pinecone/core-2020-05-10-deduplication huggingface dataset:
Focusing particles by induced charge electrokinetic flow in a microchannel

This is the peer reviewed version of the following article: Song, Y., Wang, C., Li, M., Pan, X. and Li, D. (2016), Focusing particles by induced charge electrokinetic flow in a microchannel. ELECTROPHORESIS, 37: 666–675. doi:10.1002/elps.201500361, which has been published in final form at http://dx.doi.org/10.1002/elps.201500361. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.A novel method of sheathless particle focusing by induced charge electrokinetic flow in a microchannel is presented in this paper. By placing a pair of metal plates on the opposite walls of the channel and applying an electrical field, particle focusing is achieved due to the two pairs of vortex that constrain the flow of the particle solution. As an example, the trajectories of particles under different electrical fields with only one metal plate on one side channel wall were numerically simulated and experimentally validated. Other flow focusing effects, such as the focused width ratio (focused width/channel width) and length ratio (focused length/half-length of metal plate) of the sample solution, were also numerically studied. The results show that the particle firstly passes through the gaps between the upstream vortices and the channel walls. Afterwards, the particle is focused to pass through the gap between the two downstream vortices that determine the focused particle position. Numerical simulations show that the focused particle stream becomes thin with the increases in the applied electrical field and the length of the metal plates. As regards to the focused length ratio of the focused stream, however, it slightly increases with the increase in the applied electrical field and almost keeps constant with the increase in the length of the metal plate. The size of the focused sample solution, therefore, can be easily adjusted by controlling the applied electrical field and the sizes of the metal plates
Metabolic profiling for the identification of Huntington biomarkers by on-line solid-phase extraction capillary electrophoresis mass spectrometry combined with advanced data analysis tools

In this work, an untargeted metabolomic approach based on sensitive analysis by on-line solid-phase extraction capillary electrophoresis mass spectrometry (SPE-CE-MS) in combination with multivariate data analysis is proposed as an efficient method for the identification of biomarkers of Huntington's disease (HD) progression in plasma. For this purpose, plasma samples from wild type (wt) and HD (R6/1) mice of different ages (8, 12 and 30 weeks), were analysed by C18-SPE-CE-MS in order to obtain the characteristic electrophoretic profiles of low molecular mass compounds. Then, multivariate curve resolution alternating least squares (MCR-ALS) was applied to the multiple full scan MS data sets. This strategy permitted the resolution of a large number of metabolites being characterised by their electrophoretic peaks and their corresponding mass spectra. A total number of 29 compounds were relevant to discriminate between wt and HD plasma samples, as well as to follow-up the HD progression. The intracellular signalling was found to be the most affected metabolic pathway in HD mice after 12 weeks of birth, when mice already showed motor coordination deficiencies and cognitive decline. This fact agreed with the atrophy and dysfunction of specific neurons, loss of several types of receptors and changed expression of neurotransmitters
Microemulsion electrokinetic chromatography as a suitable tool for lipophilicity determination of acidic, neutral, and basic compounds

In the present work, several MEEKC systems are studied to assess their suitability for lipophilicity determination of acidic, neutral, and basic compounds. Thus, several microemulsion compositions over a wide range of pH values (from 2.0 to 12.0), containing heptane, 1−butanol and different types and amounts of surfactant (SDS or sodium cholate: from 1.3 to 3.3%) are characterized using Abraham's solvation model. The addition of acetonitrile (up to 10%) is also studied, since it increases the resolution of the technique for the most lipophilic compounds. The system coefficients obtained are very similar to those of the 1−octanol/water, used as the reference lipophilicity index, allowing simple and linear correlations between the 1−octanol/water partition values (log Po/w) and MEEKC mass distribution ratios (log kMEEKC). Variations in the microemulsion composition (aqueous buffer, surfactant, concentration of ACN) did not significantly affect the similarity of the MEEKC systems to log Po/w partition
Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing

The presence of specific body fluids at crime scenes could be linked with particular types of crime, therefore attributing a DNA profile to a specific tissue could increase the evidential significance of a match with a suspect. Current methodologies such as tissue-specific mRNA profiling are useful but drawbacks include low tissue specificity and applicability to degraded samples. In this study, the potential of 11 tissue-specific differentially methylated regions, initially identified following large-scale methylation analysis of whole blood, buccal cells and sperm, was explored in order to identify markers for blood, saliva and semen. Bisulphite pyrosequencing analysis supported previous findings, but tissue-specific differentially methylated regions for blood and buccal cells did not show enough specificity to be proposed as markers for blood and saliva, respectively. For some CpGs, a large inter-individual variation in methylation levels was also observed. Two of the semen markers (cg04382920 and cg11768416) were used for further validation on a large set of stains. These two semen-specific assays showed high sensitivity (as low as 50 pg) and stability. Future experiments will shed light on the usefulness of these markers in forensic casework
A single step protein assay that is both detergent and reducer compatible: The cydex blue assay.

