Increase in the solubility of uvsY using a site saturation mutagenesis library for application in a lyophilized reagent for recombinase polymerase amplification

BACKGROUND

Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility.

METHODS

Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY.

RESULTS

Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY.

CONCLUSIONS

The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.

Tests of Light-Lepton Universality in Angular Asymmetries of B^{0}→D^{*-}ℓν Decays

We present the first comprehensive tests of the universality of the light leptons in the angular distributions of semileptonic B^{0}-meson decays to charged spin-1 charmed mesons. We measure five angular-asymmetry observables as functions of the decay recoil that are sensitive to lepton-universality-violating contributions. We use events where one neutral B is fully reconstructed in ϒ(4S)→BB[over ¯] decays in data corresponding to 189  fb^{-1} integrated luminosity from electron-positron collisions collected with the Belle II detector. We find no significant deviation from the standard model expectations.

Application of recombinant human pyruvate kinase in recombinase polymerase amplification

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41°C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. In this study, we attempted to use pyruvate kinase instead of creatine kinase (CK) that has been consistently used as an ATP-regenerating enzyme in RPA. Human pyruvate kinase M1 (PKM) was expressed in Escherichia coli and purified from the cells. RPA with PKM was performed at 41°C with the in vitro synthesized urease subunit β (ureB) DNA from Ureaplasma parvum serovar 3 as a standard DNA. The optimal concentrations of PKM and phosphoenolpyruvate were 20 ng/μL and 10 mM, respectively. The RPA reaction with PKM was more sensitive than that with CK. PKM exhibited higher thermostability than CK, suggesting that the RPA reagents with PKM are preferable to those with CK for onsite use.

Precise Measurement of the D_{s}^{+} Lifetime at Belle II

We measure the lifetime of the D_{s}^{+} meson using a data sample of 207  fb^{-1} collected by the Belle II experiment running at the SuperKEKB asymmetric-energy e^{+}e^{-} collider. The lifetime is determined by fitting the decay-time distribution of a sample of 116×10^{3} D_{s}^{+}→ϕπ^{+} decays. Our result is τ_{D_{s}^{+}}=(499.5±1.7±0.9)  fs, where the first uncertainty is statistical and the second is systematic. This result is significantly more precise than previous measurements.

Search for a τ^{+}τ^{-} Resonance in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} Events with the Belle II Experiment

We report the first search for a nonstandard-model resonance decaying into τ pairs in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} events in the 3.6-10  GeV/c^{2} mass range. We use a 62.8  fb^{-1} sample of e^{+}e^{-} collisions collected at a center-of-mass energy of 10.58 GeV by the Belle II experiment at the SuperKEKB collider. The analysis probes three different models predicting a spin-1 particle coupling only to the heavier lepton families, a Higgs-like spin-0 particle that couples preferentially to charged leptons (leptophilic scalar), and an axionlike particle, respectively. We observe no evidence for a signal and set exclusion limits at 90% confidence level on the product of cross section and branching fraction into τ pairs, ranging from 0.7 to 24 fb, and on the couplings of these processes. We obtain world-leading constraints on the couplings for the leptophilic scalar model for masses above 6.5  GeV/c^{2} and for the axionlike particle model over the entire mass range.

Measurement of CP Violation in B^{0}→K_{S}^{0}π^{0} Decays at Belle II

We report a measurement of the CP-violating parameters C and S in B^{0}→K_{S}^{0}π^{0} decays at Belle II using a sample of 387×10^{6}  BB[over ¯] events recorded in e^{+}e^{-} collisions at a center-of-mass energy corresponding to the ϒ(4S) resonance. These parameters are determined by fitting the proper decay-time distribution of a sample of 415 signal events. We obtain C=-0.04_{-0.15}^{+0.14}±0.05 and S=0.75_{-0.23}^{+0.20}±0.04, where the first uncertainties are statistical and the second are systematic.

Test of Light-Lepton Universality in the Rates of Inclusive Semileptonic B-Meson Decays at Belle II

We present the first measurement of the ratio of branching fractions of inclusive semileptonic B-meson decays, R(X_{e/μ})=B(B→Xeν)/B(B→Xμν), a precision test of electron-muon universality, using data corresponding to 189  fb^{-1} from electron-positron collisions collected with the Belle II detector. In events where the partner B meson is fully reconstructed, we use fits to the lepton momentum spectra above 1.3  GeV/c to obtain R(X_{e/μ})=1.007±0.009(stat)±0.019(syst), which is the most precise lepton-universality test of its kind and agrees with the standard-model expectation.

Search for an Invisible Z^{'} in a Final State with Two Muons and Missing Energy at Belle II

The L_{μ}-L_{τ} extension of the standard model predicts the existence of a lepton-flavor-universality-violating Z^{'} boson that couples only to the heavier lepton families. We search for such a Z^{'} through its invisible decay in the process e^{+}e^{-}→μ^{+}μ^{-}Z^{'}. We use a sample of electron-positron collisions at a center-of-mass energy of 10.58 GeV collected by the Belle II experiment in 2019-2020, corresponding to an integrated luminosity of 79.7  fb^{-1}. We find no excess over the expected standard-model background. We set 90%-confidence-level upper limits on the cross section for this process as well as on the coupling of the model, which ranges from 3×10^{-3} at low Z^{'} masses to 1 at Z^{'} masses of 8  GeV/c^{2}.

