Multiplex Assay of Viruses Integrating Recombinase Polymerase Amplification, Barcode-Anti-Barcode Pairs, Blocking Anti-Primers, and Lateral Flow Assay.

A multiplex assay based on recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a desirable tool for many areas. This multiplex assay could be efficiently realized using single-stranded (ss) DNAs located in separate zones on the test strip and bound complementary ssDNA tags of double-stranded (ds) DNA amplicons. Here, we investigate how to enrich multiplex assay capabilities using ssDNAs. Bifunctional oligonucleotide probes integrating (1) a forward primer for RPA, (2) a C9 spacer to stop polymerase, and (3) a ssDNA tag for binding at test strip are developed. The amplicons have a unique individual ssDNA tag at one end and a universal label of fluorescein introducing through a reverse primer at the other end. A conjugate of gold nanoparticles (GNP) with antibodies to fluorescein is used to detect all amplicons. The remainder of primers after RPA interacting with GNP conjugate was found to be a limiting factor for sensitive and specific multiplex assay. The addition of anti-RPA-primers before the use of test strips was proposed to simply and effectively eliminate remaining primers. This approach was successfully applied for the detection of three priority plant RNA viruses: potato virus Y (PVY), -S (PVS) and potato leafroll virus (PLRV). The total time of the assay is 30 min. The multiplex RPA-LFT detected at least 4 ng of PVY per g of plant leaves, 0.04 ng/g for PVS, and 0.04 ng/g for PLRV. The testing of healthy and infected potato samples showed concordance between the developed assay and reverse transcription-polymerase chain reaction. Thus, the capabilities of the proposed universal modules (ssDNA anchors, bifunctional probes, and blocking anti-primers) for multiplex detection of RNA analytes with high specificity and sensitivity were demonstrated.

PNPLA3 rs738409 associates with alcoholic liver cirrhosis but not with serum levels of IL6, IL10, IL8 or CCL2 in the Russian population.

INTRODUCTION AND AIM: Polymorphic variant rs738409 within the PNPLA3 gene associates with alcoholic liver cirrhosis (ALC) in heavy drinkers of various ancestry but has not yet been established in the Russian population characterized by high incidence of ALC. PNPLA3 rs738409 involvement in the inflammatory process has been proposed as one of the mechanisms of liver dysfunction. Relationship between the PNPLA3 polymorphism and the biochemical markers of inflammation in patients with ALC remains unclear. The current study revealed the association between the rs738409 polymorphism, liver cirrhosis and serum cytokines in heavy drinkers in the Russian population. MATERIALS AND METHODS: The serum levels of IL6, IL10, IL8, and CCL2 along with PNPLA3 rs738409 polymorphism were determined in heavy drinkers (AA, n=71) and heavy drinkers with diagnosed liver cirrhosis (ALC, n=110). All of the recruited individuals were Caucasians and belonged to the Russian population. RESULTS: Heavy drinkers carrying PNPLA3 rs738409 CG or CG+GG genotypes as compared with CC genotype carriers or G allele as compared with C allele carriers had significant risk of ALC. In ALC levels of interleukins and CCL2 increased as compared with AA. PNPLA3 rs738409 CC carriers had lower cirrhosis stage as compared with CG+GG carriers, however there were no differences of IL6, IL10, IL8 or CCL2 levels between G allele carriers and non-carriers in heavy drinkers. CONCLUSION: Thus, in the Russian population heavy drinkers carrying PNPLA3 rs738409 G allele are at higher risk of ALC, however the presence of rs738409 allele does not influence the serum cytokine levels.

Key significance of DNA-target size in lateral flow assay coupled with recombinase polymerase amplification.

The combination of isothermal nucleic acid amplification and lateral flow assay (LFA) provides highly sensitive non-laboratory ("point-of-care") detection. The aim of this study is to investigate the recognition on lateral flow membranes of DNA targets with different lengths as products of recombinase polymerase amplification (RPA). We produced double-stranded DNA with lengths of 50, 100, 150, 200, and 300 bp. Each DNA target was functionalized with biotin and fluorescein (FAM). Kinetic and equilibrium constants of the interaction of FAM at the 5'-end of DNA with anti-FAM antibodies did not depend on DNA length. Gold nanoparticles (GNPs) with diameters of 17.4 ± 1.0 nm were conjugated with anti-FAM antibodies and streptavidin. LFA was performed in two schemes: 1) anti-FAM antibodies immobilized in the test zone, GNP-streptavidin conjugates recognized as DNA; 2) streptavidin immobilized in the test zone, GNP‒anti-FAM antibodies conjugates recognized as DNA. Considering that the components of the RPA mixture caused the aggregation of the GNP-streptavidin conjugate in contradistinction to conjugate with anti-FAM antibodies, we found that 150 bp was the most promising length for the DNA target. For this length, a detection limit was achieved up to 70 pM that was approximately 10 times lower than for 50-bp DNA in the same scheme. Moreover, we showed that high concentrations of primers containing FAM or biotin competed with the DNA target on lateral flow membranes. These results demonstrated that a DNA length should be considered when designing RPA-LFA systems to detect DNA targets with high sensitivity.

