Rodrigo Sergio Wiederkehr
@imec.be
Life Sciences and Technologies
RESEARCH INTERESTS
Microfluidics
Biosensors
Lab on a Chip
Scopus Publications
Scopus Publications
Tim Stakenborg, Joren Raymenants, Ahmed Taher, Elisabeth Marchal, Bert Verbruggen, Sophie Roth, Ben Jones, Abdul Yurt, Wout Duthoo, Klaas Bombeke,et al.
Elsevier BV
Pieter Berden, Rodrigo S. Wiederkehr, Liesbet Lagae, Jan Michiels, Tim Stakenborg, Maarten Fauvart, and Willem Van Roy
American Chemical Society (ACS)
Partitions in digital PCR (dPCR) assays do not reach the detection threshold at the same time. This heterogeneity in amplification results in intermediate endpoint fluorescence values (i.e., rain) and misclassification of partitions, which has a major impact on the accuracy of nucleic acid quantification. Rain most often results from a reduced amplification efficiency or template inaccessibility; however, exactly how these contribute to rain has not been described. We developed and experimentally validated an analytical model that mechanistically explains the relationship between amplification efficiency, template accessibility, and rain. Using Monte Carlo simulations, we show that a reduced amplification efficiency leads to broader threshold cycle (Ct) distributions that can be fitted using a log-normal probability distribution. From the fit parameters, the amplification efficiency can be calculated. Template inaccessibility, on the other hand, leads to a different rain pattern, in which a distinct exponential tail in the Ct distribution can be observed. Using our model, it is possible to determine if the amplification efficiency, template accessibility, or another source is the main contributor of rain in dPCR assays. We envision that this model will facilitate and speed up dPCR assay optimization and provide an indication for the accuracy of the assay.
Senne Cornelis, Olivier Tytgat, Maarten Fauvart, Yannick Gansemans, Ann-Sophie Vander Plaetsen, Rodrigo S. Wiederkehr, Dieter Deforce, Filip Van Nieuwerburgh, and Tim Stakenborg
Springer Science and Business Media LLC
Yannick Vervoort, Rodrigo Sergio Wiederkehr, Michiel Smets, Maarten Fauvart, Tim Stakenborg, Gabrielle Woronoff, Liesbet Lagae, and Kevin J. Verstrepen
Springer Science and Business Media LLC
Qing Cai, Maarten Fauvart, Rodrigo Sergio Wiederkehr, Benjamin Jones, Piet Cools, Peter Goos, Mario Vaneechoutte, and Tim Stakenborg
Elsevier BV
Senne Cornelis, Maarten Fauvart, Yannick Gansemans, Ann-Sophie Vander Plaetsen, Frederik Colle, Rodrigo S. Wiederkehr, Dieter Deforce, Tim Stakenborg, and Filip Van Nieuwerburgh
Springer Science and Business Media LLC
Laura Powell, Rodrigo Sergio Wiederkehr, Paige Damascus, Maarten Fauvart, Federico Buja, Tim Stakenborg, Stuart C. Ray, Paolo Fiorini, and William O. Osburn
Royal Society of Chemistry (RSC)
Rapid and sensitive amplification of viral nucleic acids is feasible on a flexible silicon microchip technology platform.
Ujjal Barman, Rodrigo Sergio Wiederkehr, Paolo Fiorini, Liesbet Lagae, and Benjamin Jones
IOP Publishing
This paper presents the design and development of an optimized aluminum microheater integrated onto a biochip for the amplification of DNA using polymerase chain reaction (PCR). A coupled 3D finite element electro-thermal simulation has been used to aid in the design of the microheater and the PCR reactor. The microheater has a special shape, designed to provide a uniform temperature throughout the PCR chamber. The microreactor is fabricated at the center of a 20 mm × 20 mm silicon chip. It has a meandered shape, a volume of 1.89 µl and occupies a square area with a side of 3.8 mm. Microchannels to transport fluid in and out of the reactor are also provided. After heater design optimization, the simulated temperature of the fluid volume within the PCR chamber is very uniform (95% of the volume has a temperature within ±0.2 °C when the average temperature is 60 °C). This result is validated by DNA melting point experiments, showing a very similar uniformity. A PCR experiment, consisting of 50 cycles of amplification is conducted to demonstrate functionality of the system; amplifications is uniform across the reactor with variation of the threshold cycle within about 0.5 units.
