Plateau-linear reaction norm model analysis of number born alive in purebred Landrace pigs using meteorological data in Japan.

We performed a plateau-linear reaction norm model (RNM) analysis of number born alive (NBA) in purebred Landrace pigs, where breeding value changes according to maximum temperature at mating day, using public meteorological observation data in Japan. We analysed 52,668 NBA records obtained from 10,320 Landrace sows. Pedigree data contained 99,201 animals. Off-farm daily temperature data at the nearest weather station from each of the farms were downloaded from the Japan Meteorological Agency website. A plateau-linear RNM analysis based on daily maximum temperature on mating day (threshold temperature of 16.6°C) was performed. The percentage of the records with daily maximum temperatures at mating days of ≤16.6, ≥25.0, ≥30.0 and ≥35.0°C were 34.3%, 33.6%, 14.0% and 0.8%, respectively. The value of Akaike's information criterion for the plateau-linear RNM was lower than that for a simple repeatability model (RM). With the plateau-linear RNM, estimated value of heritability ranged from 0.14 to 0.15, while that from the RM analysis was 0.15. Additive genetic correlation between intercept and slope terms was estimated to be -0.52 from the plateau-linear RNM analysis. Estimated additive genetic correlations were >0.9 between NBA at different temperatures ranging from 16.6 to 37.6°C. For the 10,320 sows, average values of prediction reliability of the intercept and slope terms for breeding values in the plateau-linear RNM were 0.47 and 0.16, respectively. Increasing weight for slope term in linear selection index could bring positive genetic gain in the slope part, but prediction accuracy would decrease. Our results imply that genetically improving heat tolerance in sows reared in Japan focusing on NBA using RNM is possible, while RNM is more complex to implement and interpret. Therefore, further study should be encouraged to make genetic improvement for heat tolerance in sows more efficient.

Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle.

BACKGROUND: Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ([Formula: see text]) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text]), correlation between uniting gametes ([Formula: see text]), the observed vs expected number of homozygous genotypes ([Formula: see text]), runs of homozygosity (ROH) segments ([Formula: see text]) and heterozygosity by descent segments ([Formula: see text]). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle. RESULTS: The highest correlations with [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text], with range 0.33-0.55. Except for [Formula: see text] and [Formula: see text], there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text]. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for [Formula: see text]. CONCLUSIONS: Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text]. In particular, [Formula: see text] and [Formula: see text] can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.

Analysis of the trehalose synthesis pathway of Physarum polycehalum.

Desiccation is a severe survival problem for organisms. We have been studying the desiccation tolerance mechanisms in the true slime mold Physarum polycephalum. We measured the trehalose content of P. polycephalum vegetative cells (plasmodia) and drought cells (sclerotia). Surprisingly, we found that the content in sclerotia was about 473-fold greater than in the plasmodia. We then examined trehalose metabolism-related genes via RNAseq, and consequently found that trehalose 6-phosphate phosphorylase (T6pp) expression levels increased following desiccation. Next, we cloned and expressed the genes for T6pp, trehalose 6-phosphate synthase/phosphatase (Tps/Tpp), maltooligosyltrehalose trehalohydrolase (TreZ), and maltooligosyltrehalose synthase (TreY) in E. coli. Incidentally, TreY and TreZ clones have been reported in several prokaryotes, but not in eukaryotes. This report in P. polycephalum is the first evidence of their presence in a eukaryote species. Recombinant T6pp, TreY, and TreZ were purified and confirmed to be active. Our results showed that these enzymes catalyze reactions related to trehalose production, and their reaction kinetics follow the Michaelis-Menten equation. The t6pp mRNA levels of the sclerotia were about 15-fold higher than in the plasmodia. In contrast, the expression levels of TreZ and TreY showed no significant change between the sclerotia and plasmodia. Thus, T6pp is probably related to desiccation tolerance, whereas the contribution of TreY and TreZ is insufficient to account for the considerable accumulation of trehalose in sclerotia.

