High-throughput Capillary Electrophoresis Research Articles

Autonomous capillary electrophoresis processing and analysis of dried blood spots for high-throughput determination of uric acid

A new set-up for fully autonomous and high-throughput capillary electrophoresis (CE) analyses of dried blood spot (DBS) samples is presented. The DBS samples were prepared by collecting exactly 5 μL of capillary blood from a finger-prick onto a pre-punched DBS disc in a disposable plastic CE vial and by in-vial blood drying. The vials with the DBS samples were then loaded into a commercial CE instrument for a fully unmanned sample processing and analysis. A fused-silica capillary of the CE instrument was first used for the transfer of 100 μL of elution solvent to each vial, in-vial DBS elution, and in-vial eluate homogenization. The same capillary was also used for at-line injection, separation, and selective analysis of the resulting eluates. Novel CE sequences were tailor-programmed for consecutive processing and analyses of multiple DBSs, which facilitated a fully autonomous determination of uric acid with a throughput of 240 DBS samples per day (24 h). The presented analytical protocol (using 100 μm i. d./30 cm capillary; 30 mM 2-(N-morpholino)-ethanesulfonic acid, 30 mM l-histidine, and 30 μM cetyltrimethylammonium bromide background electrolyte solution; and UV detection at 292 nm) provided excellent precision at endogenous and spiked uric acid concentrations with RSD values of peak areas below 3.2%. Calibration curves were linear over the 33.3 − 1200 μM range (R2 better than 0.998), limits of detection and quantification in the original capillary blood were 10 and 33.3 μM, respectively, and were well below the uric acid clinical range (140–420 μM). The stability of uric acid in DBS samples stored at laboratory temperature for up to 2 months was also excellent demonstrating less than a 4.2% decrease in uric acid concentrations. The actual set-up might thus be highly attractive for clinical subjects and laboratories because it is minimally invasive and requires minimum intervention from laboratory staff.

High-throughput capillary electrophoresis analysis of biopharmaceuticals utilizing sequential injections.

The complexity of biotherapeutic products implies an ever-increasing list of product quality attributes that need to be monitored and characterized. In addition, the growing interest in implementing process analytical technology in biopharmaceutical production has further increased the testing burden, together with the need for rapid testing that can facilitate real-time or near-real-time decision-making. Capillary electrophoresis (CE) has made a place in biopharmaceutical analysis but is regarded as a low-throughput method, with the instrument dead time constituting more than 80% of the total time of analysis. In this study, the dead time of CE was utilized to analyse 3mAb samples in a single-CE run. This approach resulted in an up to 77% reduction in the total analysis time and increased the productivity by up to 300%, compared to traditional single CE-ultraviolet runs, without compromising resolution or relative peak areas. Additionally, good method reproducibility was observed. The compatibility of the method has been demonstrated with protein A eluate and cation exchange chromatography fractions. We, thus, propose that sequential injections can be applied for fast and robust CE analysis of biopharmaceuticals.

RNase H-based analysis of synthetic mRNA 5' cap incorporation.

Advances in mRNA synthesis and lipid nanoparticles technologies have helped make mRNA therapeutics and vaccines a reality. The 5′ cap structure is a crucial modification required to functionalize synthetic mRNA for efficient protein translation in vivo and evasion of cellular innate immune responses. The extent of 5′ cap incorporation is one of the critical quality attributes in mRNA manufacturing. RNA cap analysis involves multiple steps: generation of predefined short fragments from the 5′ end of the kilobase-long synthetic mRNA molecules using RNase H, a ribozyme or a DNAzyme, enrichment of the 5′ cleavage products, and LC-MS intact mass analysis. In this paper, we describe (1) a framework to design site-specific RNA cleavage using RNase H; (2) a method to fluorescently label the RNase H cleavage fragments for more accessible readout methods such as gel electrophoresis or high-throughput capillary electrophoresis; (3) a simplified method for post-RNase H purification using desthiobiotinylated oligonucleotides and streptavidin magnetic beads followed by elution using water. By providing a design framework for RNase H-based RNA 5′ cap analysis using less resource-intensive analytical methods, we hope to make RNA cap analysis more accessible to the scientific community.

