Multicomponent supramolecular hydrogels are constructed for sensitive, naked-eye detection of small-molecule biomarkers. A dendritic self-immolative molecule and the corresponding enzyme as a signal ...amplification system were stably embedded in a hydrogen peroxide (H2O2)-responsive supramolecular hydrogel (BPmoc-F 3 ), together with other enzymes. The nanostructure and mechanical strength of the hybrid BPmoc-F 3 gel were not substantially diminished by incorporation of these multiple components in the absence of target biomarkers, but could be destroyed by addition of the biomarker through the multiple enzymatic and chemical cascade reactions operating in combination within the gel matrix. The sensitivity to biomarkers such as H2O2, glucose, and uric acid, detected by gel–sol transition, was significantly enhanced by the signal amplification system. An array chip consisting of these multicomponent hydrogels enabled the detection of the level of hyperuricemia disease in human plasma samples.
Soft materials that exhibit stimuli-responsive behaviour under aqueous conditions (such as supramolecular hydrogels composed of self-assembled nanofibres) have many potential biological applications. ...However, designing a macroscopic response to structurally complex biochemical stimuli in these materials still remains a challenge. Here we show that redox-responsive peptide-based hydrogels have the ability to encapsulate enzymes and still retain their activities. Moreover, cooperative coupling of enzymatic reactions with the gel response enables us to construct unique stimuli-responsive soft materials capable of sensing a variety of disease-related biomarkers. The programmable gel-sol response (even to biological samples) is visible to the naked eye. Furthermore, we built Boolean logic gates (OR and AND) into the hydrogel-enzyme hybrid materials, which were able to sense simultaneously plural specific biochemicals and execute a controlled drug release in accordance with the logic operation. The intelligent soft materials that we have developed may prove valuable in future medical diagnostics or treatments.
The JRA-25 Reanalysis ONOGI, Kazutoshi; TSUTSUI, Junichi; KOIDE, Hiroshi ...
Journal of the Meteorological Society of Japan,
06/2007, Volume:
85, Issue:
3
Journal Article
Peer reviewed
Open access
A long-term global atmospheric reanalysis, named “Japanese 25-year Reanalysis (JRA-25)” was completed using the Japan Meteorological Agency (JMA) numerical assimilation and forecast system. The ...analysis covers the period from 1979 to 2004. This is the first long-term reanalysis undertaken in Asia. JMA's latest numerical assimilation system, and specially collected observational data, were used to generate a consistent and high-quality reanalysis dataset designed for climate research and operational monitoring and forecasts. One of the many purposes of JRA-25 is to enhance the analysis to a high quality in the Asian region. Six-hourly data assimilation cycles were performed, producing 6-hourly atmospheric analysis and forecast fields of various physical variables. The global model used in JRA-25 has a spectral resolution of T106 (equivalent to a horizontal grid size of around 120 km) and 40 vertical layers with the top level at 0.4 hPa. In addition to conventional surface and upper air observations, atmospheric motion vector (AMV) wind retrieved from geostationary satellites, brightness temperature from TIROS Operational Vertical Sounder (TOVS), precipitable water retrieved from orbital satellite microwave radiometer radiance and other satellite data are assimilated with three-dimensional variational method (3D-Var). JMA produced daily sea surface temperature (SST), sea ice and three-dimensional ozone profiles for JRA-25. A new quality control method for TOVS data was developed and applied in advance. Many advantages have been found in the JRA-25 reanalysis. Predicted 6-hour global total precipitation distribution and amount are well reproduced both in space and time. The performance of the long time series of the global precipitation is the best among the other reanalyses, with few unrealistic variations from degraded satellite data contaminated by volcanic eruptions. Secondly, JRA-25 is the first reanalysis to assimilate wind profiles around tropical cyclones reconstructed from historical best track information; tropical cyclones were analyzed properly in all the global regions. Additionally, low-level cloud along the subtropical western coast of continents is well simulated and snow depth analysis is also of a good quality. The article also covers material which requires attention when using JRA-25.
Biochemical diversity of venom extracts often occurs within a small number of shared protein families. Developing a sequestrant capable of broad-spectrum neutralization across various protein ...isoforms within these protein families is a necessary step in creating broad-spectrum antivenom. Using directed synthetic evolution to optimize a nanoparticle (NP) formulation capable of sequestering and neutralizing venomous phospholipase A2 (PLA2), we demonstrate that broad-spectrum neutralization and sequestration of venomous biomacromolecules is possible via a single optimized NP formulation. Furthermore, this optimized NP showed selectivity for venomous PLA2 over abundant serum proteins, was not cytotoxic, and showed substantially long dissociation rates from PLA2. These findings suggest that it may show efficacy as an in vivo venom sequestrant and may serve as a generalized lipid-mediated toxin sequestrant.
The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently ...complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering-time plasticity in a genetic mapping population grown in natural long-day field environments. Genetic loci harboring four genes originally discovered for their photoperiodic effects (
,
,
, and
) were found to differentially respond to temperature at the early growth stage to jointly determine flowering time. The effects of these plasticity genes were revealed with multiple reaction norms along the temperature gradient. By coupling genomic selection and the environmental index, accurate performance predictions were obtained. Next, we examined the allelic variation in the four flowering-time genes across the diverse accessions from the 3000 Rice Genomes Project and constructed haplotypes at both individual-gene and multigene levels. The geographic distribution of haplotypes revealed their preferential adaptation to different temperature zones. Regions with lower temperatures were dominated by haplotypes sensitive to temperature changes, whereas the equatorial region had a majority of haplotypes that are less responsive to temperature. By integrating knowledge from genomics, gene cloning and functional characterization, and environment quantification, we propose a conceptual model with multiple levels of reaction norms to help bridge the gaps among individual gene discovery, field-level phenotypic plasticity, and genomic diversity and adaptation.
