Filiz Yesilkoy

Highly efficient and gentle trapping of single cells in large microfluidic arrays for time-lapse experiments.

The isolation of single biological cells and their further cultivation in dedicated arrayed chambers are key to the collection of statistically reliable temporal data in cell-based biological experiments. In this work, we present a hydrodynamic single cell trapping and culturing platform that facilitates cell observation and experimentation using standard bio-lab equipment. The proposed design leverages the stochastic position of the cells as they flow into the structured microfluidic channels, where hundreds of single cells are then arrayed in nanoliter chambers for simultaneous cell specific data collection. Numerical simulation tools are used to devise and implement a hydrodynamic cell trapping mechanism that is minimally detrimental to the cell cycle and retains high overall trapping efficiency (∼70%) with the capability of reaching high fill factors (>90%) in short loading times (1-4 min) in a 400-trap device. A Monte Carlo model is developed using the design parameters to estimate the system trapping efficiencies, which show strong agreement with the experimentally acquired data. As proof of concept, arrayed mammalian tissue cells (MIA PaCa-2) are cultured in the microfluidic chambers for two days without viability problems.

Imaging-based molecular barcoding with pixelated dielectric metasurfaces

Metasurfaces for molecular detection Although mid-infrared (mid-IR) spectroscopy is a mainstay of molecular fingerprinting, its sensitivity is diminished somewhat when looking at small volumes of sample. Nanophotonics provides a platform to enhance the detection capability. Tittl et al. built a mid-IR nanophotonic sensor based on reflection from an all-dielectric metasurface array of specially designed scattering elements. The scattering elements could be tuned via geometry across a broad range of wavelengths in the mid-IR. The approach successfully detected and differentiated the absorption fingerprints of various molecules. The technique offers the prospect of on-chip molecular fingerprinting without the need for spectrometry, frequency scanning, or moving mechanical parts. Science, this issue p. 1105 A pixelated dielectric metasurface is used for the mid-infrared detection of molecular fingerprints. Metasurfaces provide opportunities for wavefront control, flat optics, and subwavelength light focusing. We developed an imaging-based nanophotonic method for detecting mid-infrared molecular fingerprints and implemented it for the chemical identification and compositional analysis of surface-bound analytes. Our technique features a two-dimensional pixelated dielectric metasurface with a range of ultrasharp resonances, each tuned to a discrete frequency; this enables molecular absorption signatures to be read out at multiple spectral points, and the resulting information is then translated into a barcode-like spatial absorption map for imaging. The signatures of biological, polymer, and pesticide molecules can be detected with high sensitivity, covering applications such as biosensing and environmental monitoring. Our chemically specific technique can resolve absorption fingerprints without the need for spectrometry, frequency scanning, or moving mechanical parts, thereby paving the way toward sensitive and versatile miniaturized mid-infrared spectroscopy devices.

Phase-sensitive plasmonic biosensor using a portable and large field-of-view interferometric microarray imager

Nanophotonics, and more specifically plasmonics, provides a rich toolbox for biomolecular sensing, since the engineered metasurfaces can enhance light–matter interactions to unprecedented levels. So far, biosensing associated with high-quality factor plasmonic resonances has almost exclusively relied on detection of spectral shifts and their associated intensity changes. However, the phase response of the plasmonic resonances have rarely been exploited, mainly because this requires a more sophisticated optical arrangement. Here we present a new phase-sensitive platform for high-throughput and label-free biosensing enhanced by plasmonics. It employs specifically designed Au nanohole arrays and a large field-of-view interferometric lens-free imaging reader operating in a collinear optical path configuration. This unique combination allows the detection of atomically thin (angstrom-level) topographical features over large areas, enabling simultaneous reading of thousands of microarray elements. As the plasmonic chips are fabricated using scalable techniques and the imaging reader is built with low-cost off-the-shelf consumer electronic and optical components, the proposed platform is ideal for point-of-care ultrasensitive biomarker detection from small sample volumes. Our research opens new horizons for on-site disease diagnostics and remote health monitoring.

