Microcapillary Electrophoresis Research Articles

Comprehensive Impurity Profiling of mRNA: Evaluating Current Technologies and Advanced Analytical Techniques.

In vitro transcription (IVT) of mRNA is a versatile platform for a broad range of biotechnological applications. Its rapid, scalable, and cost-effective production makes it a compelling choice for the development of mRNA-based cancer therapies and vaccines against infectious diseases. The impurities generated during mRNA production can potentially impact the safety and efficacy of mRNA therapeutics, but their structural complexity has not been investigated in detail yet. This study pioneers a comprehensive profiling of IVT mRNA impurities, integrating current technologies with innovative analytical tools. We have developed highly reproducible, efficient, and stability-indicating ion-pair reversed-phase liquid chromatography and capillary gel electrophoresis methods to determine the purity of mRNA from different suppliers. Furthermore, we introduced the applicability of microcapillary electrophoresis for high-throughput (<1.5 min analysis time per sample) mRNA impurity profiling. Our findings revealed that impurities are mainly attributed to mRNA variants with different poly(A) tail lengths due to aborted additions or partial hydrolysis and the presence of double-stranded mRNA (dsRNA) byproducts, particularly the dsRNA 3'-loop back form. We also implemented mass photometry and native mass spectrometry for the characterization of mRNA and its related product impurities. Mass photometry enabled the determination of the number of nucleotides of different mRNAs with high accuracy as well as the detection of their size variants [i.e., aggregates and partial and/or total absence of the poly(A) tail], thus providing valuable information on mRNA identity and integrity. In addition, native mass spectrometry provided insights into mRNA intact mass, heterogeneity, and important sequence features such as poly(A) tail length and distribution. This study highlights the existing bottlenecks and opportunities for improvement in the analytical characterization of IVT mRNA, thus contributing to the refinement and streamlining of mRNA production, paving the way for continued advancements in biotechnological applications.

Molecular B-cell clonality assay in minor salivary glands as a useful tool for the lymphoma risk assessment in Sjögren's syndrome

ObjectivesNon-Hodgkin's lymphoma (NHL) risk assessment is crucial in Sjögren's syndrome (SS). We studied the prevalence of clonal immunoglobulin gene rearrangements in minor salivary glands (MSG) and their correlations with lymphoma occurrence and with previously established NHL predictors. MethodsMolecular B-cell expansion was studied in fresh-frozen MSG of 207 patients with either suspected SS or with suspected lymphoma during SS, using a standardised multiplex PCR assay combined with heteroduplex analysis by microcapillary electrophoresis. The assignation of clonal cases was based on EuroClonality consortium guidelines. ResultsAmong 207 studied patients, 31 (15%) had MSG monoclonal B-cell infiltration. Monoclonality was significantly more frequent in patients with SS (28/123, 22.8%) compared with patients without SS (3/84, 3.6%, P<0.001). Monoclonal B-cell infiltration in MSG of SS patients correlated significantly with ongoing salivary gland NHL, salivary gland swelling, CD4+ T-cell lymphopenia, rheumatoid factor (RF) activity, low complement levels and type 2 mixed cryoglobulinemia. The accumulation of biological risk factors was associated with a higher rate of MSG B-cell monoclonality given that patients with only positive RF had no probability of MSG B-cell monoclonality, RF-positive patients with 1 or 2 other risk factors had a 25.0% and 85.7% probability of MSG B-cell monoclonality, respectively. ConclusionThe detection of MSG monoclonal B-cell expansion by this easy-to-perform molecular assay is useful, both at the time of diagnosis and during the course of SS. Monoclonal B-cell expansion is associated with a subset of SS patients presenting either ongoing lymphoma or other established lymphoma predictive factors.