Prognostic value of increased intraepithelial lymphocytes and lymphocytic clonality in dogs with chronic enteropathy or small-cell lymphoma

The clinical significance of severe infiltration of small intraepithelial lymphocytes (IEL) and the results of polymerase chain reaction for antigen receptor rearrangement (PARR) in dogs with chronic enteropathy (CE) and small-cell lymphoma (SCL) are controversial. This cohort study aimed to evaluate the prognostic significance of the IEL and PARR results in dogs with CE or SCL. Although definitive diagnostic histopathological criteria for SCL in dogs have yet to be established, dogs with the histopathological findings of severe IEL infiltration were diagnosed with SCL in this study. One hundred and nineteen dogs were recruited, with 23 dogs classified as having SCL and 96 dogs as having CE. The positive rate of PARR was 59.6 % (71/119) in the duodenum and 57.7 % (64/111) in the ileum. Subsequently, three dogs with SCL and four dogs with CE developed large-cell lymphoma (LCL). The median overall survival (OS) of dogs with SCL was 700 days (range, 6-1410 days), and that of dogs with CE was not reached. In the log-rank test, shorter OS was observed in cases with histopathological SCL (P = 0.035), clonal TCRγ rearrangement in the duodenum (P = 0.012), and clonal IgH rearrangement in the ileum (P < 0.0001). The Cox proportional hazards model adjusted for sex and age showed that histopathological SCL (hazard ratio [HR] 1.74; 95 % confidence interval [CI], 0.83-3.65), duodenal clonal TCRγ rearrangement (HR, 1.80; 95 % CI, 0.86-3.75), and ileal clonal IgH rearrangement (HR, 2.28; 95 % CI, 0.92-5.70) could shorten overall survival, although their 95 % CIs included 1.0. These results indicate that severe IEL infiltration could be a useful histopathological feature for diagnosing SCL, and clonality-positive results could be a negative prognostic factor in dogs with CE. Furthermore, the development of LCL should be carefully monitored in dogs with CE and SCL..

Search for Lepton-Flavor-Violating τ Decays to a Lepton and an Invisible Boson at Belle II

We search for lepton-flavor-violating τ^{-}→e^{-}α and τ^{-}→μ^{-}α decays, where α is an invisible spin-0 boson. The search uses electron-positron collisions at 10.58 GeV center-of-mass energy with an integrated luminosity of 62.8  fb^{-1}, produced by the SuperKEKB collider and collected with the Belle II detector. We search for an excess in the lepton-energy spectrum of the known τ^{-}→e^{-}ν[over ¯]_{e}ν_{τ} and τ^{-}→μ^{-}ν[over ¯]_{μ}ν_{τ} decays. We report 95% confidence-level upper limits on the branching-fraction ratio B(τ^{-}→e^{-}α)/B(τ^{-}→e^{-}ν[over ¯]_{e}ν_{τ}) in the range (1.1-9.7)×10^{-3} and on B(τ^{-}→μ^{-}α)/B(τ^{-}→μ^{-}ν[over ¯]_{μ}ν_{τ}) in the range (0.7-12.2)×10^{-3} for α masses between 0 and 1.6  GeV/c^{2}. These results provide the most stringent bounds on invisible boson production from τ decays.

Observation of e^{+}e^{-}→ωχ_{bJ}(1P) and Search for X_{b}→ωϒ(1S) at sqrt[s] near 10.75 GeV

We study the processes e^{+}e^{-}→ωχ_{bJ}(1P) (J=0, 1, or 2) using samples at center-of-mass energies sqrt[s]=10.701, 10.745, and 10.805 GeV, corresponding to 1.6, 9.8, and 4.7  fb^{-1} of integrated luminosity, respectively. These data were collected with the Belle II detector during special operations of the SuperKEKB collider above the ϒ(4S) resonance. We report the first observation of ωχ_{bJ}(1P) signals at sqrt[s]=10.745  GeV. By combining Belle II data with Belle results at sqrt[s]=10.867  GeV, we find energy dependencies of the Born cross sections for e^{+}e^{-}→ωχ_{b1,b2}(1P) to be consistent with the shape of the ϒ(10753) state. These data indicate that the internal structures of the ϒ(10753) and ϒ(10860) states may differ. Including data at sqrt[s]=10.653  GeV, we also search for the bottomonium equivalent of the X(3872) state decaying into ωϒ(1S). No significant signal is observed for masses between 10.45 and 10.65  GeV/c^{2}.

Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.

Measurement of the Λ_{c}^{+} Lifetime

An absolute measurement of the Λ_{c}^{+} lifetime is reported using Λ_{c}^{+}→pK^{-}π^{+} decays in events reconstructed from data collected by the Belle II experiment at the SuperKEKB asymmetric-energy electron-positron collider. The total integrated luminosity of the data sample, which was collected at center-of-mass energies at or near the ϒ(4S) resonance, is 207.2  fb^{-1}. The result, τ(Λ_{c}^{+})=203.20±0.89±0.77  fs, where the first uncertainty is statistical and the second systematic, is the most precise measurement to date and is consistent with previous determinations.