EP377: Enabling single-platform testing and carrier screening of the FMR1, SMN1/2, and CFTR gene trio

Carrier screening can provide valuable information for couples to help guide their reproductive decision-making. Screening studies have shown that as many as 1 in 20 individuals has pathogenic variants associated with at least 1 of 3 conditions: spinal muscular atrophy (SMA), fragile X syndrome (FXS), and cystic fibrosis (CF). Many of these conditions cause severe symptoms, and SMA and CF can lead to premature death. Early detection can both inform reproductive choices and offer early therapeutic intervention to help mitigate the most severe symptoms if implemented early enough in the course of disease progression. The three genes associated with SMA, FXS and CF (SMN1, FMR1 and CFTR, respectively) each present unique technical challenges and currently require distinct molecular diagnostic methods and analysis platforms. As a result, a simple, cost-effective, and unified screening system is not yet available for this trio. Here we demonstrate the feasibility of a common, scalable workflow for analyzing combinations of PCR products from all 3 genes on a single capillary electrophoresis (CE) instrument. DNA samples were PCR amplified using AmplideX PCR/CE SMN1/2 Plus, FMR1, and CFTR kits (Asuragen) and electrophoresed on the Applied Biosystems 3500 and 3730 Series Genetic Analyzers (Thermo Fisher Scientific). PCR products from each of the 3 assays were generated according to kit instructions, and combined onto a single CE plate for injection using harmonized conditions. A collection of 48 unique genomic DNA samples isolated from human cell lines or whole blood were tested in singleton with each assay. Samples were designed to cover the breadth of possible genotypes detected by each kit, representing 0 to ≥4 copies of SMN1 or SMN2, FMR1 categorical genotypes of normal, premutation, intermediate, or full mutation [GJL1], and at least 23 unique CFTR variants representing the minimum recommended CFTR carrier screening variant panel from ACMG. Data were processed using AmplideX Reporter Software. Samples were analyzed using a single CE plate for all 3 assays injected with a single set of injection conditions, then compared to the same amplicons injected on separate CE plates for each assay using the conditions recommended for each assay. The overall percent agreement between the genotype calls of the co-injected samples and their individually injected counterparts was >98% for SMN1/2, FMR1, and CFTR on both the 3500 and 3730 CE instruments. Concordance was similar when compared to known reference results for each sample. The co-injection of SMN1/2, FMR1, and CFTR products did not alter the genotype category or copy number calls when compared to their respective, individually assessed results. Using this approach, comprehensive trio genotypes were generated within a single day; further, the system has the potential to process up to 1000 samples per day using a single 3730 CE instrument. The co-injection of PCR products of SMN1/2, FMR1, and CFTR genes can be achieved using commonly available high throughput CE instruments. This approach consolidates existing workflows and improves run and cost efficiencies, with the flexibility to accommodate a few samples at a time or up to 1000 per day. Our study demonstrates the potential for a unified single-instrument, single-software analysis of SMN1/2, FMR1, and CFTR using an accessible, easy-to-run system that runs on equipment that labs already have and can adapt to meet the increasing needs of carrier screening. This versatility can translate to significant cost savings for screening labs that typically rely on 2, 3, or even 4 unique methodologies (with reflexes) spanning different platform requirements, workflows, and analysis tools. The workflow similarities among the 3 PCR/CE assays also simplify their implementation in labs, as the protocols are largely identical.

High-throughput and high-sensitivity capillary electrophoresis\u2013mass spectrometry method for sulfur-containing amino acids

Biological thiol amino acids have been suggested as biomarkers for pathological changes because they are reactive chemicals that participate in various physiological processes. In this study, multisegmented injection capillary electrophoresis–mass spectrometry with online sample preconcentration was used for analysis of thiol amino acids and intermediates of sulfur metabolism in human glioma cell line U-251 with high accuracy, throughput, and sensitivity. This was achieved using multiple, large-volume injections for online sample preconcentration. The 16 intermediates of sulfur metabolism had a good linear correlation coefficient range of 0.984–1 and the limit of detection range was 1.4–203.9 ng/mL. The recovery ranges of most amino acids were 88.1–114.5%, 89.0–104.3%, and 76.9–104.5% at 0.3, 0.75, and 1.5 μg/mL, respectively. The relative standard deviation ranges for the inter- and intra-day precision were 1.8–10.7% and 4.3–18.8%, respectively. Compared with the traditional injection method, the analytical time for compounds in sulfur metabolism was reduced to 4 min/sample, the method throughput was enhanced five times, and the sensitivity was increased 14.4–33.1 times. Customized injection sequences were applied in experimental optimization. The developed method simplified the experimental optimization to one injection and is suitable for the analysis of sulfur metabolites in biological samples and has high sensitivity, throughput, speed, and accuracy.

