Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches.

MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive and often requires amplification, labeling, or radioactive probes. Here, we report a single-step, nonenzymatic microRNA detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNA-activated conditional looping of engineered switches), our assay has subattomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells and multiplex our detection for several microRNAs from one biological sample. We demonstrate 1-hour detection without expensive equipment or reagents, making this assay a compelling alternative to quantitative polymerase chain reaction and Northern blotting.

Second worldwide proficiency study on variable number of tandem repeats typing of Mycobacterium tuberculosis complex.

BACKGROUND: The quality of variable number of tandem repeats (VNTR) typing of Mycobacterium tuberculosis was first investigated in 2009 in 37 laboratories worldwide. The results revealed an inter- and intra-laboratory reproducibility of respectively 60% and 72%. These data spurred an improvement in laboratory-specific assays and global standardisation of VNTR typing. OBJECTIVE: To measure the effects of the technical improvements and increased standardisation, a test panel consisting of 30 M. tuberculosis complex DNA samples was distributed for VNTR typing in 41 participating laboratories from 36 countries. RESULTS: The inter- and intra-laboratory reproducibility increased overall to respectively 78% and 88%. The 33 laboratories that participated in both the first and second proficiency studies improved their inter- and intra-laboratory reproducibility from 62% and 72% to respectively 79% and 88%. The largest improvement in reproducibility was detected in 10 laboratories that use an in-house polymerase chain reaction technique and perform amplicon sizing using gel electrophoresis. Detailed error analysis revealed a reduction in the number of systematic errors, sample exchange events and non-amplifiable loci. CONCLUSION: This second worldwide proficiency study indicates a substantial increase in the reproducibility of VNTR typing of M. tuberculosis. This will contribute to a more meaningful interpretation of molecular epidemiological and phylogenetic studies on the M. tuberculosis complex.

The gene cluster instability (GCI) assay for recombination.

A newly developed method for quantitatively detecting genomic restructuring in cultured human cell lines as the result of recombination is presented: the "gene cluster instability" (GCI) assay. The assay is physiological in that it detects spontaneous restructuring without the need for exogenous recombination-initiating treatments such as DNA damage. As an assay for genotoxicity, the GCI assay is complementary to well-established sister chromatid exchange (SCE) methods. Analysis of the U-2 OS osteosarcoma cell line is presented as an illustration of the method.

Collaborative study for the establishment of the human immunoglobulin for electrophoresis Ph. Eur. BRP batch 3.

Due to the diminished stocks of the 2(nd) batch of the European Pharmacopoeia (Ph. Eur.) Biological Reference Preparation (BRP) for human immunoglobulin for electrophoresis, in 2013, the European Directorate for the Quality of Medicines and HealthCare (EDQM) initiated an international collaborative study for the establishment of a replacement batch. The study was run under the aegis of the Biological Standardisation Programme (BSP). Seventeen laboratories participated in the collaborative study to verify the suitability of the candidate reference preparation according to the Ph. Eur. monographs 0338 and 0918 using the zone electrophoresis (ZE) method with either cellulose acetate and/or agarose as the testing medium. The candidate preparation was found suitable for the intended purpose and was subsequently adopted by the Ph. Eur. Commission as the human immunoglobulin for electrophoresis BRP batch 3 with an assigned range for immunoglobulin of 79.8 % to 86.4 % of the total protein content.

von Willebrand Factor multimers profiling with a semi-automated system.

Abnormalities in plasma von Willebrand factor (vWF) concentration and function result in von Willebrand disease (vWD). The diagnosis requires a battery of tests such as screening procedures, confirmatory tests, phenotypic characterization, and genotyping. The phenotypic testing (multimer pattern analysis) is important in order to subclassify the hereditary and the acquired forms of vWD. Only few laboratories are skilled to perform this analysis. The extreme range of protein size from 250 kDa monomer to over 20,000 kDa multimers requires a time-consuming procedure (3-4 days) and presents many technical difficulties. To standardize the method and to overcome technical difficulties, we developed a rapid and sensitive semi-automated method to visualize the multimeric structure of vWF. The semi-automated method we present performs the electrophoresis of patient's plasma in 120 min on a precast gel. Gels are suitable for the G26 Interlab instrumentation. After gel blotting, the method allows visualization of the vWF multimer pattern directly on the membrane. We reduced the time required from 72 to 8 h and we propose this test for the first level screening of vWF multimer deficiency.