International audienceDetermination of protein concentration in often an absolute pre-requisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are however present simultaneously in most denaturing extraction buffers used in proteomics and electrophoresis, and in particular in SDS electrophoresis. We found that inclusion of cyclodextrins in a Coomassie blue-based assay made it compatible with detergents, as cyclodextrins complex detergents in a 1:1 molecular ratio. As this type of assay is intrinsically resistant to reducers, we have thus developed a single step assay that is both detergent and reducer compatible. Depending on the type and concentration of detergents present in the sample buffer, either beta-cyclodextrin or alpha-cyclodextrin can be used, the former being able to complex a wider range of detergents and the latter being able to complex higher amounts of detergents due to its greater solubility in water. Cyclodextrins are used at final concentrations of 2-10 mg/mL in the assay mix. This typically allows to measure samples containing as little as 0.1 mg/mL protein, in the presence of up to 2% detergent and reducers such as 5 % mercaptoethanol or 50 mM DTT in a single step with a simple spectrophotometric assay. This article is protected by copyright. All rights reserved
Fabrication and electrokinetic motion of electrically anisotropic Janus droplets in microchannels

This is the peer reviewed version of the following article: Li, M. and Li, D. (2017), Fabrication and electrokinetic motion of electrically anisotropic Janus droplets in microchannels. ELECTROPHORESIS, 38: 287–295 which has been published in final form at http://dx.doi.org/10.1002/elps.201600310. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.This paper presents experimental investigations of the fabrication and the motion of electrically anisotropic Janus droplets in a microchannel under externally applied direct current (DC) electrical field. The fabrication method of the Janus droplets is presented first. To begin, oil droplets are coated uniformly with positively charged nanoparticles in the aluminum oxide nanoparticle suspension. The electrically anisotropic Janus droplets are formed when the nanoparticles are accumulated to one side of the droplets in response to externally applied DC electric field. The surface coverage of the Janus droplets by nanoparticles can be adjusted by controlling the concentration of the nanoparticle suspension. The flow fields around the Janus droplets moving in a microchannel were observed with tracing particles. Finally, the electrokinetic velocity of the Janus droplets in a microchannel was measured. The effects of the strength of the electrical field, the surface coverage of the Janus droplets by nanoparticles, the size of the droplets as well as the electrolyte concentration on the electrokinetic velocity of the Janus droplets were studied.Natural Sciences and Engineering Research Council of Canad
A fully automated linear polyacrylamide coating and regeneration method for capillary electrophoresis of proteins

Surface modification of the inner capillary wall in CE of proteins is frequently required to alter EOF and to prevent protein adsorption. Manual protocols for such coating techniques are cumbersome. In this paper, an automated covalent linear polyacrylamide coating and\ud
regeneration process is described to support long-term stability of fused-silica capillaries for protein analysis. The stability of the resulting capillary coatings was evaluated by a large number of separations using a three-protein test mixture in pH 6 and 3 buffer systems. The results were compared to that obtained with the use of bare fused-silica capillaries. If necessary, the fully automated capillary coating process was easily applied to regenerate the capillary to extend its useful life-time
ssDNA degradation along capillary electrophoresis process using a Tris buffer

Tris-Acetate buffer is currently used in the selection and the characterization of ssDNA by capillary electrophoresis (CE). By applying high voltage, the migration of ionic species into the capillary generates a current that induces water electrolysis. This phenomenon is followed by the modification of the pH and the production of Tris derivatives. By injecting ten times by capillary electrophoresis ssDNA (50 nM), the whole oligonucleotide was degraded. In this paper, we will show that the Tris buffer in the running vials is modified along the electrophoretic process by electrochemical reactions. We also observed that the composition of the metal ions changes in the running buffer vials. This phenomenon, never described in CE, is important for fluorescent ssDNA analysis using Tris buffer. The oligonucleotides are degraded by electrochemically synthesized species (present in the running Tris vials) until it disappears, even if the separation buffer in the capillary is clean. To address these issues, we propose to use a sodium phosphate buffer that we demonstrate to be electrochemically inactive
Tilted pillar array fabrication by the combination of proton beam writing and soft lithography for microfluidic cell capture Part 2: Image sequence analysis based evaluation and biological application

