ReactomeGSA: new features to simplify public data reuse.

MOTIVATION: ReactomeGSA is part of the Reactome knowledgebase and one of the leading multi-omics pathway analysis platforms. ReactomeGSA provides access to quantitative pathway analysis methods supporting different 'omics data types. Additionally, ReactomeGSA can process different datasets simultaneously, leading to a comparative pathway analysis that can also be performed across different species. RESULTS: We present a major update to the ReactomeGSA analysis platforms that greatly simplifies the reuse and direct integration of public data. In order to increase the number of available datasets, we developed the new grein_loader Python application that can directly fetch experiments from the GREIN resource. This enabled us to support both EMBL-EBI's Expression Atlas and GEO RNA-seq Experiments Interactive Navigator within ReactomeGSA. To further increase the visibility and simplify the reuse of public datasets, we integrated a novel search function into ReactomeGSA that enables users to search for public datasets across both supported resources. Finally, we completely re-developed ReactomeGSA's web-frontend and R/Bioconductor package to support the new search and loading features, and greatly simplify the use of ReactomeGSA. AVAILABILITY AND IMPLEMENTATION: The new ReactomeGSA web frontend is available at https://www.reactome.org/gsa with an built-in, interactive tutorial. The ReactomeGSA R package (https://bioconductor.org/packages/release/bioc/html/ReactomeGSA.html) is available through Bioconductor and shipped with detailed documentation and vignettes. The grein_loader Python application is available through the Python Package Index (pypi). The complete source code for all applications is available on GitHub at https://github.com/grisslab/grein_loader and https://github.com/reactome.

Nanoimprint Replication of Biomimetic, Multilevel Undercut Nanostructures.

The nanoimprint replication of biomimetic nanostructures can be interesting for a wide range of applications. We demonstrate the process chain for Morpho-blue-inspired nanostructures, which are especially challenging for the nanoimprint process, since they consist of multilayer undercut structures, which typically cannot be replicated using nanoimprint lithography. To achieve this, we used a specially made, proprietary imprint material to firstly allow successful stamp fabrication from an undercut master structure, and secondly to enable UV-based nanoimprinting using the same material. Nanoimprinting was performed on polymer substrates with stamps on polymer backplanes to be compatible with roller-based imprinting processes. We started with single layer undercut structures to finally show that it is possible to successfully replicate a multilayer undercut stamp from a multilayer undercut master and use this stamp to obtain multilayer undercut nanoimprinted samples.

Mastering of NIL Stamps with Undercut T-Shaped Features from Single Layer to Multilayer Stamps.

Biomimetic structures such as structural colors demand a fabrication technology of complex three-dimensional nanostructures on large areas. Nanoimprint lithography (NIL) is capable of large area replication of three-dimensional structures, but the master stamp fabrication is often a bottleneck. We have demonstrated different approaches allowing for the generation of sophisticated undercut T-shaped masters for NIL replication. With a layer-stack of phase transition material (PTM) on poly-Si, we have demonstrated the successful fabrication of a single layer undercut T-shaped structure. With a multilayer-stack of silicon oxide on silicon, we have shown the successful fabrication of a multilayer undercut T-shaped structures. For patterning optical lithography, electron beam lithography and nanoimprint lithography have been compared and have yielded structures from 10 µm down to 300 nm. The multilayer undercut T-shaped structures closely resemble the geometry of the surface of a Morpho butterfly, and may be used in future to replicate structural colors on artificial surfaces.

A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.

Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 µm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.

Investigation of Mass-Produced Substrates for Reproducible Surface-Enhanced Raman Scattering Measurements over Large Areas.

Surface-enhanced Raman scattering (SERS) is a versatile spectroscopic technique that suffers from reproducibility issues and usually requires complex substrate fabrication processes. In this article, we report the use of a simple mass production technology based on Blu-ray disc manufacturing technology to prepare large area SERS substrates (∼40 mm2) with a high degree of homogeneity (±7% variation in Raman signal) and enhancement factor of ∼6 × 106. An industrial high throughput injection molding process was used to generate periodic microstructured polymer substrates coated with a thin Ag film. A short chemical etching step produces a highly dense layer of Ag nanoparticles at the polymer surface, which leads to a large and reproducible Raman signal. Finite difference time domain simulations and cathodoluminescence mapping experiments suggest that the sample microstructure is responsible for the generation of SERS active nanostructures around the microwells. Comparison with commercial SERS substrates demonstrates the validity of our method to prepare cost-efficient, reliable, and sensitive SERS substrates.

Structural Characterization of a Capillary Microfluidic Chip Using Microreflectance.

The structural characterization of capillary microfluidic chips is important for reliable applications. In particular, nondestructive diagnostic tools to assess geometrical dimensions and their correlations with control processes are of much importance, preferably if they are implemented in situ. Several techniques to accomplish this task have been reported; namely, optical coherence tomography (OCT) jointly with confocal fluorescence microscopy (CFM) to investigate internal features of lab-on-a-chip technologies. In this paper, we report on the use of a simple optical technique, based on near-normal incidence microreflectance, which allows mapping internal features of a microfluidic chip in a straightforward way. Our setup is based on a charge-coupled device camera that allows a lateral resolution of ∼2.5 µm and allows us to measure in the wavelength range of 640-750 nm. The technique takes advantage of the Fabry-Perot interferences features in the reflectance spectra, which are further analyzed by a discrete Fourier transform. In this way, the amplitude of the Fourier coefficients is modulated by the presence of a microfluidic channel.

Optical planar waveguide for cell counting.

Low cost counting of cells has medical applications in screening, military medicine, disaster medicine, and rural healthcare. In this report, we present a shallow, buried, planar waveguide fabricated by potassium ion exchange in glass that enables low-cost and rapid counting of metal-tagged objects that lie in the evanescent field of the waveguide. Laser light transmitted through the waveguide was attenuated proportionately to the presence of metal-coated microstructures fabricated from photoresist. This technology enables the low-cost enumeration of cells from blood, urine, or other biofluids.