Identification and quantification of hemoglobins in whole blood: the analytical and organizational aspects of Capillarys 2 Flex Piercing compared with agarose electrophoresis and HPLC methods.

BACKGROUND: The present study was conducted to evaluate the analytical performance and the organizational aspects of Capillarys 2 Flex Piercing system (CFP) respect to agarose electrophoresis and HPLC methods in hemoglobinopathies screening. METHODS: The measurement of imprecision in HbA 2 and HbF quantification was verified on HbA 2 CFP control and on three samples; 74 whole blood samples were used to evaluate migration time imprecision of hemoglobin variants S, C and E (HbS, HbC, and HbE); to compare methods, 451 samples were tested on CFP and HPLC; reference values were verified as value distribution in 160 blood donors and at ROC curve analysis on 449 samples from routine analysis. RESULTS: Imprecision: the analytical CV % s ranged from 1.25 to 3.9 at HbA 2 quantification, the CV % was 3.78 at HbF quantification; the running time imprecision for HbS and HbC and HbE ranged from 0.20 to 0.69 % . Method comparison: at regression analysis findings were HbA 2: CFP=1.21×HPLC­0.64, HbF: CFP=1.31×HPLC−0.75, HbS: CFP=1.10×HPLC−3.24. Reference values: the HbA 2 95th percentile range was 2.5­2.8; HbF was undetectable in 154 out 160 samples tested; at ROC curve analysis the best combination of sensitivity and diagnostic efficiency was obtained using 2.2 and 3.0, as reference values, for HbA 2 and 1.1 as the upper reference limit for HbF. Organizational aspects: with respect to the procedures currently implemented in our laboratory CFP requires 2 h less time and obviates the need for some manual steps. CONCLUSIONS: The quantification, reproducibility and diagnostic efficiency provided by CFP in identification and quantification of hemoglobins appear accurate. In addition, the use of primary tubes allows improved safety, and the avoidance of some manual steps, that prolong working time and are a source of possible errors.

Evaluation of a microfluidics-based platform and slab electrophoresis for determination of size, integrity and quantification of in vitro transcribed RNA used as a component in therapeutic drug manufacturing.

Ribonucleic acid (RNA) is gaining utility as a key component of immunotherapeutics to transiently express antigens or to modulate endogenous gene expression for clinical applications. As a key ancillary component of clinical grade products, RNA requires a robust method for quality control. Here we evaluated the microfluidics based platform and slab electrophoresis for determination of integrity, concentration and size of four in vitro-transcribed RNA products with sizes of 1611, 808, 475 and 290 nucleotides (nts). Our data demonstrate that the Bioanalyzer can determine both size and integrity of the RNA, but the analysis suffers from a strong well position effect. For the RNAs tested, the integrity values obtained by the Bioanalyzer demonstrate a reverse correlation with the size of the molecule and are lower than those obtained using slab electrophoresis. Agarose gel electrophoresis produced the information on size of the RNA molecule with good precision, accuracy and reproducibility. We highlight observations which need to be taken into account when developing and qualifying a method of choice for assessment of in vitro-transcribed RNA using either approach.

Immunofixation electrophoresis for identification of proteins and specific antibodies.

Immunofixation electrophoresis (IFE) is a technique for the identification of proteins within complex mixtures after separation by either conventional zone electrophoresis or isoelectric focusing. Most commonly antigens (which are often immunoglobulins) are separated by electrophoresis followed by precipitation with specific antibodies in situ. However, immunoglobulins with specific reactivity can be also precipitated with the proper antigens after electrophoresis in reverse or reversed IFE. Because of its great versatility, potentially high sensitivity, ease to perform and customize, and relatively low cost with no requirement for expensive instrumentation, manual IFE remains a valuable tool for both clinical diagnostic testing and research. Any low-viscosity body fluid specimen or, possibly, culture fluid could be tested with IFE if proper antibodies (or antigens in reverse[d] IFE) are available. After pretreatment with chaotropic and/or reducing agents, even high-viscosity specimens might be amenable to testing with IFE.