As a continuation of our previously published work, this paper presents a detailed evaluation of a microfabricated cell capture device utilizing a doubly tilted micropillar array. The device was fabricated using a novel hybrid technology based on the combination of proton beam writing and conventional lithography techniques. Tilted pillars offer unique flow characteristics and support enhanced fluidic interaction for improved immuno-affinity based cell capture. The performance of the microdevice was evaluated by an image sequence analysis based in-house developed single cell tracking system. Individual cell tracking allowed in-depth analysis of the cell-chip surface interaction mechanism from hydrodynamic point of view. Simulation results were validated by using the hybrid device and the optimized surface functionalization procedure. Finally, the cell capture capability of this new generation microdevice was demonstrated by efficiently arresting cells from a HT29 cellline suspension
Fast determination of lactic, succinic, malic,\ud
tartaric, shikimic, and citric acids in red\ud
Vranec wines by CZE-ESI-QTOF-MS

Afast and simple method with CZE coupled to ESI/QTOF-MS was optimized and validated for quantitative determination of organic acids (lactic acid, succinic acid, malic acid, tartaric acid, shikimic acid, and citric acid) in red wines. The BGE was ammonium acetate and the separation of the analytes was performed in a polybrene-coated capillary in the presence of EOF. The sample preparation included dilution and ﬁltration of the wine. The method showed satisfactory performance characteristics: good linearity for each organic acid, with correlation coefﬁcients ranging from r2= 0.9902 (shikimic acid) to r2= 0.9990 (tartaric acid). The limit of quantiﬁcation was between 0.0034 mM(for shikimic acid) and 0.107 mM (for citric acid), and the recovery data fell between 95.8% (malic acid) and 102.7% (lactic acid); the total run time was less than 4 min. The RSD values for the interday repeatability and intraday reproducibility were between 3.44 and 9.50%, and between 1.75 and 8.29%, respectively. Seventeen Macedonian red Vranec wines were studied demonstrating a wide variation in the organic acids’ concentration, which should be most probably due to the variation of the climate conditions in the vine areas
Strategies towards the functionalization of subtilisin  E from bacillus subtilis for wool finishing applications

Subtilisin E is an alkaline serine protease secreted by the Gram positive bacterium Bacillus subtilis and widely used in industry as a biocatalyst for various processes. The most common application of subtilisins is in laundry detergents. However, due to environmental concerns, the application of subtilisins to treat wool, is under study. There are some reports regarding the attempts to substitute the conventional chlorine treatment by an enzymatic process capable of providing the same characteristics to the fabric, like anti-shrinking and better uptake and fixation of the dyestuff. However, the degree of uncontrolled hydrolysis due to diffusion of the enzyme inside the wool fiber causes unacceptable losses of strength. To overcome this fact, and taking advantage of the x-ray crystallographic structure, the authors have modified subtilisin E genetically, increasing its molecular weight, to restrict the hydrolysis to the surface of the wool fibers. Therefore, three genetically modified enzymes with a molecular weight 2-fold to 4-fold higher than the native subtilisin E were produced and assessed for activity. The prokaryotic expression systems, pET25b (+), pET11b and pBAD C, were explored for the production of recombinant enzymes. The results demonstrated that regardless the expression system or strain used, chimeric subtilisins were not expressed with the correct folding. No active and soluble recombinant protein was recovered under the testing conditions. Despite this drawback, a novel approach was described to increase the molecular weight of subtilisin. The reported results are noteworthy and can indicate good guidelines for future work aiming at the solubilization of recombinant chimeric subtilisins
In-situ enzymatic generation of hydrogen peroxide for bleaching purposes

Bleaching detergent formulations contain environmentally unfriendly bleaching agents (perborates and percarbonates), which cause aquatic eutrophication, although without these compounds detergents are much less efficient for the washing processes. In an effort to replace these compounds, in this study, hydrogen peroxide was generated as a bleaching compound by means of enzymatic reactions. Three different pathways were investigated. The first one was the H2O2 production from glucose by glucose oxidase. The second one was the production of H2O2 from carboxymethylcellulose (CMC) by the action of both cellulase, which promotes the hydrolysis of the polymeric chain, and glucose oxidase, which oxidizes the smaller fractions to produce H2O2. Finally, H2O2 was also obtained from ethanol, which is present in liquid detergents, by the action of the enzyme alcohol oxidase. In the search for maximal peroxide production, substrate concentration and enzymatic activities were optimized. The effect of H2O2 produced in the washing process was simulated by means of a process of cotton bleaching. Although enzymatic-reaction oxidations produced higher levels of hydrogen peroxide (up to 1 g/L after 8 h), higher improvement of cotton whiteness was achieved from CMC and from ethanol. The milder conditions of temperature and pH, biodegradability and less consumption of water and energy are advantageous for enzymes as good substitutes for H2O2 precursors and make them appropriate to be considered in detergent formulations. These enzymes could be combined with other oxidative enzymes, such as peroxidases, in order to lower the required temperature and use a pH close to the neutral value during the bleaching processes
Biological coloration of flax fabrics with flavonoids using laccase from trametes hirsuta