Towards a point-of-care nanoplasmonic biosensor for rapid and multiplexed detection of pathogenic infections

The implementation of multiplexed point-of-care biosensors is a top priority to address the current epidemic problems originated by widespread pathogenic infections, like those caused by viruses or bacteria. A rapid and accurate detection, identification, and quantification of the infectious pathogens is essential not only to facilitate a prompt treatment but also to prevent onward transmission, reduce economic expenses, and significantly promote healthcare in resource-constrained environments. We have developed a nanoplasmonic biosensor based on nanohole arrays for fast and highly sensitive analysis in a simple and direct configuration. Our microarray is integrated into a microfluidic system to allow for highthroughput detection of multiple targets in a few minutes, without the need of sample pretreatment or amplification steps. Previously, we demonstrated the utility of the biosensor for the detection of hazardous live viruses, such as the Ebola or Vaccinia viruses, measured directly in biological media. Most recently we proved the truly multiplexing capability of our plasmonic microarray with the simultaneous identification and quantification of Chlamydia trachomatis and Neisseria gonorrhoeae in urine samples. We are able to detect and distinguish the two different bacteria with detection limits in the range of 102 -103 bacteria/mL. With recent advances in plasmonics, optimized surface chemistry, and microfluidics integration, our biosensors could provide a non-invasive and rapid diagnosis at the point of care, especially when we combine the detection on a compact and low-cost optical reader.

Optofluidic nanoplasmonic biosensor for label-free live cell analysis in real time

Cell signaling activities play a critical role in physiological and disease processes. The analysis of the tumor microenvironment or the immune system activation is nowadays providing valuable insights towards disease understanding and novel therapies development. Due to the various dynamic profiles, it is essential to implement a continuous monitoring methodology for accurate analysis. The current fluorescent and colorimetric approaches hinder such applications due to their multiple time-consuming steps, molecular labeling, and the ‘snapshot’ endpoint readouts. Photonics technology, and especially nanoplasmonic biosensors offer a unique opportunity to implement lab-on-a-chip systems that provide highly sensitive and label-free analysis of cell signaling events in real time. Here, we will present a microfluidics-integrated nanoplasmonic biosensor for long-term and real-time monitoring of cell secretion activity. The biosensor consists of a gold nanohole array supporting extraordinary optical transmission (EOT), which has been optimized to enable ultra-sensitive and high-throughput biomolecular detection. The nanobiosensor is integrated with a specifically designed microfluidic system that provides well-controlled cell culture conditions for long-term monitoring. We achieved an outstanding sensitivity for the detection of vascular endothelial growth factor (VEGF) directly secreted from microfluidic-cultured cancer cells. We demonstrated real-time monitoring for over 10 hours, preserving good cell viability. The multiplexing capability of our nanobiosensor could enable simultaneous analysis of different cell types and molecules-of-interest. Thus, our innovative approach of probing live cells can be a powerful tool to evaluate cellular activities for diagnostics and novel therapy development.

Nanoparticle-Enhanced Plasmonic Biosensor for Digital Biomarker Detection in a Microarray

Nanoplasmonic devices have become a paradigm for biomolecular detection enabled by enhanced light-matter interactions in the fields from biological and pharmaceutical research to medical diagnostics and global health. In this work, we present a bright-field imaging plasmonic biosensor that allows visualization of single subwavelength gold nanoparticles (NPs) on large-area gold nanohole arrays (Au-NHAs). The sensor generates image heatmaps that reveal the locations of single NPs as high-contrast spikes, enabling the detection of individual NP-labeled molecules. We implemented the proposed method in a sandwich immunoassay for the detection of biotinylated bovine serum albumin (bBSA) and human C-reactive protein (CRP), a clinical biomarker of acute inflammatory diseases. Our method can detect 10 pg/mL of bBSA and 27 pg/mL CRP in 2 h, which is at least 4 orders of magnitude lower than the clinically relevant concentrations. Our sensitive and rapid detection approach paired with the robust large-area plasmonic sensor chips, which are fabricated using scalable and low-cost manufacturing, provides a powerful platform for multiplexed biomarker detection in various settings.