An innovative platform to improve asymmetric bispecific antibody assembly, purity, and expression level in stable pool and cell line development

Asymmetric Immunoglobulin G (IgG)-like antibody is a fast-growing class of therapeutics among various bispecific antibody formats. However, the expression of correctly assembled products with high purity and yield remains challenging. Approaches have been investigated to facilitate antibody heterodimerization, including protein engineering, cell line development (CLD) screening, and vector element customization. In this paper, an innovative CLD platform was developed to express HLX101, an asymmetric IgG antibody consisting of two different heavy chains and two common light chains. We combined Leap-In Transposase® technology, a novel transposon-based integration strategy with two ORF “dual” and four ORF “quad” expression vector designs, and a microcapillary electrophoresis (µM) based high-throughput screening method, which efficiently identified clones expressing heterodimers at early stages of CLD. In this single case study of HLX101, the percentage of single clones expressing desired heterodimer among outgrown clones isolated from the stable pool was increased from 6% to 35% by varying dual vector ratios during co-transfection. This number was further improved to 90 % by a “quad” vector design. The final titer of a single clone fed-batch production reached 6 g/L. The established CLD platform demonstrated a simple and effective way to obtain high-yield and high-quality cell lines for asymmetric antibody production.

Critical aspects of microsatellite instability testing in endometrial cancer: a comparison study

The identification of mismatch repair deficient (dMMR) and microsatellite unstable (MSI) endometrial cancers (ECs) is important in screening, diagnosis, and therapeutic stratification of patients. We compared the diagnostic performance of 4 MSI molecular tests based on fragment length assay in capillary electrophoresis (OncoMate™ MSI assay, Promega) and in microcapillary electrophoresis (TapeStation 4200, Agilent); with high-resolution melting (HRM) analysis approaches (Idylla™ MSI Test, Biocartis; EasyPGX® ready MSI, Diatech Pharmacogenetics) on a series of 56ECs, which was well characterized for MMR status with immunohistochemical approach (IHC, nonmolecular reference test). The concordance of fluorescence capillary electrophoresis with IHC (AUC 0.98) was higher respect to the other molecular methodologies. Otherwise, HRM approaches and microcapillary electrophoresis platform failed to detect MSI-ECs showing minimal microsatellite shifts. In conclusion, in colorectal site, several technologies are eligible for MSI test, whereas in ECs, MSI test should be based on fluorescent capillary electrophoresis as it identifies a higher proportion of cases that could be misdiagnosed with other strategies.

A simple and reliable microfabrication process for a programmable microvalve array

We describe our reliable methodology for fabricating a complex programmable microvalve array (PMA) and its integration with a glass microcapillary electrophoresis chip. This methodology is applicable to any device that requires multilayered PDMS, multiple alignment processes, selective PDMS bonding, and multilayered integration with downstream sensing systems. Along with the detailed step-by-step process, we discuss essential quality assurance checks that can be performed throughout fabrication to assist in troubleshooting and maximizing chip yield.•Comprehensive instructions for designing and fabricating a programmable microvalve array.•Selective bonding of PDMS and glass by microcontact printing.•Numerous quality control procedures to boost chip yield.

A handheld-type total integrated capillary electrophoresis system for SARS-CoV-2 diagnostics: Power, fluorescence detection, and data analysis by smartphone

A micro-capillary electrophoresis (μCE) system is one of the widely adopted techniques in the molecular diagnostics and DNA sequencing due to the benefits of high resolution, rapid analysis, and low reagent consumption, but due to the requirements of bulky high-power suppliers and an expensive laser-induced fluorescence detector module, the conventional set-up of μCE system is not adequate for point-of-care (POC) molecular diagnostics. In this study, we constructed a miniaturized and integrated μCE system which can be manipulated by a smartphone. The smartphone not only powers two boost converters and an excited laser, but also controls the relay for the power switch. Moreover, the complementary metal-oxide-semiconductor (CMOS) camera of the smartphone was used for detecting the fluorescence signal of amplicons amplified with reverse transcription-polymerase chain reaction (RT-PCR). We also developed a web-based application so that the raw data of the recorded fluorescence intensity versus the running time can display typical capillary electropherograms on the smartphone. The total size of the hand-held μCE system was 9.6 cm [Width] × 22 cm [Length] × 15.5 cm [Height], and the weight was ∼1 kg, which is suitable for POC DNA testing. In the integrated smartphone-associated μCE system, we could accurately analyze two genes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely N gene and S gene along with two bracket ladders in 6 min to identify SARS-CoV-2. Such an advanced μCE platform can be applied for a variety of on-site molecular diagnostics fields with user-friendliness.