Integrated workflow for urinary prostate specific antigen N-glycosylation analysis using sdAb partitioning and downstream capillary electrophoresis separation

Prostate cancer represents the second highest malignancy rate in men in all cancer diagnoses worldwide. The development and progression of prostate cancer is not completely understood yet at molecular level, but it has been reported that changes in the N-glycosylation of prostate-specific antigen (PSA) occur during tumor genesis. In this paper we report on the development and implementation of a high-throughput capillary electrophoresis based glycan analysis workflow for urinary PSA analysis. The technology utilizes selective, high yield single domain antibody based PSA capture, followed by preconcentration and capillary electrophoresis coupled with laser-induced fluorescence detection, resulting in high resolution N-glycan profiles. Urinary PSA glycan profiles were compared to a commercially available PSA standard revealing differences in their α2,3- and α2,6-sialylated isomers, proving the excellent selectivity of the suggested workflow. This is important as sialylation classification plays an important role in the differentiation between indolent, significant and aggressive forms of prostate cancer.

Profiling Thermus thermophilus Argonaute Guide DNA Sequence Preferences by Functional Screening.

Prokaryotic Argonautes (pAgo) are an increasingly well-studied class of guided endonucleases, and the underlying mechanisms by which pAgo generate nucleic acid guides in vivo remains an important topic of investigation. Recent insights into these mechanisms for the Argonaute protein from Thermus thermophilus has drawn attention to global sequence and structural feature preferences involved in oligonucleotide guide selection. In this work, we approach the study of guide sequence preferences in T. thermophilus Argonaute from a functional perspective. Screening a library of 1,968 guides against randomized single- and double-stranded DNA substrates, endonuclease activity associated with each guide was quantified using high-throughput capillary electrophoresis, and localized sequence preferences were identified which can be used to improve guide design for molecular applications. The most notable preferences include: a strong cleavage enhancement from a first position dT independent of target sequence; a significant decrease in activity with dA at position 12; and an impact of GC dinucleotides at positions 10 and 11. While this method has been useful in characterizing unique preferences of T. thermophilus Argonaute and criteria for creating efficient guides, it could be expanded further to rapidly characterize more recent mesophilic variants reported in the literature and drive their utility toward molecular tools in biology and genome editing applications.

Application of affinity capillary electrophoresis in the study of protein-DNA interactions

Protein-DNA interactions play essential roles in various biological events that determine the cell fate. Research on the molecular mechanism of protein-DNA interactions has helped elucidate diverse fundamental life processes, thereby providing theoretical guidance for establishing clinical treatment and screening potential drug of target diseases. Furthermore, well-known protein-DNA interactions have been utilized to develop advanced bioengineering and bioanalytical techniques, therefore providing robust technical support for related research. Hence, it is important to establish sensitive and rapid analytical methods to study protein-DNA interactions. High-performance capillary electrophoresis (CE) has been widely used in many research fields such as chemistry, life sciences, and environmental sciences, mainly due to its advantages including ultra-high separation efficiency, extremely low sample consumption, and short analysis time. For instance, affinity capillary electrophoresis (ACE) has become an important analytical tool for investigating molecular interactions. In this paper, we review the applications of ACE in studying protein-DNA interactions since it was first proposed in 1992, addressing previous significant work in this field. Three major aspects have been summarized in this review: (1) brief introduction to the development of ACE technique; (2) applications of ACE in the fundamental research on the molecular mechanism of protein-DNA interactions; and (3) applications of well-known protein-DNA interactions in CE-based detection of target molecules and reactions. In the first aspect, along with the concept and separation modes of ACE, general strategies to enhance the analytical ability of ACE are briefly introduced. In the second aspect, the applications of ACE in studying several important protein-DNA interactions involving transcription factors (e.g., GCN4), DNA repair proteins (e.g., UvrA, UvrB, and RecA), and methylated DNA-binding proteins (MBDs) are reviewed. In the third aspect, the applications of well-known molecular interactions (e.g., antigen-antibody, aptamer-target, etc.) to facilitate CE-based detection of target molecules (e.g., DNA adducts, DNA methylation, microRNA, single nucleotide polymorphism, etc.) and target reactions (e.g., DNA strand exchange) are addressed. Finally, we prospect and discuss the advancements of ACE that can be established in future studies. The following two aspects should be improved in future ACE analysis: (1) the advantages of extremely low volume consumption and short analysis time should be fully utilized to develop sensitive and high-throughput CE platforms for the assessment of rare biological samples and massive uncertain samples, respectively; (2) ACE should be combined with other advanced techniques, such as DNA sequencing and mass spectrometry, to rapidly screen and identify the precise interacting sites of unknown protein-DNA interactions.