Risk factor structure of heart failure in patients with cancer after treatment with anticancer agents' assessment by big data from a Japanese electronic health record.

As the prognosis of cancer patients has been improved, comorbidity of heart failure (HF) in cancer survivors is a serious concern, especially in the aged population. This study aimed to examine the risk factors of HF development after treatment by anticancer agents, using a machine learning-based analysis of a massive dataset obtained from the electronic health record (EHR) in Japan. This retrospective, cohort study, using a dataset from 2008 to 2017 in the Diagnosis Procedure Combination (DPC) database in Japan, enrolled 140,327 patients. The structure of risk factors was determined using multivariable analysis and classification and regression tree (CART) algorithm for time-to-event data. The mean follow-up period was 1.55 years. The prevalence of HF after anticancer agent administration were 4.0%. HF was more prevalent in the older than the younger. As the presence of cardiovascular diseases and various risk factors predicted HF, CART analysis of the risk factors revealed that the risk factor structures complicatedly differed among different age groups. The highest risk combination was hypertension, diabetes mellitus, and atrial fibrillation in the group aged ≤ 64 years, and the presence of ischemic heart disease was a key in both groups aged 65-74 years and 75 ≤ years. The machine learning-based approach was able to develop complicated HF risk structures in cancer patients after anticancer agents in different age population, of which knowledge would be essential for realizing precision medicine to improve the prognosis of cancer patients.

Maternal effect on body measurement and meat production traits in purebred Duroc pigs.

We investigated maternal effect on nine body measurement traits (body height, body length, front width (FW), chest width (CW), hind width (HW), chest depth, chest girth (CHG), front cannon circumference (FCC) and rear cannon circumference (RCC)) measured at the end of performance testing and five meat production traits (ages at the start and end of performance testing (D30 and D105), average daily gain (ADG), backfat thickness and loin muscle area) in purebred Duroc pigs. Genetic parameters for each trait were estimated by using six single-trait models with and without common litter environmental effect, maternal genetic effect and direct-maternal genetic correlation. The value of Akaike's information criterion was lowest with the model including direct additive genetic and common litter environmental effects for 10 traits. The estimated proportion of common litter environmental variance to phenotypic variance was approximately ≥0.1 for D30, D105, ADG, FW, CW, HW, CHG, FCC and RCC. Using a model without common litter environmental effect would overestimate the direct heritability of most traits. Standard errors of estimated genetic parameters tended to be larger in models including maternal genetic effect. The results indicate that a compromise could be made for accurate genetic parameter estimation for body measurement traits, as well as meat production traits, in pigs by considering common litter environmental effect.

An ascovirus isolated from Spodoptera litura (Noctuidae: Lepidoptera) transmitted by the generalist endoparasitoid Meteorus pulchricornis (Braconidae: Hymenoptera).

The family Ascoviridae is a recently described virus family whose members are transmitted by parasitoids and cause chronic and lethal infections in lepidopteran insects. Little is known about the biology and ecology of ascoviruses, and few isolates have been found outside the United States. We report here the isolation of a new ascovirus variant from Spodoptera litura in Japan. Full genome sequence and phylogenetic analyses showed that this virus was closely related to variants in Heliothis virescens ascovirus-3a, and it was named HvAV-3j. HvAV-3j has a DNA genome of 191 718 bp, with 189 putative ORFs and a GC content of 45.6 %, and is highly similar to HvAV-3h, which was isolated in China. In a field survey, the endoparasitoid Meteorus pulchricornis caused a high percentage of parasitization in populations of S. litura larvae, and under laboratory conditions M. pulchricornis was able to transmit HvAV-3j from infected to uninfected larvae by oviposition. Meteorus pulchricornis is thus likely to be a major vector for HvAV-3j transmission in Japan. This species is recognized here for the first time as a vector of ascoviruses that parasitizes a range of host species that extends across families.

Sequencing of individual chromosomes of plant pathogenic Fusarium oxysporum.

