Separation of parasites from human blood using deterministic lateral displacement

We present the use of a simple microfluidic technique to separate living parasites from human blood. Parasitic trypanosomatids cause a range of human and animal diseases. African trypanosomes, responsible for human African trypanosomiasis (sleeping sickness), live free in the blood and other tissue fluids. Diagnosis relies on detection and due to their often low numbers against an overwhelming background of predominantly red blood cells it is crucial to separate the parasites from the blood. By modifying the method of deterministic lateral displacement, confining parasites and red blood cells in channels of optimized depth which accentuates morphological differences, we were able to achieve separation thus offering a potential route to diagnostics.     

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

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Band-broadening effects in preparative free-flow zone electrophoresis

Recently, we proposed a novel preparative free flow zone electrophoresis cell with extremely short residence time, which does not require external cooling (Poggel, M., Melin, T., Electrophoresis 2001, 22, 1008-1015). Within the new cell the smallest chamber dimension is not orientated perpendicular but in direction of the electric field. This alteration provides straight forward scale up opportunities. In this paper, new experimental results are reported, from which the limits of stable flow can be determined. The data suggest that not density differences but electrohydrodynamic effects are responsible for the disturbance of the laminar flow pattern, which is observed above a critical field strength. To demonstrate the efficiency of the new system, a three-component mixture consisting of bovine serum albumin (BSA), myoglobin and cytochrome c is processed, resulting in relatively high recovery and purity values of the different proteins, although a complete separation is not achieved.     

Identification of anhydroecgonine methyl ester N-oxide,a new metabolite of anhydroecgonine methyl ester,using electrospray mass spectrometry

Cocaine is transformed into hepatotoxic metabolites through oxidative pathways. For anhydroecgonine methyl ester (AEME), the main constituent in crack smoke, the oxidative metabolism has not been studied. Therefore, incubation of AEME with rat liver microsomes was performed and a metabolite of AEME, anhydroecgonine methyl ester N-oxide (AEMENO), was identified. The chemical structure of this new metabolite was confirmed by synthesis and by comparative interpretation of electrospray multiple-stage mass spectra, which were obtained in the positive ion mode. This metabolite was also detected in whole blood, serum and urine samples from crack users. The application of liquid chromatography/electrospray mass spectrometry or nanoelectrospray mass spectrometry was necessary because AEMENO is susceptible to thermal degradation during gas chromatographic/mass spectrometric analysis. This study demonstrated that AEMENO is produced by rat hepatic microsomal metabolism in vitro and is present in body fluids from crack users.     

Design,synthesis, and evaluation of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-ribitylaminolumazines as inhibitors of riboflavin synthase and lumazine synthase

A series of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-D-ribityllumazine were synthesized as inhibitors of both Escherichia coli riboflavin synthase and Bacillus subtilis lumazine synthase. The compounds were designed to bind to both the ribitylpurine binding site and the phosphate binding site of lumazine synthase. In the carboxyalkyl series, maximum activity against both enzymes was observed with the 3'-carboxypropyl compound 22. Lengthening or shortening the chain linking the carboxyl group to the lumazine by one carbon resulted in decreased activity. In the phosphonoxyalkyl series, the 3'-phosphonoxypropyl compound 33 was more potent than the 4'-phosphonoxybutyl derivative 39 against lumazine synthase, but it was less potent against riboflavin synthase. Molecular modeling suggested that the terminal carboxyl group of 6-(3'-carboxypropyl)-7-oxo-8-D-ribityllumazine (22) may bind to the side chains of Arg127 and Lys135 of the enzyme. A hypothetical molecular model was also constructed for the binding of 6-(2'-carboxyethyl)-7-oxolumazine (15) in the active site of E. coli riboflavin synthase, which demonstrated that the active site could readily accommodate two molecules of the inhibitor.     

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies,aqueous p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript>, and cyclohexane–water log <Emphasis Type="Italic">D</Emphasis>

We predict cyclohexane–water distribution coefficients (log D _7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pK _a) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the “Minnesota Solvation Database” (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol^?1 for water and 0.8–0.9 kcal mol^?1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pK _a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2–3 for each solvent and two for the pK _a) for training solvation and acidity models. Applying the final models to the log D _7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0–2.1 for the RMSE with the first and 2.2–2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.     

Comparative study of 8-hydroxyquinoline derivatives as chelating reagents for flow-injection preconcentration of cobalt in a knotted reactor

8-Hydroxyquinoline (HQ), 2-methyl-8-hydroxyquinoline (CH₃-HQ), 5,7-dichloro-2-methyl-8-hydroxyquinoline (Cl₂-CH₃-HQ), 5,7-dibromo-8-hydroxyquinoline (Br₂-HQ), 5-sulfo-7-iodo-8-hydroxyquinoline (ferron) and 5-sulfo-8-hydroxyquinoline (SO₃H-HQ) were compared as chelating reagents for on-line sorption preconcentration of cobalt in a knotted reactor (KR) precoated with the reagent. The results obtained with the different HQ derivatives reveal those properties of the chelating reagent responsible for the processes taking place in the KR. The influence of hydrophobicity, acidity, stability of the cobalt chelate and type of substituents in the HQ ring system on the separate steps of the flow injection (FI) preconcentration procedure are discussed. According to the performance characteristics of the different HQ derivatives, the most important parameters for on-line preconcentration in a KR are the hydrophobicity of the reagent and the stability of the chelate complex with the analyte.