Abstract
Summary
Supervised learning is widely used in biology for prediction, and ensemble learning, including stacking, is a promising technique for increasing and stabilizing the prediction ...accuracy. In this study, we developed an R package for stacking. This package depends on the R package caret and can handle models supported by caret. Stacking involves cross-validation of training data with multiple base learners, and the predicted values are used as explanatory variables for the meta-learner. In the prediction, the testing data were fed into the base models, and the returned values were averaged for each base learner. The averaged values were then fed into the meta-model, and the final predictions were returned. Using this package, the training and prediction procedures for stacking can be conducted using one-row scripts.
Availability and implementation
The R package stacking is available at the Comprehensive R Archive Network (CRAN) (https://cran.r-project.org/) and GitHub (https://github.com/Onogi/stacking). R scripts to reproduce the presented results are also reposited at GitHub.
BK polyomavirus (BKPyV) was the first human polyomavirus to be isolated from an immunosuppressed kidney transplant recipient in 1971. BKPyV reactivation causes BKPyV‐associated nephropathy and ...hemorrhagic cystitis. However, the mechanisms underlying BKPyV replication remain unclear. In the present study, we performed the long‐term cultivation of COS‐7 cells transfected with archetype KOM‐5 DNA, which were designated as COS‐BK cells. BKPyV derived from COS‐BK cells was characterized by analyzing the amount of the virus based on hemagglutination, viral replication, and the production of viral protein 1 (VP1). Immunostaining showed that VP1‐positive cells accounted for a small percentage of COS‐BK cells. The nucleotide sequences encompassing the origin of the DNA replication of BKPyV derived from COS‐BK cells were generated from KOM‐5 by the deletion of an 8‐bp sequence, which did not involve T antigen binding sites. BKPyV replicated most efficiently in COS‐BK cells in DMEM containing 2% fetal bovine serum. These results indicate that COS‐BK cells are a suitable culture system for studying the persistent infection of archetype BKPyV.
Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of ...non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6-19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.
Abstract Study question Does fatty acid (FA) supplementation into warming solutions influence maternal and obstetric outcomes after single vitrified-warmed cleavage stage embryo transfer (SVCT)? ...Summary answer FA-supplemented warming solutions improve the live birth rate after SVCTs without exerting any adverse effects on maternal and obstetric outcomes. What is known already Vitrification procedures decrease the intracellular lipid content and impair developmental competence. Adding fatty acids (FAs) to the warming solution has been shown to recover the lipid content of the cytoplasm and improve developmental competence and clinical pregnancy by stimulating the beta-oxidation pathway in warmed embryos. Recently, the FA-supplemented warming solutions have been commercially released. However, influence of the FA-supplemented supplementation on live birth rate after embryo transfers and perinatal outcomes remains unknown. Study design, size, duration The clinical records of 701 treatment cycles in 701 women who underwent SVCTs were retrospectively analysed. Vitrified embryos were warmed using solutions (from April 2022 to June 2022, control group, n = 340) or FA-supplemented solutions (from July 2022 to September 2022, FA group, n = 361). All pregnant women were invited to respond to the questionnaire at 9 weeks of gestation and after delivery. Maternal and obstetric outcomes were obtained from a self-reported questionnaire completed by the patients. Participants/materials, setting, methods The embryos in the FA group were warmed with the FA-supplemented solutions (VT526, Kitazato Corporation) while the embryos in the control group were warmed with the non-supplemented solutions (VT506, Kitazato Corporation). SVCTs were performed on day 2 after ovulation in natural cycles. The live birth rate, incidence of pregnancy complications, and neonatal outcomes were compared between the control and FA groups. Main results and the role of chance The live birth rate was higher in the FA group than in the control group (P = 0.0399). The miscarriage rates were comparable between the groups. Multivariate logistic regression analysis also demonstrated a higher probability of live births in the FA group than in the control group (adjusted odds ratio, 1.46; P = 0.0404). Patients were stratified by median maternal age for further analysis (37 years). This subgroup analysis showed that the live birth rate was significantly higher in the FA group than in the control group in women younger than 37 years of age. However, the live birth rate was comparable between the two groups for women aged 37 years or older. The incidence and types of pregnancy complications were comparable between the control and FA groups. Furthermore, caesarean section rates were similar between the groups. The average gestational age and incidence of preterm delivery were comparable between the groups. Birth length and weight, incidence of low birth weight, incidence of small for gestational age and large for gestational age, and infant sex were comparable between the groups. The incidence of birth defects was similar between the groups. Multivariate logistic regression analysis revealed a similar trend. Limitations, reasons for caution The single-centre retrospective study limits the strength of the study, necessitating further multicentre studies to ascertain the generalizability of these findings to other clinics with different protocols and/or patient demographics. Furthermore, the number of perinatal cycles was low. Wider implications of the findings The FA-supplemented warming solutions improved the live birth rates after SVCTs, particularly in young patients. Furthermore, the incidence of pregnancy complications and infant health was not affected by the FA-supplemented solutions. Therefore, FA-supplemented solutions can be considered safe and effective at improving clinical outcomes and reducing the patient burden. Trial registration number not applicable
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