A small chromosome in reference isolate 4287 of F. oxysporum f. sp. lycopersici (Fol) has been designated as a 'pathogenicity chromosome' because it carries several pathogenicity related genes such as the Secreted In Xylem (SIX) genes. Sequence assembly of small chromosomes in other isolates, based on a reference genome template, is difficult because of karyotype variation among isolates and a high number of sequences associated with transposable elements. These factors often result in misassembly of sequences, making it unclear whether other isolates possess the same pathogenicity chromosome harboring SIX genes as in the reference isolate. To overcome this difficulty, single chromosome sequencing after Contour-clamped Homogeneous Electric Field (CHEF) separation of chromosomes was performed, followed by de novo assembly of sequences. The assembled sequences of individual chromosomes were consistent with results of probing gels of CHEF separated chromosomes with SIX genes. Individual chromosome sequencing revealed that several SIX genes are located on a single small chromosome in two pathogenic forms of F. oxysporum, beyond the reference isolate 4287, and in the cabbage yellows fungus F. oxysporum f. sp. conglutinans. The particular combination of SIX genes on each small chromosome varied. Moreover, not all SIX genes were found on small chromosomes; depending on the isolate, some were on big chromosomes. This suggests that recombination of chromosomes and/or translocation of SIX genes may occur frequently. Our method improves sequence comparison of small chromosomes among isolates.

Comprehensive analysis of epigenetically regulated genes in anergic T cells.

T cell anergy is one of the important mechanisms for immune tolerance. The results of many studies investigating the mechanism for T cell anergy induction have revealed that the expression of several genes was up-regulated in anergic T cells. It has also been demonstrated that the molecules encoded on those genes played a critical role in anergy induction. However, the mechanism for their up-regulation has not previously been clarified. We examined in this study the changes in gene expression and DNA methylation status caused by anergy induction. Our results demonstrate that the expression of many genes was changed by anergy induction, and that the DNA methylation status of some of these genes was also changed. We show here by a GO analysis that the extent of the change in methylation status caused by anergy induction was distinct between the groups of genes that were categorized.

Double-stranded RNA-binding protein DRB3 negatively regulates anthocyanin biosynthesis by modulating PAP1 expression in Arabidopsis thaliana.

The model plant Arabidopsis thaliana has five double-stranded RNA-binding proteins (DRB1-DRB5), two of which, DRB1 and DRB4, are well characterized. In contrast, the functions of DRB2, DRB3 and DRB5 have yet to be elucidated. In this study, we tried to uncover their functions using drb mutants and DRB-over-expressed lines. In over-expressed lines of all five DRB genes, the over-expression of DRB2 or DRB3 (DRB2ox or DRB3ox) conferred a downward-curled leaf phenotype, but the expression profiles of ten small RNAs were similar to that of the wild-type (WT) plant. Phenotypes were examined in response to abiotic stresses. Both DRB2ox and DRB3ox plants exhibited salt-tolerance. When these plants were exposed to cold stress, drb2 and drb3 over-accumulated anthocyanin but DRB2ox and DRB3ox did not. Therefore, the over-expression of DRB2 or DRB3 had pleiotropic effects on host plants. Microarray and deep-sequencing analyses indicated that several genes encoding key enzymes for anthocyanin biosynthesis, including chalcone synthase (CHS), dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS), were down-regulated in DRB3ox plants. When DRB3ox was crossed with the pap1-D line, which is an activation-tagged transgenic line that over-expresses the key transcription factor PAP1 (Production of anthocyanin pigmentation1) for anthocyanin biosynthesis, over-expression of DRB3 suppressed the expression of PAP1, CHS, DFR and ANS genes. DRB3 negatively regulates anthocyanin biosynthesis by modulating the level of PAP1 transcript. Since two different small RNAs regulate PAP1 gene expression, a possible function of DRB3 for small RNA biogenesis is discussed.

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch).