Quantitative microcapillary electrophoresis immunoassay (mCE IA) for end-to-end analysis of pertactin within in-process samples and Quadracel® vaccine

Protein concentration is an important attribute in the production of subunit or component-based vaccine antigens. Rigorous monitoring of protein concentration is required to identify potential areas for yield improvement. The current GMP method for quantitation is the plate-based ELISA which requires numerous hands-on steps and has low sensitivity in comparison to new microfluidic systems. To address this issue, a sensitive automated microCapillary Electrophoresis ImmunoAssay (mCE IA) method was developed to accurately separate and quantitate pertactin (PRN), an important antigen of the modern acellular Pertussis (aP) vaccine. PRN is reported to be a low-yielding antigen; thus, it is critical to observe its concentration throughout its manufacturing process. First, a primary antibody for PRN was identified to establish suitable immunoprobing conditions for detection of PRN over a wide linear dynamic range that spans 3 orders of magnitude. Next, the pre-adsorbed PRN Drug Substance (DS) was used as a reference standard to quantitate PRN samples against a calibration curve with adequate accuracy and precision. Four representative samples including three in-process steps and final adjuvanted drug product: Quadracel®, were examined to demonstrate the capability of mCE IA to quantitate PRN with high sensitivity and specificity. The matrices of the selected samples contain additional components (e.g. other proteins, growth factors, cell culture media, residual ammonium sulfate, and aluminum adjuvant) often making the quantitation of PRN challenging. The specificity and method linearity were demonstrated by spiking pre-adsorbed PRN DS into the four representative samples. In addition, it was shown that reportable concentrations of PRN for nine downstream process steps as analyzed by our method is comparable to concentrations obtained with ELISA. Most importantly, this study demonstrated that our method’s quantitative accuracy is independent of matrix components, as each sample undergoes extensive dilution. This allows for seamless end-to-end analysis of PRN from fermenter harvest, through to complex downstream process samples to adjuvanted drug products. Finally, for the first time the developed and qualified mCE IA method was shown to quantify PRN throughout the entire manufacturing process to provide rapid feedback for process optimizations allowing for accurate yield and step-loss calculations.

A modular, easy-to-use microcapillary electrophoresis system with laser-induced fluorescence for quantitative compositional analysis of trace organic molecules.

Microcapillary electrophoresis (μCE) enables high-resolution separations in miniaturized, automated microfluidic devices. Pairing this powerful separation technique with laser-induced fluorescence (LIF) enables a highly sensitive, quantitative, and compositional analysis of organic molecule monomers and short polymers, which are essential, ubiquitous components of life on Earth. Improving methods for their detection has applications to multiple scientific fields, particularly those related to medicine, industry, and space science. Here, a modular benchtop system using μCE with LIF detection was constructed and tested by analyzing standard amino acid samples of valine, serine, alanine, glycine, glutamic acid, and aspartic acid in multiple borate buffered solutions of increasing concentrations from 10 mM to 50 mM, all pH 9.5. The 35 mM borate buffer solution generated the highest resolution before Joule heating dominated. The limits of detection of alanine and glycine using 35 mM borate buffer were found to be 2.12 nM and 2.91 nM, respectively, comparable to other state-of-the-art μCE-LIF instruments. This benchtop system is amenable to a variety of detectors, including a photomultiplier tube, a silicon photomultiplier, or a spectrometer, and currently employs a spectrometer for facile multi-wavelength detection. Furthermore, the microdevice is easily exchanged to fit the desired application of the system, and optical components within the central filter cube can be easily replaced to target alternative fluorescent dyes. This work represents a significant step forward for the analysis of small organic molecules and biopolymers using μCE-LIF systems.