Recombinase polymerase amplification combined with a magnetic nanoparticle-based immunoassay for fluorometric determination of troponin T.

The authors describe a method for the improvement of the sensitivity of immunoassays. This was achieved by a combination of immunoassay and an amplification based on the use of a multiplied DNA probe. The immunoassay was enhanced via recombinant polymerase amplification (RPA). It enables fast (35 min) isothermal multiplication of DNA at 37 °C. This concept was demonstrated for a sandwich immunoassay that is making use of magnetic nanoparticles conjugated to first specific antibodies and then to second specific antibodies linked to reporter DNA via biotin-streptavidin binding. Reporter DNA multiplied by RPA was quantified fluorometrically via the carboxyfluorescein label. Human cardiac troponin T (cTnT), a biomarker for acute myocardial infarction, was used as the target of the immunoRPA (iRPA). The assay can detect cTnT in serum and in plasma within 2 h, with detection limits as low as 12.5 ± 1.1 pg•mL-1 and 9.4 ± 2.1 pg•mL-1, respectively. This represents increased sensitivity and decreased assay time compared to classical ELISAs (3.5 ± 0.3 ng•mL-1) or immuno-PCR (4.3 ± 0.8 ng•mL-1) that were carried out using the same immunoreagents and reporter DNA. The good performance of this iRPA was underlined by its successful application to the analysis of plasma samples. The iRPA has significant advantages relative to other DNA amplification-based immunoassays due to isothermal conditions and analysis at 37 °C. Graphical abstract Schematic representation of a new kind of immunoassay that is enhanced by making use of recombinase polymerase amplification (immunoRPA). Reporter DNA was conjugated with specific antibodies, then amplified and finally quantified fluorometrically. Limit of detection of troponin T in plasma within 2 h was 9.4 ± 2.1 pg•mL-1.

Identifying the Infarct-Related Artery in Patients With Non-ST-Segment-Elevation Myocardial Infarction.

BACKGROUND: Determining the infarct-related artery (IRA) in non-ST-segment-elevation myocardial infarction (MI) can be challenging. Delayed-enhancement cardiac magnetic resonance (DE-CMR) can accurately identify small MIs. The purpose of this study was to determine whether DE-CMR improves the ability to identify the IRA in patients with non-ST-segment-elevation MI. METHODS AND RESULTS: In this 3-center, prospective study, we enrolled 114 patients presenting with their first MI. Patients underwent DE-CMR followed by coronary angiography. The interventional cardiologist was blinded to the DE-CMR results. Later, coronary angiography and DE-CMR images were reviewed independently and blindly for identification of the IRA. The pattern of DE-CMR hyperenhancement was also used to determine whether there was a nonischemic pathogenesis for myocardial necrosis. The IRA was not identifiable by coronary angiography in 37% of patients (n=42). In these, the IRA or a new noncoronary artery disease diagnosis was identified by DE-CMR in 60% and 19% of patients, respectively. Even in patients with an IRA determined by coronary angiography, a different IRA or a noncoronary artery disease diagnosis was identified by DE-CMR in 14% and 13%, respectively. Overall, DE-CMR led to a new IRA diagnosis in 31%, a diagnosis of nonischemic pathogenesis in 15%, or either in 46% (95% CI, 37%-55%) of patients. Of 55 patients undergoing revascularization, 27% had revascularization solely to nonculprit coronary artery territories as determined by DE-CMR. CONCLUSIONS: Identification of the IRA by coronary angiography can be challenging in patients with non-ST-segment-elevation MI. In nearly half, DE-CMR may lead to a new IRA diagnosis or elucidate a nonischemic pathogenesis. Revascularization solely of coronary arteries that are believed to be nonculprit arteries by DE-CMR is not uncommon.

The Analogy Between the Tradition Chinese Acupuncture and Phlebotomy in Medieval Bohemia.