Biological environmentally friendly concepts are emerging to replace chemical treatments of fabrics. In this work, a new process for the coloration of flax fabrics via enzymatic oxidation of natural flavonoids (morin, quercetin) has been developed. Laccase from Trametes hirsuta is able to react with flavonoids and polymerize them, resulting in a strongly colored polymeric solution which can be applied to the coloration of flax fabrics. Two methods were investigated: (i) the simultaneous enzymatic polymerization and coloration of fabrics and (ii) the polymerization of flavonoids with laccase, followed by a further coloration of the flax fabrics. Factors such as temperature, reaction time, presence of NaCl or the use of bleached or unbleached fabrics were evaluated in order to increase the color of the fabrics and the color fastness. The increase of temperature, the presence of salt and the use of unbleached fabrics allowed the final color to be improved. Colorized flax fabrics with oxidized quercetin solution showed a color fixation two times higher than the fabrics colorized with oxidized morin. Finally, the polymerization of flavonoids and their binding to fibers were verified using Fourier transform infrared spectroscopy (FT-IR). The results confirmed this environmentally friendly process as useful for the coloration of flax fabrics. A similar technique could also be extended to the treatment of other types of fabrics in textile processes
Downstream processing of high chain length polysialic acid using membrane adsorbers and clay minerals for application in tissue engineering

Polysialic acid (polySia) is a carbohydrate polymer of varying chain length. It is a promising scaffold material for tissue engineering. In this work, high chain length polySia was produced by an Escherichia coli K1 strain in a 10-L bioreactor in batch and fed-batch mode, respectively. A new downstream process for polySia is presented, based on membrane adsorber technology and use of inorganic anion exchanger. These methods enable the replacement of precipitation steps, such as acetone, cetavlon, and ethanol precipitation of the already established purification process. The purification process was simplified, while process efficiency and product qualities were improved. The overall yield of polySia from a 10-L batch cultivation process was 61% and for 10-L fed-batch cultivation process the yield was 40% with an overall purity of 98%. The endotoxin content was determined to be negligible (14 EU mg-1). The main advantage of this new downstream process is that polySia with high chain length of more than 130 degree of polymerization can be obtained. In fed-batch cultivation, chain lengths up to 160 degree of polymerization were obtained.DFG/FOR/54
Evolution of fluorinated enzymes: an emerging trend for biocatalyst stabilization

Nature uses remarkably limited sets of chemistries in its repertoire, especially when compared to synthetic organic chemistry. This limits both the chemical and structural diversity that can ultimately be achieved with biocatalysis, unless the powers of chemical synthesis are merged with biological systems by integrating nonnatural synthetic chemistries into the protoplasma of living cells. Of particular interest, here is the fluorous effect that has recently established the potential to generate enzymes with an increased resistance toward both high temperature and organic solvents. For these reasons, we are witnessing a rapid development of efficient methodologies for the incorporation of fluorinated amino acids in protein synthesis, using both in vivo and in vitro strategies. In this review, we highlight relevant and trendsetting results in the design and engineering of stable fluorinated proteins and peptides along with whole-cell biocatalysis as an economically attractive and convenient application with exclusive focus on industrial biocatalysis. Finally, we envision new strategies to improve current achievements and enable the field to progress far beyond the current state-of-the-art.DFG, EXC 314, Unifying Concepts in Catalysi
3D-printed individual labware in biosciences by rapid prototyping: In vitro biocompatibility and applications for eukaryotic cell cultures

Three-dimensional (3D) printing techniques are continuously evolving, thus their application fields are also growing very fast. The applications discussed here highlight the use of rapid prototyping in a dedicated biotechnology laboratory environment. The combination of improving prototypes using fused deposition modeling printers and producing useable parts with selective laser sintering printers enables a cost- and time-efficient use of such techniques. Biocompatible materials for 3D printing are already available and the printed parts can directly be used in the laboratory. To demonstrate this, we tested 3D printing materials for their in vitro biocompatibility. To exemplify the versatility of the 3D printing process applied to a biotechnology laboratory, a normal well plate design was modified in silico to include different baffle geometries. This plate was subsequently 3D printed and used for cultivation. In the near future, this design and print possibility will revolutionize the industry. Advanced printers will be available for laboratories and can be used for creating individual labware or standard disposables on demand. These applications have the potential to change the way research is done and change the management of stock-keeping, leading to more flexibility and promoting creativity of the scientists