The genetic relationships of Indian jujube (Ziziphus mauritiana Lam.) cultivars using SSR markers

The genetic relationships among 24 Indian jujube cultivars (Ziziphus mauritiana Lam.) were evaluated by genotyping the microsatellite loci using simple sequence repeat (SSR) markers. The SSR loci were scored by fluorescent labelling and automated detection systems for the high-throughput capillary electrophoresis and high-resolution gel electrophoresis. Out of the 29 newly characterized SSR loci, 26 were considered as polymorphic with a total of 181 alleles obtained. The number of alleles ranged from 2–12, while the polymorphism information content ranged from 0.08–0.83, and the expected and observed heterozygosity were 0.04–0.83 and 0.04–0.82, respectively. The allele pattern of Indian jujube for all SSR loci confirmed its karyotype as tetraploid. Similarity coefficients and UPGMA dendrogram revealed that the Taiwanese cultivars consisted of a large ‘A’ clade, which is further divided into ‘A1’ and ‘A2’ groups, and the ‘B’ clade where both are rooted by the wild accession, ‘Chad native’. These four genetic clusters were supported by the results of PCoA and the assignment test. The excess of heterozygotes based on F-statistics was attributed to its mating system as outcrossing and self-incompatible, and the introgression of the presumed mutation-derived cultivars with genetic admixture. Based on this study, SSR markers offer valuable information on the genetic relationship of this tropical fruit tree which is basically in agreement with the genealogy of its breeding history.

Analyzing editosome function in high-throughput.

Mitochondrial gene expression in African trypanosomes and other trypanosomatid pathogens requires a U-nucleotide specific insertion/deletion-type RNA-editing reaction. The process is catalyzed by a macromolecular protein complex known as the editosome. Editosomes are restricted to the trypanosomatid clade and since editing is essential for the parasites, the protein complex represents a near perfect target for drug intervention strategies. Here, we report the development of an improved in vitro assay to monitor editosome function. The test system utilizes fluorophore-labeled substrate RNAs to analyze the processing reaction by automated, high-throughput capillary electrophoresis (CE) in combination with a laser-induced fluorescence (LIF) readout. We optimized the assay for high-throughput screening (HTS)-experiments and devised a multiplex fluorophore-labeling regime to scrutinize the U-insertion/U-deletion reaction simultaneously. The assay is robust, it requires only nanogram amounts of materials and it meets all performance criteria for HTS-methods. As such the test system should be helpful in the search for trypanosome-specific pharmaceuticals.

Genotypic Expansion Within the Population Structure of Classical Brucella Species Revealed by MLVA16 Typing of 1404 Brucella Isolates From Different Animal and Geographic Origins, 1974-2006.

Previous studies have shown the usefulness of MLVA16 as a rapid molecular identification and classification method for Brucella species and biovars including recently described novel Brucella species from wildlife. Most studies were conducted on a limited number of strains from limited geographic/host origins. The objective of this study was to assess genetic diversity of Brucella spp. by MLVA16 on a larger scale. Thus, 1404 animal or human isolates collected from all parts of the world over a period of 32 years (1974-2006) were investigated. Selection of the 1404 strains was done among the approximately 4000 strains collection of the BCCN (Brucella Culture Collection Nouzilly), based on classical biotyping and on the animal/human/geographic origin over the time period considered. MLVA16 was performed on extracted DNAs using high throughput capillary electrophoresis. The 16 loci were amplified in four multiplex PCR reactions. This large scale study firstly confirmed the accuracy of MLVA16 typing for Brucella species and biovar identification and its congruence with the recently described Extended Multilocus Sequence Analysis. In addition, it allowed identifying novel MLVA11 (based upon 11 slowly evolving VNTRs) genotypes representing an increase of 15% relative to the previously known Brucella MLVA11 genotypes. Cluster analysis showed that among the MLVA16 genotypes some were genetically more distant from the major classical clades. For example new major clusters of B. abortus biovar 3 isolated from cattle in Sub-Saharan Africa were identified. For other classical species and biovars this study indicated also genotypic expansion within the population structure of classical Brucella species. MLVA proves to be a powerful tool to rapidly assess genetic diversity of bacterial populations on a large scale, as here on a large collection of strains of the genomically homogeneous genus Brucella. The highly discriminatory power of MLVA appears of particular interest as a first step for selection of Brucella strains for whole-genome sequencing. The MLVA data of this study were added to the public Brucella MLVA database at http://microbesgenotyping.i2bc.paris-saclay.fr. Current version Brucella_4_3 comprises typing data from more than 5000 strains including in silico data analysis of public whole genome sequence datasets.