Smart phone-powered capillary electrophoresis on a chip for foodborne bacteria detection

Due to the requirement of high-voltage power supply, on-chip micro-capillary electrophoresis (μCE) suffers from practical on-site bioapplications. In this paper, we introduced a smart phone based electric power system for μCE on a chip with simple electrical operations and improved portability of a μCE device. Since the power of the smart phone is limited to 5 V, we utilized a boost converter circuit to increase up to 250 V, which enables μCE on a chip. The typical μCE channel with a cross design was patterned on the PMMA substrate, and the sample, the waste, the anode and the cathode reservoirs were fabricated. Two steps of μCE consisting of the injection and the separation were performed to separate two amplicons (121 bp FliC gene of Escherichia coli and 161 bp InvA gene of Salmonella serovar Typhimurium). During the injection step, the voltages applied in the sample and waste reservoirs were 0 V and 250 V, respectively, and the amplicons were filled in the injection channel (6.8 mm length) in 50 s. We switched the power supply to the anode reservoir with 250 V and the cathode reservoir with 0 V. Two amplicons were successfully separated in the separation channel (17 mm length) in 4 min. In order to assign the peak in the electropherogram, we added two bracket ladders with the amplicon sample, so that we could accurately identify the target peak based on a relative migration time.

Effects of Quantification Methods, Isolation Kits, Plasma Biobanking, and Hemolysis on Cell-Free DNA Analysis in Plasma.

Cell-free DNA (cfDNA) has become a promising noninvasive clinical marker widely studied in early disease detection, monitoring, and therapy selection. However, there is lack of data on a number of cfDNA-associated procedural features such as blood plasma biobanking conditions, isolation, and quantification methods that should be taken into account as they can affect downstream applications. In this study cfDNA from 125 plasma samples from healthy individuals were isolated using three different commercial kits (bead and vacuum based). Yield of cfDNA, distribution of cfDNA fragments and absolute amount of miR-223 were estimated. Moreover, the impact of different plasma biobanking conditions and hemolytic plasma were evaluated. In conclusion, results showed that quantification method (fluorescence or microcapillary electrophoresis based) has a major impact in estimating cfDNA amount. Samples isolated by QIAamp showed a higher amount of larger (around 300 bp) DNA fragments and miRNA yield, suggesting possible applications for multiomics approach. On the other hand, the highest cfDNA yield was obtained in samples isolated by the MagMAX Isolation Kit. This kit also showed lowest coefficient of variation and low miRNA yield. Plasma storage conditions and hemolysis affected performance of isolation kits differently.

Microcapillary electrophoresis chip with a bypass channel for autonomous compensation of hydrostatic pressure flow

The application of chip-based microcapillary electrophoresis (µCE) to determine the electrophoretic mobility of molecules and particles has been intensively studied in the last two decades. Balancing the hydrostatic pressure between both ends of the microchannel is essential for free-zone electrophoresis and highly accurate measurement. This balancing operation appears simple on a macroscale (e.g., > 10−3 m); however, on a microscale (e.g., 10−6–10−3 m), it is not straightforward because of the complexity of the interface dynamics at the meniscus. The hydrostatic pressure flow is unstable because of the small size of the microchannel, which is smaller than a single droplet of water. In this study, a µCE chip design was proposed by adding an extra bypass channel to balance the fluid level of the two open reservoirs and inhibit the generation of hydrostatic pressure flow within the microchannel. The fluid behaviors in the microchannel and current and voltage (I–V) characterization were experimentally studied. In addition, a numerical simulation of the electroosmotic flow and hydrostatic flow in the µCE chip was performed. The comparison between the µCE chip with and without the bypass channel showed that the bypass channel did not produce a disturbance in the microchannel for the electrophoretic measurement. The simple microchannel design enabled autonomous compensation of the hydrostatic pressure from the instability of the meniscus, and thus improved the usability of the chip-based µCE chip and the accuracy in the electrophoretic measurement.

An integrated slidable direct polymerase chain reaction-capillary electrophoresis microdevice for rapid Y chromosome short tandem repeat analysis

We have developed an integrated slidable direct polymerase chain reaction-capillary electrophoresis (Direct PCR-CE) microdevice to analyze mini-Y chromosome short tandem repeat (mini-Y STR) typing without a DNA purification step. The Direct PCR has been recently commercialized as a simple DNA amplification technique, which does not require any sample preparation steps such as cell lysis, DNA extraction and purification for amplifying specific target genes. By implementing the advantages of Direct PCR on a microdevice, we can amplify target min-Y STR loci directly from human whole blood in a micro-reactor (2μL) and the amplicons were successively separated by micro-capillary electrophoresis. The utilization of a slidable plate enables us to manually control the fluid without use of microvalves and microtubes, and the functional units of sample injection, Direct PCR, and CE analysis were sequentially and independently performed by switching the slidable plate to each unit. On the integrated slidable Direct PCR-CE microdevice, we could complete monoplex and multiplex mini-Y STR typing directly using human whole blood within 1 h.

