Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n = 28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection

Characterization and polarization resolved simulation of diffractive optical elements

We present our activity on the characterization and simulation of diffractive optical elements (DOEs) for near infrared spectroscopy. The DOE surface is designed to direct and focus light of a limited set of wavelengths onto a detector. In order to perform this, the surface pattern has a complicated structure and varies significantly over the element. This leads to a variation in the diffraction efficiency if the incident light only illuminates certain parts of the DOE. For the use of a DOE in a spectrometer, it is for some applications important that the local diffraction efficiency of each wavelength component relative to the others is as uniform as possible over the DOE. Otherwise, the spectroscopic measurement can become unreliable. A measurement setup was built at SINTEF to characterize the DOEs. This setup uses a movable aperture in front of the DOE, so that it is possible to measure the diffraction efficiency in different positions on the DOE. The simulations were carried out using the PCGrate software [1], which computes the diffraction efficiency for a periodic diffraction grating, employing full vectorial representation of the optical field. We carried out the simulations for one wavelength and position at a time, modeling the DOE surface by a perfectly periodic diffraction grating, with a period and an orientation designed to yield a surface with the same performance as the fabricated DOE. This yields a simple model that gives variations of local diffraction efficiency of the same order of magnitude as the measurements.Characterization and polarization resolved simulation of diffractive optical element

Wood's anomalies and spectral uniformity of focusing diffractive optical elements

-We report on simulations and measurements of focusing diffractive optical elements, fabricated as two-level binary optics. The diffractive optical elements are designed to separate and focus four specific wavelengths in the infrared. The simulations are based on a local linear grating model, and predict anomalies similar to Wood’s anomalies known from grating diffraction theory. The anomalies are also seen in the measurements, and are excited at the DOE locations predicted by the simulations. The given examples illustrate the usefulness of the model for evaluation of DOE designs. We also present a comparison of the response and spectral uniformity between two different versions of the four-wavelength diffractive optical elements. In the first version, the optical functions for all the four wavelengths are incorporated into the same surface pattern, covering the whole patterned area. In the second version the pattern, each wavelength is kept separate, and cover one fourth of the area, forming a mosaic of the four individual patterns

Detection of single nano-defects in photonic crystals between crossed polarizers

-We investigate, by simulations and experiments, the light scattering of small particles trapped in photonic crystal membranes supporting guided resonance modes. Our results show that, due to amplified Rayleigh small particle scattering, such membranes can be utilized to make a sensor that can detect single nano-particles. We have designed a biomolecule sensor that uses cross-polarized excitation and detection for increased sensitivity. Estimated using Rayleigh scattering theory and simulation results, the current fabricated sensor has a detection limit of 26 nm, corresponding to the size of a single virus. The sensor can potentially be made both cheap and compact, to facilitate use at point-of-care

Photonic-crystal membranes for optical detection of single nano-particles, designed for biosensor application

-A sensor designed to detect bio-molecules is presented. The sensor exploits a planar 2D photonic crystal (PC) membrane with sub-micron thickness and through holes, to induce high optical fields that allow detection of nano-particles smaller than the diffraction limit of an optical microscope. We report on our design and fabrication of a PC membrane with a nano-particle trapped inside. We have also designed and built an imaging system where an optical microscope and a CCD camera are used to take images of the PC membrane. Results show how the trapped nano-particle appears as a bright spot in the image. In a first experimental realization of the imaging system, single particles with a radius of 75 nm can be detected