The common opinion is that in Europe acupuncture was introduced in China at the end of the XVII century. However there are some publications, which describe the similar treatment method in the Stone Age Europe. From ancient to late middle century theoretical and practical aspects of medieval medicine in Europe were very similar to the Tradition Chinese medicine. So it is possible that historical phlebotomy in Europe (bloodletting) played the same role as the acupuncture in the Chinese therapy and they had one scientific source. In this article we are comparing the modern acupuncture with some Bohemian medical tractates (Practica medicinalis by Sigismundus Albicus from 1408-1424, De sanguinis minucione by Cristannus de Prachaticz from 1430). We can see the close relationship between localizations and indications of medieval phlebotomy and modern acupuncture points. 40% of the bloodletting points have close localization with the modern acupuncture points and 57% of their indications are common or very similar. The similarity of two methods may be explained in two ways. First is a common scientific source and intensive interaction and crosscultural transmission of knowledge during medical development in China and Europe up to the beginning of the XV century. This possibility indicates also some linguistic coincidences. On the other hand, both methods could have been developed separately based on common clinical empire and objective neuro-physiological patterns of human body.

Polyadenylate-binding protein-interacting proteins PAIP1 and PAIP2 affect translation termination.

Polyadenylate-binding protein (PABP) stimulates translation termination via interaction of its C-terminal domain with eukaryotic polypeptide chain release factor, eRF3. Additionally, two other proteins, poly(A)-binding protein-interacting proteins 1 and 2 (PAIP1 and PAIP2), bind the same domain of PABP and regulate its translation-related activity. To study the biochemistry of eRF3 and PAIP1/2 competition for PABP binding, we quantified the effects of PAIPs on translation termination in the presence or absence of PABP. Our results demonstrated that both PAIP1 and PAIP2 prevented translation termination at the premature termination codon, by controlling PABP activity. Moreover, PAIP1 and PAIP2 inhibited the activity of free PABP on translation termination in vitro However, after binding the poly(A) tail, PABP became insensitive to suppression by PAIPs and efficiently activated translation termination in the presence of eRF3a. Additionally, we revealed that PAIP1 binds eRF3 in solution, which stabilizes the post-termination complex. These results indicated that PAIP1 and PAIP2 participate in translation termination and are important regulators of readthrough at the premature termination codon.

Implementation of Fast Healthcare Interoperability Resources for an Integration of Laboratory and Hospital Information Systems.

Electronic exchange of medical data between clinics and test centers makes the testing process more efficient, enables continuity of care record and reuse of medical data. The presented project employs HL 7 FHIR approach to model clinical concepts for the medical data exchange between a test center and different hospitals. Using a standard FHIR editor we have modeled 1226 observation profiles, 2396 commercial tests profiles that are mapped to 3249 production tests profiles. We have also defined a concept of an order and developed RESTfull API protocol to facilitate the ordering process. Now the data exchange system is in production and processes more than 20 000 test orders with more than 40 000 tests a day.

PABP enhances release factor recruitment and stop codon recognition during translation termination.

Poly(A)-binding protein (PABP) is a major component of the messenger RNA-protein complex. PABP is able to bind the poly(A) tail of mRNA, as well as translation initiation factor 4G and eukaryotic release factor 3a (eRF3a). PABP has been found to stimulate translation initiation and to inhibit nonsense-mediated mRNA decay. Using a reconstituted mammalian in vitro translation system, we show that PABP directly stimulates translation termination. PABP increases the efficiency of translation termination by recruitment of eRF3a and eRF1 to the ribosome. PABP's function in translation termination depends on its C-terminal domain and its interaction with the N-terminus of eRF3a. Interestingly, we discover that full-length eRF3a exerts a different mode of function compared to its truncated form eRF3c, which lacks the N-terminal domain. Pre-association of eRF3a, but not of eRF3c, with pre-termination complexes (preTCs) significantly increases the efficiency of peptidyl-tRNA hydrolysis by eRF1. This implicates new, additional interactions of full-length eRF3a with the ribosomal preTC. Based on our findings, we suggest that PABP enhances the productive binding of the eRF1-eRF3 complex to the ribosome, via interactions with the N-terminal domain of eRF3a which itself has an active role in translation termination.

Friedel-Crafts Alkylation of Arenes with 2-Halogeno-2-CF3-styrenes under Superacidic Conditions. Access to Trifluoromethylated Ethanes and Ethenes.