Masahiko Tsukuda, Rodrigo Sergio Wiederkehr, Qing Cai, Bivragh Majeed, Paolo Fiorini, Tim Stakenborg, and Toshinobu Matsuno
IOP Publishing
A silicon microfluidic chip was developed for microRNA (miRNA) quantitative analysis. It performs sequentially reverse transcription and polymerase chain reaction in a digital droplet format. Individual processes take place on different cavities, and reagent and sample mixing is carried out on a chip, prior to entering each compartment. The droplets are generated on a T-junction channel before the polymerase chain reaction step. Also, a miniaturized fluorescence detector was developed, based on an optical pick-up head of digital versatile disc (DVD) and a micro-photomultiplier tube. The chip integrated in the detection system was tested using synthetic miRNA with known concentrations, ranging from 300 to 3,000 templates/µL. Results proved the functionality of the system.
L. Zhang, Q. Cai, R. S. Wiederkehr, M. Fauvart, P. Fiorini, B. Majeed, M. Tsukuda, T. Matsuno, and T. Stakenborg
Royal Society of Chemistry (RSC)
We present a silicon-based integrated microsystem combining a blood lysis chamber, a cross-flow filter, a T-junction mixer, and a microreactor for quantitative polymerase chain reaction. The detection of multiple single nucleotide polymorphisms was demonstrated in the system from human blood.
Rodrigo S. Wiederkehr and Sergio B. Mendes
Royal Society of Chemistry (RSC)
We report here the fabrication, characterization, and application of a single-mode integrated optical waveguide (IOW) spectrometer capable of acquiring optical absorbance spectra of surface-immobilized molecules in the visible and ultraviolet spectral region down to 315 nm.
Hiroyuki Tanaka, Paolo Fiorini, Benjamin Jones, Sara Peters, Rodrigo S. Wiederkehr, Bivraph Majeed, Hidenobu Yaku, Maki Hiraoka, Toshinobu Matsuno, and Ichiro Yamashita
IOP Publishing
We developed an electrochemical (EC) sensor having dry reagents to detect pyrophosphoric acid (PPi) produced as a by-product of a polymerase-chain-reaction (PCR) amplicon for single nucleotide polymorphism (SNP) detection. The EC sensor is implementable in a lab-on-chip (LoC) system, and a sensor chip having side-wall electrical connections that enable electrical contacts from the top of the LoC has been developed. We also developed separated on-chip placement of dry reagents divided into three groups in a sensor cavity to suppress background current when there is no PPi. Using this chip, we successfully demonstrated SNP detection in the ABO gene from human blood samples, in combination with the allele-specific PCR amplification method using our developed LoC system.
Geoffrey C. Hoops
SPIE-Intl Soc Optical Eng
In this work, we experimentally investigated the effects of sodium chloride on the molar absorptivity and surface density of a sub- monolayer of chlorophyll a adsorbed onto hydrophilic and hydrophobic solid/liquid interfaces. Those investigations were made possible by a broadband spectroscopic platform based on single-mode, integrated op- tical waveguides, which allows for extremely sensitive spectroscopic de- tection of analytes immobilized at submonolayer levels. Chlorophyll a with a constant bulk concentration (1.4 μM) was dissolved in phosphate buffer solutions (7 mM) of neutral pH, but with different sodium chloride concen- trations. For a buffer solution of 1 mM of sodium chloride, the measured surface density of chlorophyll a was 0.209 pmol/cm 2 for a hydrophilic and 0.125 pmol/cm 2 for a hydrophobic surface. For a phosphate buffer solution of 10 mM of sodium chloride, the measured surface density of chlorophyll a was 0.528 pmol/cm 2 for a hydrophilic and 0.337 pmol/cm 2 for a hy- drophobic surface. Additionally, a hypsochromic shift of the Soret band was observed for the adsorbed pigment in correlation with an increase in buffer ionic strength. The adsorption of chlorophyll a onto different sur- faces can play an important role to elucidate several processes found in nature and provide a rationale for bio-inspired new material technologies.