Search for a Dark Photon and an Invisible Dark Higgs Boson in μ^{+}μ^{-} and Missing Energy Final States with the Belle II Experiment

The dark photon A^{'} and the dark Higgs boson h^{'} are hypothetical particles predicted in many dark sector models. We search for the simultaneous production of A^{'} and h^{'} in the dark Higgsstrahlung process e^{+}e^{-}→A^{'}h^{'} with A^{'}→μ^{+}μ^{-} and h^{'} invisible in electron-positron collisions at a center-of-mass energy of 10.58 GeV in data collected by the Belle II experiment in 2019. With an integrated luminosity of 8.34  fb^{-1}, we observe no evidence for signal. We obtain exclusion limits at 90% Bayesian credibility in the range of 1.7-5.0 fb on the cross section and in the range of 1.7×10^{-8}-200×10^{-8} on the effective coupling ϵ^{2}×α_{D} for the A^{'} mass in the range of 4.0  GeV/c^{2}<M_{A^{'}}<9.7  GeV/c^{2} and for the h^{'} mass M_{h^{'}}<M_{A^{'}}, where ϵ is the mixing strength between the standard model and the dark photon and α_{D} is the coupling of the dark photon to the dark Higgs boson. Our limits are the first in this mass range.

Study on ammonia generation from digested sludge by subcritical water treatment

Organic sludge has recently attracted attention as a renewable energy source. While the organic matter contained in sludge can be utilized as various renewable energy sources, its nitrogen component has limited use. In this study, subcritical water treatment was conducted to recover ammonia from digested sludge. While ammonia recovered via stripping is limited to soluble components, subcritical water treatment can convert solid components and dissolved organic nitrogen sludge into ammonia. Digested sludge was treated at several reaction temperatures, reaction pressures, treatment times, and oxygen ratios to determine the ammonia generation rate. Among the conditions tested in this study, an ammonium generation rate of 84.0% was obtained at 400 °C, 10 MPa, a treatment time of 5 min, and at an oxygen ratio of 1.2.

Modified uvsY by N-terminal hexahistidine tag addition enhances efficiency of recombinase polymerase amplification to detect SARS-CoV-2 DNA

Background

Methods

Results

Conclusions

Supplementary Information

Development of robust isothermal RNA amplification assay for lab-free testing of RNA viruses

Simple tests of infectiousness that return results in minutes and directly from samples even with low viral loads could be a potential game-changer in the fight against COVID-19. Here, we describe an improved isothermal nucleic acid amplification assay, termed the RICCA (RNA Isothermal Co-assisted and Coupled Amplification) reaction, that consists of a simple one-pot format of ‘sample-in and result-out’ with a primary focus on the detection of low copy numbers of RNA virus directly from saliva without the need for laboratory processing. We demonstrate our assay by detecting 16S rRNA directly from E. coli cells with a sensitivity as low as 8 CFU/μL and RNA fragments from a synthetic template of SARS-CoV-2 with a sensitivity as low as 1740 copies/μL. We further demonstrate the applicability of our assay for real-time testing at the point of care by designing a closed format for paper-based lateral flow assay and detecting heat-inactivated SARS-COV-2 virus in human saliva at concentrations ranging from 28,000 to 2.8 copies/μL with a total assay time of 15–30 min.

P–145 usefulness of morphokinetic data to predict pregnancy rates of day–6 blastocyst transfers

Study question

Can a scoring model based on morphokinetic data developed to predict pregnancy rates of day–5 blastocyst transfers (KIDSCORE™D5) predict pregnancy rates of day–6 blastocyst transfers?

Summary answer

KIDSCORE™D5 was able to predict the clinical pregnancy rates of embryo transfers done on day 6 with an area under the curve (AUC) of 0.72.

What is known already

KIDSCORE™D5 is a scoring model based on morphokinetic data developed to predict the pregnancy rates of day–5 blastocysts. In 2019, Regnier et al. reported that the AUC of KIDSCORE™D5 for predicting clinical pregnancy rates of day–5 blastocyst transfers was 0.6. However, as KIDSCORE™D5 is constructed based on morphological characteristics and developmental dynamics of day–5 blastocysts, it is unclear whether KIDSCORE™D5 can predict pregnancy rates of day–6 blastocyst transfers. Since there are many cases of day–6 blastocyst transfers, it is important to know if KIDSCORE™D5 can predict pregnancy rates of day–6 blastocyst transfers.

Study design, size, duration

This retrospective single-center study, which included 162 day–5 and 72 day–6 blastocyst transfers, respectively, was conducted at Takahashi Women’s clinic from January to December 2019. Blastocysts derived from 146 patients who underwent intracytoplasmic sperm injection. All blastocysts were cryopreserved and were transferred singly.

Participants/materials, setting, methods

We used EmbryoScope+™ (Vitrolife) for in-vitro culture and calculated KIDSCORE™D5 (ver.3) using Embryoviewer™ (Vitrolife). Blastocyst scoring was done from 1.0 to 9.9. Clinical pregnancy was defined as the presence of a gestational sac confirmed by transvaginal ultrasonography. Statistical analysis was performed with JMP Pro 15.00 (SAS). The relationship between KIDSCORE™D5 and clinical pregnancy was evaluated by the AUC using ROC curve analysis and multivariate analysis adjusted for patient age.