The formation of the corresponding benzyl cations [ArHC(+)-CH(X)CF3] takes place under protonation of E-/Z-2-halogeno-2-CF3 styrenes [ArCH═C(X)CF3, X = F, Cl, Br] in superacids. The structures of these new electrophiles were studied by means of NMR and theoretical DFT calculations. According to these data, in the case of bromo derivatives, the formed cations, most probably, exist as cyclic bromonium ions; however, in the cases of chloro and fluoro derivatives, open forms are more preferable. Subsequent reaction of these benzyl cations with arenes proceeds as Friedel-Crafts alkylation to afford 1,1-diaryl-2-halo-3,3,3-trifluoropropanes [Ar(Ar')CH-CH(X)CF3] in high yields (up to 96%) as a mixture of two diastereomers. The prepared halogenopropanes were easily converted into the corresponding mixtures of E-/Z-trifluoromethylated diarylethenes [Ar(Ar')C═CCF3] (in yields up to 96%) by dehydrohalogenation with base (KOH or t-BuOK). The mechanism of elimination (E2 and Ecb) depends on the nature of the leaving group and reaction conditions.

Transformations of Conjugated Enynones in the Superacid CF3SO3H. Synthesis of Butadienyl Triflates, Indanones, and Indenes.

Conjugated 1,5-diarylpent-2-en-4-yn-1-ones add the superacid CF3SO3H to the acetylenic bond with formation of the corresponding butadienyl triflates. Under superacidic reaction conditions, these triflates are transformed into indanone or indene derivatives depending on which substituents on the aromatic ring are conjugated with the butadiene fragment. In a less acidic system (10% vol pyridine in CF3SO3H) only the formation of butadienyl triflates takes place. Cationic reaction intermediates were studied by means of NMR and DFT calculations.

Beauty will save the world, but will the world save beauty? The case of the highly endangered Vavilovia formosa (Stev.) Fed.

MAIN CONCLUSION: Vavilovia formosa (Stev.) Fed. is a scientifically valuable common ancestor of the plant tribe Fabeae and also important in breeding and agronomy studies of the cultivated Fabeae, but it is close to extinction. A concerted academic and geovernmental effort is needed to save it. Since 2007, an informal international group of researchers on legumes has been working to increase awareness of Vavilovia formosa (Stev.) Fed., a relict and endangered wild-land relative to crop plant species. A majority of the modern botanical classifications place it within the tribe Fabeae, together with the genera vetchling (Lathyrus L.), lentil (Lens Mill.), pea (Pisum L.) and vetch (Vicia L.). V. formosa is encountered at altitudes from 1,500 m up to 3,500 m in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia, Syria and Turkey. This species may be of extraordinary importance for broadening current scientific knowledge on legume evolution and taxonomy because of its proximity to the hypothetical common ancestor of the tribe Fabeae, as well as for breeding and agronomy of the cultivated Fabeae species due to its perenniality and stress resistance. All this may be feasible only if a concerted and long-term conservation strategy is established and carried out by both academic and geovernmental authorities. The existing populations of V. formosa are in serious danger of extinction. The main threats are domestic and wild animal grazing, foraging, and early frosts in late summer. A long-term strategy to save V. formosa from extinction and to sustain its use in both basic and applied research comprises much improved in situ preservation, greater efforts for an ex situ conservation, and novel approaches of in vitro propagation.

Interaction of Gram-negative bacteria with cationic proteins: Dependence on the surface characteristics of the bacterial cell.

Gram-negative bacteria can enter the bloodstream and interact with serum cationic proteins. The character of interaction will depend on the surface characteristics of bacterial cells, which are determined by bacterial chemotype and density of lipopolysaccharide (LPS) packing in the cell wall. It was shown that the lysozyme treatment resulted in the increase sensitivity to hypotonic shock. Significant differences to this effect were found between Escherichia coli strain D21 and D21f2 under treatment with physiological protein concentration. On the basis of electrokinetic measurements and studies of the interaction of cells with lysozyme, the hypothesis was formed that the cell wall of the E. coli strain D21f2 contains more LPS and has a higher density of their packing than the cell wall of the E. coli D21 cells. The effect of lysozyme and lactoferrin on the viability of E. coli cells of two different strains was examined. Lysozyme was found to more effectively inhibit the growth of the E. coli D21 bacteria, and lactoferrin suppressed mainly the growth of the E. coli D21f2 bacteria. These results indicate that the differences in LPS core structure of bacterial R-chemotype, which determines surface charge and density of LPS packing, plays an essential role in the mechanisms of interaction of the cationic proteins with the cell wall.