A repeat-primed PCR assay for pentanucleotide repeat alleles in spinocerebellar ataxia type 37.

Spinocerebellar ataxia 37 (SCA37) is caused by an (ATTTC)n insertion in a polymorphic ATTTT repeat in the non-coding region of DAB1. The non-pathogenic alleles have a configuration [(ATTTT)7-400], whereas pathogenic alleles have a complex structure of [(ATTTT)60-79(ATTTC)31-75(ATTTT)58-90]. Molecular diagnosis of SCA37 is laborious because about 7% of the pentanucleotide repeat alleles in DAB1 are larger than 30 units and, thus, fail to amplify with standard PCR conditions, resulting in apparently homoallelism or in complete lack of PCR amplification in several cases. The molecular test currently available requires long-range PCR and sequencing analysis for the detection and characterization of these large alleles. We developed a simple assay capable of rapidly detecting the presence or absence of large pentanucleotide repeat sizes. This assay is based on repeat-primed PCR followed by high-throughput capillary electrophoresis. Combining the standard PCR with RP-PCR allows completion of the diagnosis in more than 80% of individuals, minimizing the number of samples that require long-range PCR followed by Sanger sequencing analysis. This assay meets many of the requirements for pre-screening of large cohorts of affected individuals.

Rapid Protein Analysis and Western Blotting by Capillary Gel Electrophoresis

Capillary gel electrophoresis has been used since the early 1980s to separate analytes based upon their mass to charge ratio. However, optical limitations prevented high sensitivity instruments from being developed, limiting functionality. As manufacturing capabilities have improved the high‐throughput, hands‐off nature of parallel capillary gel electrophoresis has made it a desirable technique for analysis of DNA, RNA, and protein. Traditionally, protein analysis and Western blotting have been accomplished using SDS‐PAGE followed by staining of proteins in the gel or by downstream transfer of proteins to a blotting membrane, respectively. The trademark feature of these methods is their labor‐intensive nature with many hours or days passing between sample loading and results. Additionally, manual analysis prevents processing of large numbers of samples.Advanced Analytical Technologies, Inc, (AATI) has developed a high‐throughput capillary electrophoresis instrument capable of running 12 samples in parallel with analysis of a complete 96‐well plate without user intervention. This method relies on the rapid fluorescent labeling (~5 min hands on, 15 min total) of total protein sample, with a linear labeling dynamic range of 1 ng − 1000 ng protein input, followed by heat denaturing of the sample in an SDS buffer. The samples are then separated electrophoretically through a proprietary gel matrix (~30 min run time). Sizing of samples is provided using internal markers and comparison to a standardized ladder, allowing for sizing of samples from 14 kDa to greater than 200 kDa with an accuracy of ≤5% and precision of less ≤5%. Relative quantification of proteins is accomplished by comparing the corrected peak area of sample peaks with a precision of ≤10%. Absolute quantification of proteins can be accomplished through a calibration curve using the same protein as the unknown, as each unique protein species will label at varying efficiencies.Capillary gel electrophoresis coupled with total protein labeling can be used to replace traditional Western blots by analyzing and quantifying immunoprecipitations. Analysis of immunoprecipitations by SDS‐PAGE and Coomassie staining are limited due to sensitivity and the copious amounts of antibody present in the sample. By using an unlabeled antibody coupled with labeled total protein, the capillary electrophoresis instrument will only detect the labeled protein of interest isolated by the immunoprecipitation. This provides relative concentration and size information analogous to that provided by the traditional western in a fraction of the time. The AATI protocol eliminates signal bleeding which allows for a greater dynamic range than film. A pull down of endogenous GAPDH demonstrated a 3‐fold dynamic response (0.01 μg – 10 μg protein input).By harnessing capillary gel electrophoresis, AATI has developed a high sensitivity SDS‐PAGE/Western blot replacement with a 3‐fold dynamic range, allowing for rapid analysis of total and purified protein. Please contact the authors at AATI‐us.com if you have interest in this technology.Support or Funding InformationThis work was funded by Advanced Analytical Technologies, Inc.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Triple-Internal Standard Based Glycan Structural Assignment Method for Capillary Electrophoresis Analysis of Carbohydrates.