Optical MEMS filter for infrared gas detection

An optical filter is proposed, which can be adapted to infrared detection of various gases. The filter is based on a diffraction grating structured on a micro-electro-mechanical system (MEMS) which can be switched between two states by applying an external actuation voltage of 0-5V. The optical grating is etched into silicon, and has a period and a depth adapted to the gas to be detected. The grating presented in this poster is a two-level binary grating designed to give a reflection spectrum centred at a 2μm wavelength. It has 500nm deep grooves and has a period of 5- 10μm. The grating is structured on top of an array of silicon beams, where every second beam can be moved vertically. The filter switches between two states by applying an actuation voltage of 0V and 5V. The optical spectrum of the diffracted light changes according to actuation voltage. By deflecting every second grating element 500nm (λ/4) vertically, the filter can be switched between a function with a single band which peaks at a certain centre wavelength, and a function with two sidebands positioned on either side of the centre wavelength. The single band can be designed to coincide with the absorption lines of the gas to be detected, while the sidebands are positioned outside of the absorption region of the gas. By illuminating the gas with light diffracted off this filter and switching between the two filter states, an intensity modulation of the light is achieved which is dependent upon the amount of gas present in the transmission path of the light. The proposed filter provides a robust, flexible, and potentially low cost solution for infrared gas detection of a wide range of gases.Optical MEMS filter for infrared gas detectio

Two-state Optical Filter Based on Micromechanical Diffractive Elements

We have designed a robust two-state filter for infrared gas measurement, where the filter transmittance alternates between a single bandpass function, and a double-band offset reference. The device consists of fixed and movable diffractive sub-elements, micromachined in the device layer of a bonded silicon on insulator (BSOI) wafer. Switching between the two states of the filter is obtained by actuation of the movable sub- elements between idle and pull-in positions, which affects the interference of reflected light The characteristics of the filter are defined by a diffractive microrelief pattern etched on top of the sub-elements and by the position of the movable sub-elements at pull-in, the latter mechanically defined by the buried oxide layer. Thus, no accurate electrical control is needed to operate the filter. The first test components operate at 2 mum wavelength using a displacement of 500 nm and an actuation voltage of 5 V. No sticking or change in filter characteristics have been observed after repeated pull-in operations. The simplicity of fabrication and operation is likely to make the two-state filter an attractive component for sensors such as non-dispersive infrared gas detector.Two-state Optical Filter Based on Micromechanical Diffractive Element

Finite-size limitations on quality factor of guided resonance modes in 2D photonic crystals

-High-Q guided resonance modes in two-dimensional photonic crystals, enable high field intensity in small volumes that can be exploited to realize high performance sensors. We show through simulations and experiments how the Q-factor of guided resonance modes varies with the size of the photonic crystal, and that this variation is due to loss caused by scattering of in-plane propagating modes at the lattice boundary and coupling of incident light to fully guided modes that exist in the homogeneous slab outside the lattice boundary. A photonic crystal with reflecting boundaries, realized by Bragg mirrors with a band gap for in-plane propagating modes, has been designed to suppress these edge effects. The new design represents a way around the fundamental limitation on Q-factors for guided resonances in finite photonic crystals. Results are presented for both simulated and fabricated structures

Detection of single nano-defects in photonic crystals between crossed polarizers

We investigate, by simulations and experiments, the light scattering of small particles trapped in photonic crystal membranes supporting guided resonance modes. Our results show that, due to amplified Rayleigh small particle scattering, such membranes can be utilized to make a sensor that can detect single nano-particles. We have designed a biomolecule sensor that uses cross-polarized excitation and detection for increased sensitivity. Estimated using Rayleigh scattering theory and simulation results, the current fabricated sensor has a detection limit of 26 nm, corresponding to the size of a single virus. The sensor can potentially be made both cheap and compact, to facilitate use at point-of-care

Photonic-crystal membranes for optical detection of single nano-particles, designed for biosensor application

A sensor designed to detect bio-molecules is presented. The sensor exploits a planar 2D photonic crystal (PC) membrane with sub-micron thickness and through holes, to induce high optical fields that allow detection of nano-particles smaller than the diffraction limit of an optical microscope. We report on our design and fabrication of a PC membrane with a nano-particle trapped inside. We have also designed and built an imaging system where an optical microscope and a CCD camera are used to take images of the PC membrane. Results show how the trapped nano-particle appears as a bright spot in the image. In a first experimental realization of the imaging system, single particles with a radius of 75 nm can be detected