Main results and the role of chance

The mean KIDSCORE™D5 of day–5 and day–6 blastocysts was 7.1±1.7 and 3.7±1.5, respectively. KIDSCORE™D5 of day–6 blastocysts was significantly lower than that of day–5 blastocysts (p &lt; 0.0001, Wilcoxon test). ROC curve analysis showed that the KIDSCORE™D5 could predict clinical pregnancy rates with an AUC of 0.62 for day–5 blastocysts and 0.72 for day–6 blastocysts. The cut-off values for KIDSCORE™D5 were 5.7 and 4.9 for day–5 and day–6 blastocysts, respectively. Blastocysts above the cut off value on both day–5 and day–6 had a significantly higher pregnancy rate than those below the cut off value (day–5: 61.9% vs. 33.3%(p = 0.0023), day–6: 47.4% vs. 7.6%(p = 0.0003)). Multivariate analysis adjusted for patient age showed that KIDSCORE™D5 correlated with clinical pregnancy rates of days 5 and 6 of blastocyst transfer with AUCs of 0.66 and 0.73, respectively.

Limitations, reasons for caution

This study had a small sample size, and it was a retrospective single-center study. In addition, the relationship between KIDSCORE™D5 and clinical pregnancy rates may vary among facilities. Therefore, a prospective multicenter validation is necessary.

Wider implications of the findings: Our study results indicated that KIDSCORE™D5 predicted clinical pregnancy and that morphokinetic parameters related to clinical pregnancy were similar between day–5 and day–6 blastocysts. Hence, morphokinetic evaluation can serve as a criterion for deciding which of multiple day–6 blastocysts can be transferred.

Trial registration number

Not applicable

Insight into the collagen-degrading activity of a serine protease in the latex of Ficus carica cultivar Masui Dauphine

Ficus carica produces, in addition to the cysteine protease ficin, a serine protease. Earlier study on a serine protease from F. carica cultivar Brown Turkey showed that it specifically degraded collagen. In this study, we characterized the collagenolytic activity of a serine protease in the latex of F. carica cultivar Masui Dauphine. The serine protease degraded denatured, but not undenatured, acid-solubilized type I collagen. It also degraded bovine serum albumin, while the collagenase from Clostridium histolyticum did not. These results indicated that the serine protease in Masui Dauphine is not collagen-specific. The protease was purified to homogeneity by two-dimensional gel electrophoresis, and its partial amino acid sequence was determined by liquid chromatography-tandem mass spectrometry. BLAST searches against the Viridiplantae (green plants) genome database revealed that the serine protease was a subtilisin-like protease. Our results contrast with the results of the earlier study stating that the serine protease from F. carica is collagen-specific.

Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E

The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillus sp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.

Improvement of Moloney murine leukemia virus reverse transcriptase thermostability by introducing a disulfide bridge in the ribonuclease H region

Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) is widely used in research and clinical diagnosis. Improvement of MMLV RT thermostability has been an important topic of research for increasing the efficiency of cDNA synthesis. In this study, we attempted to increase MMLV RT thermostability by introducing a disulfide bridge in its RNase H region using site-directed mutagenesis. Five variants were designed, focusing on the distance between the two residues to be mutated into cysteine. The variants were expressed in Escherichia coli and purified. A551C/T662C was determined to be the most thermostable variant.

Analyses of putative anti-cancer potential of three STAT3 signaling inhibitory compounds derived from Salvia officinalis

The extract of Salvia officinalis (Common Sage) exhibited inhibitory activity of STAT3 signal after screening of several plants extracts using the STAT3-responsive reporter system. Cirsiliol, luteolin, and carnosol were identified from the methanol extract of Silvia officinalis as inhibitors of STAT3 signaling and the effects of these three compounds on STAT3 protein or growth inhibition on cancer cells was compared. Luteolin at the dose of 90 μM clearly suppressed the phosphorylation of STAT3 induced by IL-6, while carnosol was prone to decrease total STAT3 proteins at high doses (>90 μM). Cirsiliol had almost no effect. Since the three compounds exhibited similar concentration-dependent suppression patterns in the reporter assay except for cirsiliol became plateau beyond 30 μM, these compounds appeared to function as STAT3 inhibitory factors in different ways. The direct anti-proliferative activity of three compounds was examined with or without the anti-cancer drug gefitinib using HepG2 and A549 cells. The anti-proliferative effect of the three compounds was additively enhanced by gefitinib. At the doses of 3.6 μM, statistically significant suppression of proliferation was observed in HepG2 cells only by cirsiliol among the three compounds in the absence of gefitinib but all three compounds were prone to suppress the proliferation of HepG2 cells and A549 cells dose-dependently although cirsiliol showed a modest dose-dependency and this suppression of proliferation was enhanced by the addition of gefitinib. Cirsiliol, a dimethyoxylated flavone, activated the natural killer activity of KHYG-1 cells against erythroleukemia K562 cells like a hexamethoxylated flavone, nobiletin, suggesting that it may also have an indirect anti-cancer potential through activation of NK cells. These results shed light on the putative anti-cancer potential of Salvia officinalis.

•

Carnosol, luteolin and cirsiliol were identified as STAT3 signal inhibitors in S. officinalis.