Isoelectric focusing in agarose gel for detection of oligoclonal bands in cerebrospinal and other biological fluids.

Isoelectric focusing (IEF) coupled with immunodetection (immunofixation or immunoblotting) has become the leading technique for the detection and study of oligoclonal bands (OCBs) in cerebrospinal fluid (CSF) and also is increasingly used in other body fluids such as the tear and serum. Limited commercial availability of precast agarose IEF gels for research and a need for customization prompted reporting a detailed general protocol for the preparation and casting of agarose IEF gel along with sample, control, and isoelectric point marker preparation and carrying out the focusing itself for CSF OCBs. However, the method is readily adaptable to the use of other body fluid specimens and, possibly, research specimens such as culture fluids as well.

Immunoelectrophoresis: a method with many faces.

Immunoelectrophoresis (IEP) was the first practical method that combined electrophoresis and -immunoprecipitation for identifying and characterizing proteins within complex mixtures. Over the years, IEP has been extended to include a variety of techniques and, as a general name, has been applied to virtually any technique that involves electrophoresis and antigen-antibody precipitin reaction for proteins. Because of the diversity in technical details of different IEP versions, the method described here deals only with classic IEP. Although it requires some manual expertise, IEP is versatile, relatively easy to customize, and economical with no need for expensive instrumentation. Further, it can discern identity, partial identity, and nonidentity of the proteins. Any low-viscosity body fluid specimen or, possibly, culture fluid and tissue extract could be tested with IEP if proper antibodies are available. With these attributes, classic IEP remains a valuable tool for clinical diagnostic testing, purity checking of biochemical and pharmaceutical products, and research.

Comparison of reverse transcriptase PCR, reverse transcriptase loop-mediated isothermal amplification, and culture-based assays for Salmonella detection from pork processing environments.

Novel rapid Salmonella detection assays without the need for sophisticated equipment or labor remain in high demand. Real-time reverse transcriptase PCR (RT-PCR) assays, though rapid and sensitive, require expensive thermocyclers, while a novel RT loop-mediated isothermal amplification (RT-LAMP) method requires only a simple water bath. Our objective was to compare the detection sensitivity of Salmonella Typhimurium from the pork processing environment by RT-LAMP, RT-PCR, and culture-based assays. Carcass and surface swabs and carcass rinses were obtained from a local processing plant. Autoclaved carcass rinses (500 ml) were spiked with Salmonella Typhimurium and filtered. Filters were placed in stomacher bags containing tetrathionate broth (TTB) and analyzed with or without 10-h enrichment at 37 °C. Natural swabs were stomached with buffered peptone water, and natural carcass rinses were filtered, preenriched, and further enriched in TTB. Serially-diluted enriched samples were enumerated by spread plating on xylose lysine Tergitol 4 agar. RNA was extracted from 5 ml of enriched TTB with TRIzol. RT-LAMP assay using previously described invA primers was conducted at 62 °C for 90 min in a water bath with visual detection and by gel electrophoresis. SYBR Green I-based-real-time RT-PCR was carried out with invA primers followed by melt temperature analysis. The results of RT-LAMP detection for spiked carcass rinses were comparable to those of RT-PCR and cultural plating, with detection limits of 1 log CFU/ml, although they were obtained significantly faster, within 24 h including preenrichment and enrichment. RT-LAMP showed 4 of 12 rinse samples positive, while RT-PCR showed 1 of 12 rinse samples positive. For swabs, 6 of 27 samples positive by RT-LAMP and 5 of 27 by RT-PCR were obtained. This 1-day RT-LAMP assay shows promise for routine Salmonella screening by the pork industry.

Interpretation of capillary zone electrophoresis compared with cellulose acetate and agarose gel electrophoresis: reference intervals and diagnostic efficiency in dogs and cats.