Evaluation of Accuracy, Precision and Agreement of Five Hba1c Measurement Methods with HPLC Reference Method

Background and Objective: The current challenge of diabetes mellitus is to prevent its complications. These complications are directly associated with hyperglycemia in diabetics. The HbA1c measurement is essential for long-term glycemic control. Synchronization of HbA1c measurement is important in order to avoid discrepancies between results reported by laboratories. This study aimed to evaluate the accuracy, precision and agreement of five HbA1c measurement methods with HPLC reference method. Methods: HbA1c levels of 55 samples were measured using six methods of microcapillary electrophoresis (Sepia), enzymatic method (Pishtaz Teb), immunoturbidometry (Pars Azmoon), boronate affinity (Nycocard), immunofluorescence (ichroma) and Tosoh G8 HPLC. Results: The five tested methods showed a good agreement with the HPLC method with correlation coefficient of less than 95%. Regression testing of HPLC method and other methods showed slope of 0.99 (P<0.05) for Sebia, 1.02 (P<0.05) for Pishtaz Teb, 0.79 (P<0.05) for Pars Azmoon, 0.82 (P<0.05) for Nycocard and 0.89 (P<0.05) for ichroma. Average inaccuracy for the Sebia, Pishtaz Teb, Pars Azmoon, Nycocard and ichroma in comparison with the HPLC reference method were -0.09, -0.004, -0.75, -0.79 and -0.78, respectively. Conclusion: The Sebia microcapillary method and Pishtaz teb enzymatic method have appropriate accuracy and precision. Therefore, these methods can be used as alternatives to the HPLC method for HbA1c measurement. Other methods such as Pars Azmoon, Nycocard and ichroma have significant shortcomings in terms of accuracy.

Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping

A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1μL whole human blood within 60min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer.

On-chip immunoelectrophoresis of extracellular vesicles released from human breast cancer cells.

Extracellular vesicles (EVs) including exosomes and microvesicles have attracted considerable attention in the fields of cell biology and medicine. For a better understanding of EVs and further exploration of their applications, the development of analytical methods for biological nanovesicles has been required. In particular, considering the heterogeneity of EVs, methods capable of measuring individual vesicles are desired. Here, we report that on-chip immunoelectrophoresis can provide a useful method for the differential protein expression profiling of individual EVs. Electrophoresis experiments were performed on EVs collected from the culture supernatant of MDA-MB-231 human breast cancer cells using a measurement platform comprising a microcapillary electrophoresis chip and a laser dark-field microimaging system. The zeta potential distribution of EVs that reacted with an anti-human CD63 (exosome and microvesicle marker) antibody showed a marked positive shift as compared with that for the normal immunoglobulin G (IgG) isotype control. Thus, on-chip immunoelectrophoresis could sensitively detect the over-expression of CD63 glycoproteins on EVs. Moreover, to explore the applicability of on-chip immunoelectrophoresis to cancer diagnosis, EVs collected from the blood of a mouse tumor model were analyzed by this method. By comparing the zeta potential distributions of EVs after their immunochemical reaction with normal IgG, and the anti-human CD63 and anti-human CD44 (cancer stem cell marker) antibodies, EVs of tumor origin circulating in blood were differentially detected in the real sample. The result indicates that the present method is potentially applicable to liquid biopsy, a promising approach to the low-invasive diagnosis of cancer.

Improving the application of SSR polymorphism analysis coupled with Lab-on-a-chip® capillary electrophoresis to assess food authenticity: Italian pigmented rice as case study

Genetic distances evaluated via SSR-based profiling can be usefully assessed by using capillary electrophoresis. In order to set up a method to distinguish pure Italian rice varieties from imported Asian blends, seven Italian rice genotypes and seven uncharacterized rice samples coming from outside Italy were studied using a classical SSR polymorphism analysis coupled with Lab-on-a-chip® microcapillary electrophoresis. A special algorithm for the elaboration of the raw outputs provided by the software was generated, thus overcoming the problems connected to the instrument intrinsic limits of resolution. The results showed that even considering just the smallest verifiable genetic distance between the employed samples, locally cultivated Italian rice varieties clustered separately from other foreign cultivars. Moreover, it was possible to clearly identify an artificial blend formed by Venere rice mixed with a black variety from Thailand, thus confirming the usefulness of this new post-analysis approach.

