurements. The noise immunity, sensitivity and linearity of LAMP is benchmarked against several other signal processing methods by applying the different techniques to a large set of simulated porous silicon thin film optical spectra that contain various types of noise signatures. The LAMP signal processing technique opens up new applications in disease detection and environmental monitoring for thin film sensors previously precluded by insufficient detection limits.

When dealing with sensing of (bio)molecules the length scale of targets may vary over more than 2 orders of magnitude moving from elementary ions and molecules (0.1 to 1 nm) to complex proteins and virus (1 to 100 nm). A number of technologies have been proposed to prepare fluidic structures and systems with length scales enabling an effective interaction with the specific molecular target. Among these, electrochemical micro and nano structuring of silicon is increasingly attracting attention at research level for biosensing and microfluidics. In this talk, state-of-the-art research on silicon nano-micro structures and systems prepared by electrochemical etching for high-sensitivity (bio)sensing, among which, interferometers for ultra-high-sensitivity ion measurements in water, optical platforms for point-of-care clinical diagnostics, drop-and-measure photonic crystal systems for in-field optical biosensing, microneedles for transdermal biosensing, is presented and discussed.

An objective of the present research was to conduct specific monitoring of sanitary conditions via the study of liquids from wash swabs of door handles in a public place building, which is can be important in the context of fast-spreading of infectious diseases to model and understand how tightening and weakening preventive measures (cleaning) affect this dangerous process. Surface-enhanced Raman scattering (SERS) spectroscopy was selected as an analytical method since it provides ultrahigh sensitivity, facilitates an express-analysis, and does not require specially-trained staff. To overcome the problem of irreproducibility of the SERS-spectra of multicomponent liquids typical for traditional SERS-active substrates based on nanoparticles we used the metal-coated nanovoids with a diameter of 1 m. The geometry of nanovoids facilitated excitation of the volumetric electromagnetic field inside them that provided a collection of reproducible SERS-patterns for each swab liquid sample. We were able to distinguish the samples constituted by skin secretion from fingers and those enriched with bacteria because of the long unclean period of the door handle and its frequent touching with dirty hands.