BACKGROUND: Serum protein electrophoresis is widely used for diagnostic and research purposes. Cellulose acetate (CAE) and agarose gel (AGE) electrophoresis are the most frequently used methods, but capillary zone electrophoresis (CZE) is beginning to be used more in veterinary laboratories. However, reference intervals for CZE in animals and comparison studies with the other electrophoretic techniques are lacking, compromising the diagnostic utility of CZE. OBJECTIVES: The aims of this study were to compare results obtained using CAE, AGE, and CZE; to establish reference intervals for CZE in dogs and cats; and to assess the capacity of CZE to detect abnormalities identified by AGE. METHODS: Serum samples from 204 dogs, including 104 healthy animals, and 62 cats, including 28 healthy animals, were analyzed using automated systems for CAE, AGE, and CZE. Descriptive statistics and Passing-Bablok and Bland-Altman tests were used to compare results. For each technique, reference intervals were calculated based on results from healthy animals. Concordance between CZE and AGE in detecting pathologic changes was assessed using Cohen's k coefficient. RESULTS: For most protein fractions, values obtained by CAE, AGE, and CZE were significantly different from each other, and constant and proportional errors were often detected. Nevertheless, reference intervals obtained by the 3 techniques overlapped. Moreover, Cohen's k coefficient demonstrated that the capacity of CZE and AGE to detect pathologic changes was comparable. CONCLUSIONS: CZE performs comparably to AGE and CAE as long as CZE-specific reference intervals are used for interpretation and distinctive visual patterns for albumin, gaps between fractions, and subpeaks found on CZE tracings are recognized. In addition, CZE offers several technical advantages, such as ease of use and complete automation.

Unit cloning and amplification as novel and universal strategies for complex vector construction and small DNA fragment preparation.

With a novel and universal strategy for the cloning of multiple DNA fragments, a complex synthetic vector (pVEC100), harboring the target DNA fragments in conventional 100-bp DNA ladder, was constructed for efficient and large-scale production of 100-bp DNA marker through bacteria fermentation, plasmid extraction and restrictive digestion. Since the restrictive digestion of complex vectors yields insufficient small DNA fragments, an innovative PCR model was developed as an alternative. The PCR model comprised a specially designed template vector and a unit amplification model for producing groups of small DNA fragments. The unit amplification model improved the efficiency of the PCR protocol and made it more economical and easier for small DNA fragment amplification. The approach presented in this paper--a unit cloning model for constructing complex synthetic vectors combined with the modular design of unit amplification by PCR--is a powerful method for preparing small DNA fragments of DNA molecular weight standards.

Distinction of Plasmodium falciparum recrudescence and re-infection by MSP2 genotyping: a caution about unstandardized classification criteria.

BACKGROUND: Plasmodium falciparum genotyping with molecular polymorphic markers is widely employed to distinguish recrudescence from re-infection in antimalarial drug efficacy monitoring programmes. However, limitations occur on agarose gel DNA measurements used to resolve the polymorphisms. Without empirical data, the current distinction of pre- and post-treatment bands, as persistent or new infection, is subjective and often varying by author. This study measures empirical tolerance limits for classifying different-sized bands as same or different alleles during MSP2 genotyping. METHODS: P. falciparum field samples from 161 volunteers were genotyped by nested PCR using polymorphic MSP2 family-specific primers. Data were analysed to determine variability of band size measurements between identical MSP2 alleles randomized into different agarose lanes. RESULTS: The mean (95% CI) paired difference in band size between identical alleles was 9.8 bp (1.48 - 18.16 bp, p = 0.022) for 3D7/IC and 2.54 (-3.04 - 8.05 bp, p = 0.362) for FC27. Based on these findings, pre- and post-treatment samples with 3D7/IC alleles showing less than 18 bp difference corresponded to recrudescence, with 95% confidence, while greater difference indicated new infection. FC27 allele differences were much narrower. For both 3D7/IC and FC27 amplicon, allele detection sensitivity was significantly higher with 13 mul compared to 20 mul or 30 mul lane loading volumes. CONCLUSION: During MSP genotyping, it is useful to standardize classifications against measurement of background variability on identical alleles, in order to obtain reliable findings. It is critical to use a fixed optimal lane loading volume for constant allele patency, to avoid the disappearance or false appearance of new infection.

Evaluation of the BAX gel and fluorometric systems for the detection of foodborne Salmonella.