Despite the ever growing use of capillary electrophoresis in biomedical research and the biopharmaceutical industry, the development of data interpretation methods is lagging behind. In this paper we report the design and implementation of a coinjected triple-internal standard method to alleviate the need of an accompanying run of the maltooligosaccharide ladder for glucose unit (GU) calculation. Based on the migration times of the coinjected standards of maltose, maltotriose, and maltopentadecaose (bracketing the peaks of interest), a data processing approach was designed and developed to set up a virtual ladder that was used for GU calculation. The data processing was tested in terms of the calculated GU values of human IgG glycans, and the resulting relative standard deviation was ≤1.07%. This approach readily supports high-throughput capillary electrophoresis systems by significantly speeding up the processing time for glycan structural assignment.

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.

Capillary electrophoresis (CE) is a powerful approach for structural analysis of nucleic acids, with recent high-throughput variants enabling three-dimensional RNA modeling and the discovery of new rules for RNA structure design. Among the steps composing CE analysis, the process of finding each band in an electrophoretic trace and mapping it to a position in the nucleic acid sequence has required significant manual inspection and remains the most time-consuming and error-prone step. The few available tools seeking to automate this band annotation have achieved limited accuracy and have not taken advantage of information across dozens of profiles routinely acquired in high-throughput measurements. We present a dynamic-programming-based approach to automate band annotation for high-throughput capillary electrophoresis. The approach is uniquely able to define and optimize a robust target function that takes into account multiple CE profiles (sequencing ladders, different chemical probes, different mutants) collected for the RNA. Over a large benchmark of multi-profile datasets for biological RNAs and designed RNAs from the EteRNA project, the method outperforms prior tools (QuSHAPE and FAST) significantly in terms of accuracy compared with gold-standard manual annotations. The amount of computation required is reasonable at a few seconds per dataset. We also introduce an 'E-score' metric to automatically assess the reliability of the band annotation and show it to be practically useful in flagging uncertainties in band annotation for further inspection. The implementation of the proposed algorithm is included in the HiTRACE software, freely available as an online server and for download at http://hitrace.stanford.edu. sryoon@snu.ac.kr or rhiju@stanford.edu Supplementary data are available at Bioinformatics online.

Microanalytical study of sub-nanoliter samples by capillary electrophoresis – mass spectrometry with 100 % injection efficiency

A method is presented for conducting fast capillary electrophoresis (CE) with ultrasmall sample volumes (<10 nL) and subsequent determination of target analytes by time-of-flight mass spectrometry (TOF-MS). Furthermore, an approach towards preconcentration by solvent evaporation of samples as small as 500 nL is shown. Ultrasmall samples of biologically important cyclic nucleotides (cyclic guanosine monophosphate, cyclic adenosine monophosphate, cyclic cytidine monophosphate) served as model compounds. Sample volumes as small as 500 pL were used to perform sample uptake and CE injections by capillary batch injection (CBI). This resulted in detection limits between 2 and 5 fmol. The fast rate of sample evaporation prevents the operation of nano-/subnano-liter samples under room temperature conditions. A CBI-CE-TOF-MS setup incorporating a Peltier element and a thermostat was used for the handling of very small samples. In combination with tapered fused silica injection capillaries and the high-precision guiding system of the CBI setup, nearly 100 % efficient injections of ultrasmall samples into funnelled separation capillaries could be managed. The overall system allowed for high-throughput CE separations from densely arranged sample droplets or vials with RSD of peak heights ranging from 6 to 8 % (n = 5). CE-TOF-MS separations of mixtures of cyclic nucleotides were carried out in capillaries as short as 20 cm (25 μm ID) in less than 55 s with high separation efficiency. We report details of the setup and optimizations with respect to etching of capillaries (tapering and funnelling), sample uptake and injection as well as separation of the model compounds. Moreover, the capabilities of the experimental setup for preconcentration of target analytes by solvent evaporation are described. Preconcentration factors of up to 100 could be achieved. This approach was successfully used for the determination of the cyclic nucleotide cGMP in (spiked) human urine samples.