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Cirsiliol inhibited the STAT3-responsive reporter expression at 7.5 μM but showed low dose-dependency at higher doses.

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Cirsiliol at 90 μM showed almost no effect on phosphorylation of STAT3 and weakly suppressed total STAT3.

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Cirsiliol exhibited anti-proliferative activity at 3.6 μM against HepG2 cells and A549 cells but showed low dose-dependency.

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Cirsiliol activated NK cells by stimulating exocytosis of granules for cytolysis.

Solvent engineering studies on recombinase polymerase amplification

Recombinase polymerase amplification (RPA) is a technique that is used to specifically amplify a target nucleic acid sequence. Unlike the polymerase chain reaction (PCR), RPA is performed at a constant temperature between 37 and 42°C. Therefore, it can be potentially used for the onsite detection of various pathogens when combined with DNA extraction and amplicon detection techniques. In this study, we prepared recombinant recombinase and single-stranded DNA-binding protein from T4 phage and used them to examine the effects of reaction conditions and additives on the efficiency of RPA. The results revealed that the optimal pH was 7.5-8.0, optimal potassium acetate concentration was 40-80 mM, and optimal reaction temperature was 37-45°C although dimethyl sulfoxide at 5% v/v and formamide at 5% v/v inhibited the reaction. Our results suggest that RPA could be conducted using a wider range of optimal reaction conditions than those required for PCR and that RPA is highly suitable for point-of-care use.

Kinetic analysis of inhibition of α-glucosidase by leaf powder from Morus australis and its component iminosugars

Abbreviations

1-DNJ: 1-deoxynojirimycin; GAL-DNJ: 2-O-α-D-galactopyranosyl-DNJ

The roles of histidine and tyrosine residues in the active site of collagenase in Grimontia hollisae

Collagenase from the Grimontia hollisae strain 1706B (Ghcol) is a zinc metalloproteinase with the zinc-binding motif H492EXXH496. It exhibits higher collagen-degrading activity than the collagenase from Clostridium histolyticum, which is widely used in industry. We previously examined the pH and temperature dependencies of Ghcol activity; Glu493 was thought to contribute acidic pKa (pKe1), while no residue was assigned to contribute alkaline pKa (pKe2). In this study, we introduced nine single mutations at the His or Tyr residues in and near the active site. Our results showed that H412A, H485A, Y497A, H578A and H737A retained the activities to hydrolyze collagen and gelatin, while H426A, H492A, H496A and Y568A lacked them. Purification of active variants H412A, H485A, H578A and H737A, along with inactive variants H492A and H496A, were successful. H412A preferred (7-methoxycoumarin-4-yl)acetyl-L-Lys-L-Pro-L-Leu-Gly-L-Leu-[N3-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH2 to collagen, while H485A preferred collagen to the peptide, suggesting that His412 and His485 are important for substrate specificity. Purification of the active variant Y497A and inactive variants H426A and Y568A were unsuccessful, suggesting that these three residues were important for stability. Based on the reported crystal structure of clostridial collagenase, Tyr568 of Ghcol is suggested to be involved in catalysis and may be the ionizable residue for pKe2.

Val143 of human ribonuclease H2 is not critical for, but plays a role in determining catalytic activity and substrate specificity

Ribonuclease H2 (RNase H2) exhibits both single ribonucleotide excision activity (activity A) and RNA strand degrading activity (activity B). Val143 of human RNase H2 is located at the active site and is conserved in eukaryotic RNase H2. In this study, we explored the role of Val143 in catalytic activity and substrate specificity. Nineteen single variants at amino acid position 143 were expressed in E. coli, and all variants except for V143C and V143M were purified from the cells. When the activity of the wild-type human RNase H2 (WT) was set as 100%, the relative activities A and B of the 17 variants were in the range of 0.05–130 and 0.02–42%, respectively. When the ratio of the relative activity A to the relative activity B of WT was set as 1, the ratios of the 17 variants were in the range of 0.2–5.7. This indicates that valine is optimal for balancing the two activities. The ratios for V143Y and V143W were relatively high (5.6 and 5.5, respectively), suggesting that the bulky residues like tyrosine and tryptophan at position 143 caused steric hindrance with the 2’-OH of the sugar moiety of the ribonucleotide at the 5’ side of the scissile phosphodiester bond. The ratio for V143Q was relatively low (0.2). These results suggested that Val143 is not critical for, but plays a role in determining catalytic activity and substrate specificity.

Characterization of six recombinant human RNase H2 bearing Aicardi-Goutiéres syndrome causing mutations

Mammalian RNase H2 is a heterotrimeric enzyme consisting of one catalytic subunit (A) and two accessory subunits (B and C). RNase H2 is involved in the removal of a single ribonucleotide embedded in genomic DNA and removal of RNA of RNA/DNA hybrids. In humans, mutation of the RNase H2 gene causes a severe neuroinflammatory disorder Aicardi-Goutières syndrome (AGS). Here, we examined the activity and stability of six recombinant human RNase H2 variants bearing one AGS-causing mutation, A-G37S (Gly37 in the A subunit is replaced with Ser), A-N212I, A-R291H, B-A177T, B-V185G, or C-R69W. The activity of A-G37S was 0.3-1% of that of the wild-type RNase H2 (WT), while those of other five variants were 51-120%. In circular dichroism measurement, the melting temperatures of variants were 50-53°C, lower than that of WT (56°C). These results suggested that A-G37S had decreased activity and stability than WT, while other five variants had decreased stability but retained activity. In gel filtration chromatography of the purified enzyme preparation, WT migrated as a heterotrimer, while A-R291H eluted in two separate peaks containing either the heterotrimer or only the A subunit, suggesting that some AGS-causing mutations affect the heterotrimer-forming stability of RNase H2.