The present study compared the sensitivity of the BAX automated fluorometric and the recently discontinued BAX gel electrophoresis systems with a standard culture method to detect Salmonella in 333 high-moisture and 171 low-moisture foods. A total of 95 naturally contaminated foods, including 63 high-moisture and 32 low-moisture foods, were detected by the standard culture method. No contaminated samples were identified exclusively by the BAX systems. By means of the analytical protocol stipulated by the manufacturer, the BAX fluorometric system detected 36 (57.1%) and 29 (90.6%) of the contaminated high- and low-moisture foods, respectively. Similar results were obtained with the BAX gel electrophoresis system, which identified 40 (63.5%) and 26 (81.3%) of the contaminated high- and low-moisture foods. The rate of false-positive reactions with the BAX systems was low. Our results indicate that the low sensitivity of the BAX systems with high-moisture foods, notably raw meats and poultry products, was serovar-independent. The high levels of background microflora that commonly occur in raw meat and on fresh fruit and vegetable products, and the high successive dilutions of test materials for PCR analysis, suggestively undermined the sensitivity of the gel and the fluorometric BAX assays. The potential benefits of immunomagnetic separation of Salmonella in preenrichment cultures, of selective broth enrichment following preenrichment to markedly reduce levels of background microflora in PCR test materials, and the use of larger portions of test materials in PCR analyses should be investigated.

DNA damage quantitation by alkaline gel electrophoresis.

Quantifying DNA lesions provides a powerful way to assess the level of endogenous damage or the damage level induced by radiation, chemical or other agents, as well as the ability of cells to repair such damages. Quantitative gel electrophoresis of experimental DNAs along with DNA length standards, imaging the resulting dispersed DNA and calculating the population average length allows accurate measurement of lesion frequencies. Number average length analysis provides high sensitivity and does not require any specific distribution of lesions within the DNA molecules. These methods are readily applicable to strand breaks and ultraviolet radiation induced pyrimidine dimers, but can also be used-with appropriate modifications-for ionizing radiation-induced lesions such as oxidized bases and abasic sites.

Multiplex nested PCR for Brazilian Alphavirus diagnosis.

A reverse-transcriptase PCR (RT-PCR) and a multiplex nested PCR were developed for the rapid detection and identification of 14 Brazilian alphaviruses. Using Alphavirus genus-specific primers in a RT-PCR, we obtained amplified products of 434 bp. Species-specific primers were selected and simultaneously tested in a multiplex nested PCR. The nested PCR increased the test sensitivity 1000-fold and was capable of identifying Brazilian Alphavirus showing the expected bands with diagnostic sizes for Venezuelan (400 bp), Eastern (124 bp), and Western (208 bp) equine encephalitis, Aura (86 bp), and Mayaro (270 bp) viruses. This strategy for diagnosis is fast, sensitive, specific and it can be used as a reliable alternative for routine Brazilian Alphavirus diagnosis.

A combined AFLP-multiplex PCR assay for molecular typing of Escherichia coli strains using variable bacterial interspersed mosaic elements.

The original method for molecular typing of E. coli strains was developed using the polymorphism in chromosomal sequences of bacterial interspersed mosaic elements (BIMEs) detected by multiplex PCR and analysed by AFLP assay. The applicability of the method in the epidemiology of E. coli was tested on a group of 524 strains of human and veterinary origin. In the studied group 18 different genotypes were detected. Significant differences were found in the frequencies of the genotypes among various groups of strains, suggesting the method could be a promising tool in the epidemiology of E. coli.

Vertical agarose gel electrophoresis and electroblotting of high-molecular-weight proteins.

The electrophoretic separation of high-molecular-weight proteins (> 500 kDa) using polyacrylamide is difficult because gels with a large enough pore size for adequate protein mobility are mechanically unstable. A 1% vertical sodium dodecyl sulfate (SDS)-agarose gel electrophoresis (VAGE) system has been developed that allows titin (a protein with the largest known SDS subunit size of 3000-4000 kDa) to migrate over 10 cm in a approximately 13 cm resolving gel. Such migration gives clear and reproducible separation of titin isoforms. Proteins ranging in size from myosin heavy chain ( approximately 220 kDa) up to titin can be resolved on this gel system. Electroblotting of these very large proteins was nearly 100% efficient. This VAGE system has revealed two titin size variants in rabbit psoas muscle, two N2BA bands in rabbit cardiac muscle, and species differences between titins from rat and rabbit muscle. Agarose electrophoresis should be the method of choice for separation and blotting of proteins with very large subunit sizes.