A fully open source software program for automated two‐dimensional and one‐dimensional data reduction and preliminary analysis of isotropic small‐angle X‐ray scattering (SAXS) data is presented. The program is freely distributed, following the open‐source philosophy, and does not rely on any commercial software packages. BioXTAS RAW is a fully automated program that, via an online feature, reads raw two‐dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averaging, error bar calculation, artifact removal, normalization and q calibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easy via the graphical user interface. BioXTAS RAW also provides preliminary analysis of one‐dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair‐distance distribution function, PDDF, and is thereby a free and open‐source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII‐format input files and is currently compatible with one‐dimensional data files from SAXS beamlines at a number of synchrotron facilities. BioXTAS RAW is written in Python with C++ extensions.

Flow cytometry is widely used for analyzing microparticles, such as cells and bacteria. In this paper, we report an innovative microsystem, in which several different optical elements (waveguides, lens and fiber-to-waveguide couplers) are integrated with microfluidic channels to form a complete microchip flow cytometer. All the optical elements, the microfluidic system, and the fiber-to-waveguide couplers were defined in one layer of polymer (SU-8, negative photoresist) by standard photolithography. With only a single mask procedure required, all the fabrication and packaging processes can be finished in one day. Polystyrene beads were measured in the microchip flow cytometer, and three signals (forward scattering, large angle scattering and extinction) were measured simultaneously for each bead. To our knowledge this is the first time forward scattered light and incident light extinction were measured in a microsystem using integrated optics. The microsystem can be applied for analyzing different kinds of particles and cells, and can easily be integrated with other microfluidic components.

Taking the next step from individual functional components to higher integrated devices, we present a feasibility study of a lab-on-a-chip system with five different components monolithically integrated on one substrate. These five components represent three main domains of microchip technology: optics, fluidics and electronics. In particular, this device includes an on-chip optically pumped liquid dye laser, waveguides and fluidic channels with passive diffusive mixers, all defined in one layer of SU-8 polymer, as well as embedded photodiodes in the silicon substrate. The dye laser emits light at 576 nm, which is directly coupled into five waveguides that bring the light to five different locations along a fluidic channel for absorbance measurements. The transmitted portion of the light is collected at the other side of this cuvette, again by waveguides, and finally detected by the photodiodes. Electrical read-out is accomplished by integrated metal connectors. To our knowledge, this is the first time that integration of all these components has been demonstrated.

In this paper, we investigate the use of a commercial CO 2 laser system for fabrication of microfluidic systems in polymers. We discuss the cutting process with the laser system and present a straightforward model for the channel depth of microchannels dependent on the fabrication parameters. In particular, we examine the influence of the cutting sequence, the number of cut passes, the laser beam velocity and the laser radiant flux. The model allows the prediction of microchannel depths within a maximum deviation of 8 µm for channels that are up to 210 µm in depths. It was shown that, at constant channel depth, the channel width could be varied by 27% by using different cutting parameters. The optimum cutting sequence for the production of a channel T-junction is also presented in the paper. The laser system is shown to be a flexible and rapid tool for the production of polymer microfluidic prototypes.

This manuscript presents, for the first time, the method of automated structural analysis of biomolecules in solution on a microfluidic chip. A polymer-based micrototal analysis system for high-throughput Small-Angle X-ray Scattering (SAXS) data collection from biological macromolecules has been developed. The bioXTAS chip features an integrated X-ray transparent 200 nL sample chamber and diffusion-based mixing of protein and buffer solutions. Software for fully automated fluidic control, data acquisition, and data analysis has been developed. The proof-of concept is based on data using bovine serum albumin as the model system. It confirms the quality of SAXS data generated from small sample volumes and furthermore validates the on-chip mixing capabilities. SAXS data on the gradual unfolding of BSA induced by an anionic surfactant exemplifies how the bioXTAS chip can be used to follow and identify structural changes and proves the feasibility of high-throughput structural analysis in solution. In total, this shows that the bioXTAS chip has the potential for becoming a powerful tool for automated high-throughput structural analysis of macromolecular systems.

Electro membrane extraction was demonstrated in a microfluidic device. The device was composed of a 25 μm thick porous polypropylene membrane bonded between two poly(methyl methacrylate) (PMMA) substrates, each having 50 μm deep channel structures facing the membrane. The supported liquid membrane (SLM) consisted of 2-nitrophenyl octyl ether (NPOE) immobilized in the pores of the membrane. The driving force for the extraction was a 15 V direct current (DC) electrical potential applied across the SLM. Samples containing the basic drugs pethidine, nortriptyline, methadone, haloperidol, loperamide, and amitriptyline were used to characterize the system. Extraction recoveries were typically in the range of 65-86% for the different analytes when the device was operated with a sample flow of 2.0 μL/min and an acceptor flow of 1.0 μL/min. With the sample flow at 9.0 μL/min and the acceptor flow at 0.0 μL/min, enrichment factors exceeding 75 were obtained during 12 min of operation from a total sample volume of only 108 μL. The on-chip electro membrane system was coupled online to electrospray ionization mass spectrometry and used to monitor online and real-time metabolism of amitriptyline by rat liver microsomes.

This paper presents the first downscaling of electro membrane extraction (EME) to a chip format. The voltage-controlled extraction for sample preparation on microfluidic devices has several advantages such as selective extraction removing the high ionic strength of biological samples, preconcentration, fast kinetics with exact control of the beginning, and termination of the extraction. The device comprises a 25 lm thick porous polypropylene membrane bonded in-between two polymethyl methacrylate (PMMA) substrates with channel structures toward the membrane. The supported liquid membrane (SLM) was created by locally filling the pores of the membrane with 2-nitrophenyl octyl ether (NPOE). The sample solution, containing five basic model analytes in 10 mM HCl or urine was pumped through the 50 lm deep donor channel on one side of the membrane. With 15 V applied across the membrane, the protonated basic drugs were selectively extracted from the flowing sample solution, into the organic phase SLM, and further into just 7 ll of 10 mM HCl, serving as acceptor solution. Subsequently, the acceptor solution was analyzed by capillary electrophoresis. The electro membrane chip was highly efficient and even with flow rates resulting in the sample being in contact with the SLM for less than 4 s (3 ll min -1 ), 20-60% of the amount of the respective drugs in the sample was extracted. The large span in recovery was dependent on the physical properties of the drug substances compared to the SLM, and the individual drug substances were extracted with a RSD in the recovery of less than 5%.

Here, we describe a multi-parametric study of DNA hybridization to probes with 20–70% G + C content. Probes were designed towards 71 different sites/mutations in the phenylalanine hydroxylase gene. Seven probe lengths, three spacer lengths and six stringencies were systematically varied. The three spacer lengths were obtained by placing the gene-specific sequence in discrete steps along the 60-mer probes. The study was performed using Agilent 8 × 15 000 probes custom-made arrays and a home-built array washer providing different stringencies to each of the eight sub-arrays on the slides. Investigation of hybridization signals, specificity and dissociation curves indicated that probes close to the surface were influenced by an additional stringency provided by the microarray surface. Consistent with this, probes close to the surface required 4 × SSC, while probes placed away from the surface required 0.35 × SSC wash buffers in order to give accurate genotyping results. Multiple step dissociation was frequently observed for probes placed furthest away from surface, but not for probes placed proximal to the surface, which is consistent with the hypothesis that there is different stringency along the 60-mer. The results have impact on design of probes for genotyping, gene expression and comparative genome hybridization analysis.