Interlaboratory Evaluation of Two Enzyme-Linked Immunosorbent Assay Kits for the Determination of Crustacean Protein in Processed Foods

The labeling of foods containing material derived from crustaceans such as shrimp and crab is to become mandatory in Japan because of increases in the number of allergy patients. To ensure proper labeling, 2 novel sandwich enzyme-linked immunosorbent assay (ELISA) kits for the determination of crustacean protein in processed foods, the N kit (Nissui Pharmaceutical Co., Ltd, Ibaraki, Japan) and the M kit (Maruha Nichiro Holdings, Inc., Ibaraki, Japan), have been developed. Five types of model processed foods containing 10 and/or 11.9 g/g crustacean soluble protein were prepared for interlaboratory evaluation of the performance of these kits. The N kit displayed a relatively high level of reproducibility relative standard deviation (interlaboratory precision; 4.08.4 RSDR) and sufficient recovery (6586) for all the model processed foods. The M kit displayed sufficient reproducibility (17.620.5 RSDR) and a reasonably high level of recovery (82103). The repeatability relative standard deviation (RSDr) values regarding the detection of crustacean proteins in the 5 model foods were mostly &lt;5.1 RSDr for the N kit and 9.9 RSDr for the M kit. In conclusion, the results of this interlaboratory evaluation suggest that both these ELISA kits would be very useful for detecting crustacean protein in processed foods.

Determination of Walnut Protein in Processed Foods by Enzyme-Linked Immunosorbent Assay: Interlaboratory Study

Because food allergens from tree nuts, including walnuts, are a frequent cause of adverse food reactions for allergic patients, the labeling of foods containing ingredients derived from tree nuts is required in numerous countries. According to Japanese regulations, the labeling of food products containing walnuts is recommended. To ensure proper labeling, a novel sandwich ELISA kit for the determination of walnut protein in processed foods (Walnut Protein [2S-Albumin] Kit; Morinaga Institute of Biological Science, Inc.; walnut kit) has been developed. We prepared seven types of incurred samples (model processed foods: biscuits, bread, sponge cake, orange juice, jelly, chicken meatballs, and rice gruel) containing 10 g walnut soluble protein/g of food for use in interlaboratory evaluations of the walnut kit. The walnut kit displayed sufficient reproducibility relative standard deviations (interlaboratory precision: 5.89.9 RSDR) and a high level of recovery (81119) for all the incurred samples. All the repeatability relative standard deviation (RSDr) values for the incurred samples that were examined were less than 6.0. The results of this interlaboratory evaluation suggested that the walnut kit could be used as a precise and reliable tool for determination of walnut protein in processed foods.

Enzyme-Linked Immunosorbent Assay Kit for the Determination of Soybean Protein in Processed Foods: Interlaboratory Evaluation

The labeling of foods containing ingredients derived from soybean is recommended in Japan because of an increasing number of patients who are allergic to soybeans. To ensure proper labeling, a novel sandwich ELISA kit for the determination of soybean protein in processed foods (FASTKIT Ver. II, Soybean, Nippon Meat Packers, Inc.; soy kit) has been developed. Five types of incurred samples (model processed foods: rice gruel, sausage, sweet adzuki bean soup, sweet potato cake, and tomato sauce) containing 10 g soybean soluble protein/g food were prepared for use in interlaboratory evaluations of the soy kit. The soy kit displayed a sufficient RSDR value (interlaboratory precision: 9.313.4 RSDR) and a high level of recovery (97114) for all the incurred samples. The RSDr value for the incurred samples was mostly &lt;4.8. The results of this interlaboratory evaluation suggest that the soy kit can be used as a precise and reliable tool for the determination of soybean proteins in processed foods.

P1828Aortic calcification detected by computed tomography and aortic vulnerable plaques: aortic angioscopy study

Background

Aortic calcification is associated with atherosclerotic risk factors and an increased risk of death and cardiovascular disease. However, the relationships aortic calcification and aortic plaque instability are not yet elucidated. Recently, some reports showed non-obstructive aortic angioscopy seemed to visualize atherosclerotic changes of aortic wall more clearly compared with computed tomography (CT). The purpose of this study was to evaluate whether aortic calcification is associated with aortic vulnerable plaques in patients with cardiovascular disease.

Methods

We investigated 60 consecutive patients with confirmed or suspected coronary artery disease who underwent both aortic angioscopy and CT. The AC volume (ACV) was measured using the volume-rendering method by extracting the area >130 HU within the whole aorta. ACV index (ACVI) was defined as ACV divided by the body surface area. We evaluated the number of ruptured plaque (RP), ulceration and fissure by aortic angioscopy in the whole aorta. We excluded 4 hemodialysis patients. All patients were divided into the median value of ACVI.