Mustafa M. Aslan, Nathan A. Webster, Courtney L. Byard, Marcelo B. Pereira, Colin M. Hayes, Rodrigo S. Wiederkehr, and Sergio B. Mendes
Elsevier BV
Rodrigo S. Wiederkehr, Geoffrey C. Hoops, Mustafa M. Aslan, Courtney L. Byard, and Sergio B. Mendes
IEEE
In this work we report experimental results on the molar absorptivity of cytochrome c adsorbed at different submonolayer levels onto an aluminum oxide waveguide surface. The spectra was acquired using the broadband, single-mode, integrated optical waveguide spectroscopic technique, which is an extremely sensitive tool able to reach submonolayer levels of detection required for this type of studies. For a protein surface density of 2.3 pmol/cm<sup>2</sup> the molar absorptivity measured at 695 nm was 335 M<sup>−1</sup> cm<sup>−1</sup>, and for a surface density of 14.6 pmol/cm<sup>2</sup> was 720 M<sup>−1</sup> cm<sup>−1</sup> which is much closer to the value of cyt c dissolved in an aqueous neutral buffer (830 M<sup>−1</sup> cm<sup>−1</sup>). Our data show a clear dependence of the protein optical properties on its surface density. The modification of the protein molar absorptivity can most likely be attributed to conformational changes of the surface-adsorbed species.
Rodrigo S. Wiederkehr, Geoffrey C. Hoops, Mustafa M. Aslan, Courtney L. Byard, and Sergio B. Mendes
American Chemical Society (ACS)
In this work, we report experimental results on the molar absorptivity of cytochrome c adsorbed at different submonolayer levels onto an aluminum oxide waveguide surface; our data show a clear dependence of the protein optical properties on its surface density. The measurements were performed using the broadband, single-mode, integrated optical waveguide spectroscopic technique, which is an extremely sensitive tool able to reach submonolayer levels of detection required for this type of studies. This investigation focuses on the molar absorptivity at the Q-band (centered at 525 nm) and, for the first time to our knowledge, the weak charge transfer (CT) band (centered at 695 nm) of surface-adsorbed cyt c. Polarized light in the spectral region from 450 to 775 nm was all-coupled into an alumina thin film, which functioned as a single-mode planar optical waveguide. The alumina thin-film waveguide used for this work had a thickness of 180 nm and was deposited on a glass substrate by the atomic layer deposition process. The protein submonolayer was formed on the alumina waveguide surface through electrostatic adsorption from an aqueous buffer solution at neutral pH. The optical properties of the surface-adsorbed cyt c were investigated for bulk protein concentrations ranging from 5 nM to 8200 nM in the aqueous buffer solution. For a protein surface density of 2.3 pmol/cm(2), the molar absorptivity measured at the charge transfer band was 335 M(-1) cm(-1), and for a surface density of 15 pmol/cm(2) was 720 M(-1) cm(-1), which is much closer to the value of cyt c dissolved in an aqueous neutral buffer (830 M(-1) cm(-1)). The modification of the protein molar absorptivity and its dependence on the surface density can most likely be attributed to conformational changes of the surface-adsorbed species.
Rodrigo Sergio Wiederkehr, Maria Cecilia Salvadori, Fernando Massa Fernandes, and Mauro Cattani
IEEE
Gas flow through a conical micronozzle integrated with a piezoelectric actuator has been numerically studied using continuum methods. Experimental data of air flow through a converging-diverging nozzle of throat diameter 245 mum with and without actuator at its outlet side were used for reference. The inlet pressure was kept constant at 266 Pa in all measurements. The actuator at the nozzle outlet was fabricated from poli(vinylidene fluoride) (PVDF), a piezoelectric polymer, and has a 3 mm x 6 mm rectangular shape. A voltage of +300 V DC was used to open the device, and -200 V to close it. The micronozzle with actuator is a microvalve, since the gas flow rate can be controlled by the actuator. We used Ansys/CFX software to solve the Navier Stokes equations for this valve system. The Mach number was obtained for both cases, micronozzle with and without actuator at the outlet.