Combination of biobarcode assay with on-chip capillary electrophoresis for ultrasensitive and multiplex biological agent detection

Early diagnosis of biological agents is of paramount importance to prevent the casualties and fatal disease in human during bioterrorism or biological warfare. In this study, we reported an efficient and sensitive multiplex biological agent detection method based on the DNA biobarcode assay and the micro-capillary electrophoresis (μCE) technology. Monoplex as well as multiplex pathogen identification was performed using five targets including Bacillus anthracis, Francisella tularensis, Yersinia pestis, Vaccinia virus and Botulinum toxin A. Through the DNA biobarcode assay process, the magnetic microparticle–pathogen–polystyrene microbead complexes were formed, and the FAM labeled single stranded barcode DNA could be released from the complexes upon denaturation. Different lengths of a barcode DNA were designed to designate each pathogen, so that the specific peak elution time in the capillary electrophoresis on a chip allows us to distinguish the target with high accuracy within 3min. We improved the assignment accuracy of the peak in the electropherogram by adding two bracket ladders. Owing to the abundant amount of barcode DNAs, the presence of B. anthracis, F. tularensis, Y. pestis, Vaccinia virus was confirmed with a limit of detection of 50CFU/mL, while Botulinum toxin A was analyzed even at a concentration of 12.5ag/mL. Multiple pathogen detection was also successfully conducted in a phosphate buffered saline (PBS) as well as a serum medium with background of other pathogens. Thus, our analytical platform based on the biobarcode assay and on-chip CE analysis provides rapid, sensitive, multiplex, and accurate biological agent identification.

Evaluation of desialylation effect on zeta potential of extracellular vesicles secreted from human prostate cancer cells by on-chip microcapillary electrophoresis

Extracellular vesicles including exosomes have the potential to be used in therapeutic and diagnostic applications. Towards the noninvasive diagnosis of prostate cancer using urinary exosomes, technical challenges lie in developing precise methods of analyzing exosomes. Previously, we developed an on-chip microcapillary electrophoresis (µCE) system equipped with a laser dark-field microscope. The zeta potential of exosomes of cancer cells was found to be larger than that of normal cells. In this study, the zeta potential of exosomes of normal and cancer prostate cells was evaluated using this system after treating with sialidase. The large negative charge of cancer exosomes was found to be due to the large amount of sialic acids. These results suggest that an on-chip µCE system is useful for the accurate evaluation of events that occur on the exosome surfaces at the single-particle level and promising for the prescreening of prostate cancer exosomes without the need for labeling.

Highly sensitive detection of cancer cells based on the DNA barcode assay and microcapillary electrophoretic analysis

Considering rarity of circulating tumor cells (CTCs) in human blood, the development of highly sensitive detection techniques for cancer cells is crucial for prediction, diagnosis, and prognosis of cancers. In this study, we propose an advanced cellular detection method by combining a biobarcode assay and microcapillary electrophoresis (μCE) technology. While the DNA biobarcode assay can provide ultrasensitive and multiplex detection platforms, the μCE chip can analyze barcode DNAs with high speed and accuracy according to the DNA size. We designed the barcode DNA size as 20 bp for indicating the expression of epithelial cell adhesion molecules (EpCAM) biomarkers and 30 bp for assigning CDX2 expression which is specific for colorectal cancer cells with addition to two bracket ladders (15 and 45 bp). Using MCF-7 (breast cancer) and SW620 (colorectal cancer) as models, we conducted a biobarcode assay and analyzed the resultant biobarcode DNA on the μCE chip. We could detect the 20 bp CE peak in the electropherogram even with ten MCF-7 and SW620 cells in a volume of 200 μL, thereby demonstrating the highly sensitive detection of cancer cells. We furthermore identified the type of colorectal cancer by observing two positive peaks (20 bp for EpCAM and 30 bp for CDX2) in the μCE analysis.

Reprint of “Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)”

This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.