Results

The mean age of patients was 68±10. The median of ACVI was 10.7 ml/m2 [3.9–22.7]. High ACVI patients had significantly greater number of RP, ulceration and atheromatous plaques detected by aortic angioscopy compared with those of low ACVI (2.2±2.7 vs 0.8±1.1, p=0.033, 1.6±1.2 vs 0.9±1.0, p=0.041, 4.0±3.1 vs 1.9±1.8, p=0.009, respectively). Furthermore, the patients without aortic calcification did not have RP at all. In a multivariate model, the number of the atheromatous plaques was independently associated with high ACVI (odds ratio 1.57, 95% confidence interval 1.07–2.69, p=0.018)

Conclusions

Aortic calcification detected by CT was related to aortic vulnerable plaques in patients with cardiovascular disease.

6125High wall shear stress predicts plaque rupture of the aortic arch: computational fluid dynamics model and non-obstructive general angioscopy study

Background

Wall shear stress (WSS) has been considered as a major determinant of aortic atherosclerosis. Recently, non-obstructive general angioscopy (NOGA) was developed to be able to visualize a variety of its atherosclerotic pathology, including in vivo ruptured plaque (RP) in the aorta. We, therefore, investigated the relationship between NOGA derived RP in the aortic arch and the stereographic distribution of WSS by using computational fluid dynamics modeling (CFD) on three-dimensional CT angiography (3D-CT).

Methods

We investigated 30 consecutive patients who underwent 3D-CT before and NOGA during coronary angiography. WSS in the aortic arch was measured with an application of CFD based on finite element method by using uniform inlet and outlet flow conditions. Aortic RP was detected by NOGA.

Results

The maximum and mean values of WSS were 67.2±29.2 Pa and 2.4±0.6 Pa. A total of 18 RPs was detected by NOGA. The patients with a distinct RP showed a significantly higher maximum WSS in the whole aortic arch, and the greater and lesser curvature of the aortic arch than those without it (73.3±29.0 Pa vs 50.4±15.2 Pa, p=0.035, 95.0±27.5 Pa vs 42.8±25.2 Pa, p=0.003, 70.8±29.3 Pa vs 46.1±11.9 Pa, p=0.013, respectively), whereas there was no significant difference in the mean WSS between those with and without it. In a multivariate analysis, the maximum value of WSS was an independent predictor of RP in the aortic arch (odds ratio 1.05, 95% confidence interval 1.01–1.13, p=0.019).

Representative picture of WSS and NOGA

Conclusions

Aortic RP detected by NOGA was strongly associated with the higher maximum WSS in the aortic arch derived by CFD using 3D-CT. Maximum WSS may explain the underlying mechanism of not only aortic atherosclerosis, but also aortic RP.

P1831Prediction of cardiovascular events by atheromatous plaques detected by non-obstructive general angioscopy: two-year results of EAST-NOGA Registry

Background

Non-obstructive general angioscopy (NOGA) has revealed the intimal damages or atheromatous plaques as well as its spontaneous rupture of the aorta. Recent study revealed that plaque debris or different size of cholesterol crystals were detected in the blood above the spontaneous ruptured aortic plaque observed by NOGA and these plaque materials might cause the peripheral organ damages as the embolic source. These various morphological changes may cause the acute aortic events or atheroembolic events on the peripheral organs, such as brain, kidney, peripheral artery and so on.

Purpose

EAST-NOGA (Evaluation of AtheroSclerotic and rupture events by Non-Obstructive General Angioscopy) is a multi-center prospective observational study to assess the relationship between the findings of NOGA and future cardiovascular events.

Methods

Five hundred and seventy-seven patients with atherosclerotic cardiovascular disease who underwent NOGA study. The major cerebrocardiovascular events including cardiovascular death, non-fatal myocardial infarction, non-fatal cerebral infarction, and acute aortic syndrome were accumulated during the 2-year follow-up after NOGA study.

Results

The median number of aortic atheromatous plaques was 6 [IQR: 3–12]. A total of 514 patients were followed up (89.1%). The mean follow-up duration was 757±120 days. Major adverse cardiovascular events developed in 23 (4.5%) during 2 years follow-up. Patients with MACE and cerebral infarction, had significantly greater number of aortic atheromatous plaques (11 [5–19] vs. 6 [3–11], p<0.001, 12 [4–20] vs. 6 [3–12], p=0.014, respectively). In a univariate analysis, the number of aortic atheromatous plaques and ruptured plaque were significant predictors of MACE (HR: 1.09 95% confidence interval 1.05–1.14, p<0.001) and (HR: 1.12, 95% confidence interval 1.02–1.23, p=0.02). In a multivariate logistic analysis, the number of aortic atheromatous plaques is one of the independent predictors of MACE (HR 1.05, 95% confidence interval 1.00–1.10, p=0.032).

Conclusion

The number of atheromatous plaques identified by NOGA has a significant relation to the onset of cerebral infarction, which suggest the atheromatous plaque were vulnerable and ruptured spontaneously, then cause the aortogenic cerebral infarction. The NOGA study would be useful for predicting the futured atheroembolic events.