CZE Separation of New Drugs for Treatment of Leukemia

Imatinib, bosutinib, dasatinib, pazopanib, erlotinib, canertinib and vatalanib are new developed anticancer drugs, especially for treatment of leukemia. In this article, a fast and high throughput capillary zone electrophoresis method has been developed and validated for analysis of these new drugs in pharmaceutical formulas. The method can be easily utilized for determination of all the drugs in one run what is advantageous for the quality control in pharmaceutical industry because there is no need for changing and optimization of separation conditions when changing the analyte. The separation was performed using an uncoated fused silica capillary with 100 mmol L−1 sodium phosphate buffer pH 2.75, voltage of 25 kV, hydrodynamic injection time of 5 s by 50 mbar, and detection at 214 nm. Under these conditions, the analysis took about 8 min. The validation of all the drugs resulted in recoveries in the range of 84–100 %. The method showed to be precise for all the drugs with RSDs of migration times lower than 0.9 % (interday precision). A very good linearity in the validated range (5–100 μg mL−1) and the limits of detection (LODs) in the range of 0.5–2.0 (μg mL−1) were achieved. Finally, we proved that the method is robust by the Youden’s test. Therefore, our method can be successfully applied for analysis of the real pharmaceutical samples.

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis.

To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis). HiTRACE has been used extensively for quantitating data from RNA and DNA structure mapping experiments, including mutate-and-map contact inference, chromatin footprinting, the Eterna RNA design project and other high-throughput applications. However, HiTRACE is based on a suite of command-line MATLAB scripts that requires nontrivial efforts to learn, use and extend. Here, we present HiTRACE-Web, an online version of HiTRACE that includes standard features previously available in the command-line version and additional features such as automated band annotation and flexible adjustment of annotations, all via a user-friendly environment. By making use of parallelization, the on-line workflow is also faster than software implementations available to most users on their local computers. Free access: http://hitrace.org.

A SIMPLE AND ROBUST APPROACH FOR GENOTYPING IN MUSACEAE

Banana and plantain (Musa spp.) are seed-sterile vegetatively propagated crops, which originated as intraspecific hybrids of Musa acuminate and interspecific hybrids between M. acuminate and Musa balbisiana. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changing farming practices. To set up an efficient and effective strategy for breeding improved banana cultivars and support the choice of crossing-parents, a solid understanding of the genetic diversity of available resources is needed, underlining the need for characterization and conservation of this genetic diversity. With the aim to provide a simple and robust approach for genotyping in Musa, we have developed an optimized genotyping platform using SSR markers. The genotyping system is based on 19 microsatellite loci, originally developed by CIRAD, which are scored using fluorescently labeled primers and high-throughput capillary electrophoresis separation with high resolution. The knowledge gained during the course of this study is used by the Musa Genotyping Centre, which serves the Musa research and breeding community by determining DNA ploidy and SSR profiles of unknown samples. The Centre operates on a cost-recovery basis and guarantees that all analyses are performed under strictly controlled conditions, enabling direct comparison of various accessions from different parts of the world.

The dynamics of natural Plasmodium falciparum infections.

BackgroundNatural immunity to Plasmodium falciparum has been widely studied, but its effects on parasite dynamics are poorly understood. Acquisition and clearance rates of untreated infections are key elements of the dynamics of malaria, but estimating these parameters is challenging because of frequent super-infection and imperfect detectability of parasites. Consequently, information on effects of host immune status or age on infection dynamics is fragmentary.MethodsAn age-stratified cohort of 347 individuals from Northern Ghana was sampled six times at 2 month intervals. High-throughput capillary electrophoresis was used to genotype the msp-2 locus of all P. falciparum infections detected by PCR. Force of infection (FOI) and duration were estimated for each age group using an immigration-death model that allows for imperfect detection of circulating parasites.ResultsAllowing for imperfect detection substantially increased estimates of FOI and duration. Effects of naturally acquired immunity on the FOI and duration would be reflected in age dependence in these indices, but in our cohort data FOI tended to increase with age in children. Persistence of individual parasite clones was characteristic of all age-groups. Duration peaked in 5–9 year old children (average duration 319 days, 95% confidence interval 318;320).ConclusionsThe main age-dependence is on parasite densities, with only small age-variations in the FOI and persistence of infections. This supports the hypothesis that acquired immunity controls transmission mainly by limiting blood-stage parasite densities rather than changing rates of acquisition or clearance of infections.