Acknowledgement/Funding

None

A Polymorphism rs6726395 in Nrf2 Contributes to the Development of Emphysema-Associated Age in Smokers Without COPD

INTRODUCTION

Several studies have reported that single nucleotide polymorphisms (SNPs) in the gene encoding NF-E2-related factor 2 (Nrf2) contribute to airflow limitations in smokers without COPD. Although small airway lesions and emphysema contribute cooperatively to airflow limitation, the relationship between Nrf2 SNPs and the development of emphysema in smokers without COPD is not well understood.

METHODS

Healthy subjects who underwent an annual health checkup with computed tomography (CT) of the chest at Osaka City University Hospital were prospectively recruited. The percentage of low-attenuation area (%LAA) on chest CT was quantified, and correlations between %LAA, Nrf2 SNP [rs6726395 (G/A)] genotypes, and clinical characteristics were examined.

RESULTS

A total of 245 subjects without COPD [non-/light-smoker: 153 (62.4%) and smoker: 92 (37.6%)] were enrolled. The %LAA in the upper lung field was higher than that in the lower lung field (p < 0.001). The %LAA in smokers was significantly higher than that in non-/light-smokers (p = 0.021). The %LAA showed significant but weak correlation with age in all subjects (r = 0.141, p = 0.028). Divided by genotype, the %LAA of the upper lung field was significantly correlated with age in smokers with genotype GG (wild type) (r = 0.333, p = 0.022), but was not significantly correlated with age in smokers with genotype AG/AA. These correlations were not observed in non-/light smokers.

CONCLUSION

A polymorphism rs6726395 in Nrf2 can contribute to the development of emphysema-associated aging in smokers. The Nrf2 SNP may be a predictive factor for smoking-induced emphysema, and genotyping of Nrf2 SNP may serve as biomarker for emphysema prevention.

Construction and characterization of ribonuclease H2 knockout NIH3T3 cells

Ribonuclease H (RNase H) specifically hydrolyzes the 5'-phosphodiester bonds of the RNA of RNA/DNA hybrid. Both types 1 and 2 RNases H act on the RNA strand of the hybrid, while only type 2 acts on the single ribonucleotide embedded in DNA duplex. In this study, to explore the role of mammalian type 2 RNase H (RNase H2) in cells, we constructed the RNase H2 knockout NIH3T3 cells (KO cells) by CRISPR/Cas9 system. KO cells hydrolyzed RNA strands in RNA/DNA hybrid, but not single ribonucleotides in DNA duplex, while wild-type NIH3T3 cells (WT cells) hydrolyzed both. Genomic DNA in the KO cells was more heavily hydrolyzed than in the WT cells by the alkaline or RNase H2 treatment, suggesting that the KO cells contained more ribonucleotides in genomic DNA than the WT cells. The growth rate of the KO cells was 60% of that of the WT cells. Expression of interferon-stimulated genes (ISGs) in the KO cells was not markedly elevated compared with the WT cells. These results suggest that in NIH3T3 cells, RNase H2 is crucial for suppressing the accumulation of ribonucleotides in genomic DNA but not for the expression of ISGs.

High sensitive RNA detection by one-step RT-PCR using the genetically engineered variant of DNA polymerase with reverse transcriptase activity from hyperthermophilies

One-step RT-PCR has not been widely used even though some thermostable DNA polymerases with reverse transcriptase (RT) activity were developed from bacterial and archaeal polymerases, which is owing to low cDNA synthesis activity from RNA. In the present study, we developed highly-sensitive one-step RT-PCR using the single variant of family A DNA polymerase with RT activity, K4pol_L329A (L329A), from the hyperthermophilic bacterium Thermotoga petrophila K4 or the 16-tuple variant of family B DNA polymerase with RT activity, RTX, from the hyperthermophilic archaeon Thermococcus kodakarensis. Optimization of reaction condition revealed that the activities for cDNA synthesis and PCR of K4pol_L329A and RTX were highly affected by the concentrations of MgCl₂ and Mn(OCOCH₃)₂ as well as those of K4pol_L329A or RTX. Under the optimized condition, 300 copies/μl of target RNA in 10 μl reaction volumes were successfully detected by the one-step RT-PCR with K4pol_L329A or RTX, which was almost equally sensitive enough compared with the current RT-PCR condition using retroviral RT and thermostable DNA polymerase. Considering that K4pol_L329A and RTX are stable even at 90-100°C, our results suggest that the one-step RT-PCR with K4pol_L329A or RTX is more advantageous than the current one.

RNA/DNA structures recognized by RNase H2

Ribonuclease H (RNase H) [EC 3.1.26.4] is an enzyme that specifically degrades RNA from RNA/DNA hybrids. Since its discovery in 1969, the enzyme has been extensively studied for its catalytic mechanism and physiological role. RNase H has been classified into two major families, Type 1 and Type 2. Type 1 enzymes are designated RNase HI in prokaryotes and RNase H1 in eukaryotes, while Type 2 enzymes are designated RNase HII in prokaryotes and RNase H2 in eukaryotes. Type 2 enzymes are able to cleave the 5′-phosphodiester bond of one ribonucleotide embedded in a DNA double strand. Recent studies have shown that RNase H2 is involved in excision of a single ribonucleotide embedded in genomic DNA and removal of an R-loop formed in cells. It is also involved in double-strand break of DNA and its repair. In this review, we aim to outline the structures recognized by RNase H2.