BACKGROUND: Ornamental peaches cv. 'Yaguchi' (Prunus persica (L.) Batsch) can be propagated via seeds. The establishment of efficient seed treatments for early germination and seedling growth is required to shorten nursery and breeding periods. It is important, therefore, to identify potential candidate genes responsible for the effects of rinsing and chilling on seed germination. We hypothesized that longer rinsing combined with chilling of seeds can alter the genes expression in related to dormancy and then raise the germination rate in the peach. To date, most molecular studies in peaches have involved structural genomics, and few transcriptome studies of seed germination have been conducted. In this study, we investigated the function of key seed dormancy-related genes using next-generation sequencing to profile the transcriptomes involved in seed dormancy in peaches. De novo assembly and analysis of the transcriptome identified differentially expressed and unique genes present in this fruit. RESULTS: De novo RNA-sequencing of peach was performed using the Illumina Miseq 2000 system. Paired-end sequence from mRNAs generated high quality sequence reads (9,049,964, 10,026,362 and 10,101,918 reads) from 'Yaguchi' peach seeds before rinsed (BR) and after rinsed for 2 or 7 days with a chilling period of 4 weeks (termed 2D4W and 7D4W), respectively. The germination rate of 7D4W was significantly higher than that of 2D4W. In total, we obtained 51,366 unique sequences. Differential expression analysis identified 7752, 8469 and 506 differentially expressed genes from BR vs 2D4W, BR vs 7D4W and 2D4W vs 7D4W libraries respectively, filtered based on p-value and an adjusted false discovery rate of less than 0.05. This study identified genes associated with the rinsing and chilling process that included those associated with phytohormones, the stress response and transcription factors. 7D4W treatment downregulated genes involved in ABA synthesis, catabolism and signaling pathways, which eventually suppressed abscisic acid activity and consequently promoted germination and seedling growth. Stress response genes were also downregulated by the 7D4W treatment, suggesting that this treatment released seeds from endodormancy. Transcription factors were upregulated by the BR and 2D4W treatment, suggesting that they play important roles in maintaining seed dormancy. CONCLUSIONS: This work indicated that longer rinsing combined with chilling affects gene expression and germination rate, and identified potential candidate genes responsible for dormancy progression in seeds of 'Yaguchi' peach. The results could be used to develop breeding programs and will aid future functional genomic research in peaches and other fruit trees.

Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes.

BACKGROUND: For plant species with unsequenced genomes, cDNA contigs created by de novo assembly of RNA-Seq reads are used as reference sequences for comparative analysis of RNA-Seq datasets and the detection of differentially expressed genes (DEGs). Redundancies in such contigs are evident in previous RNA-Seq studies, and such redundancies can lead to difficulties in subsequent analysis. Nevertheless, the effects of removing redundancy from contig assemblies on comparative RNA-Seq analysis have not been evaluated. RESULTS: Here we describe a method for removing redundancy from raw contigs that were primarily created by de novo assembly of Arabidopsis thaliana RNA-Seq reads. Specifically, the contigs with the highest bit scores were selected from raw contigs by a homology search against the gene dataset in the TAIR10 database. The two existing methods for removal of redundancy based on contig length or clustering analysis used to eliminate redundancies from raw contigs. Contig number was reduced most effectively with the method based on homology search. In a comparative analysis of RNA-Seq datasets, DEGs detected in contigs that underwent redundancy removal via the homology search method showed the highest identity to the DEGs detected when the TAIR10 gene dataset was used as an exact reference. Redundancy in raw contigs could also be removed by a homology search against integrated protein datasets from several plant species other than A. thaliana. DEGs detected using contigs that underwent such redundancy-removed also showed high homology to DEGs detected using the TAIR10 gene dataset. CONCLUSION: Here we describe a method for removing redundant contigs within raw contigs; this method involves a homology search against a gene or protein database. In principal, this method can be used with unsequenced plant genomes that lack a well-developed gene database. Redundant contigs were not removed adequately via either of two existing methods, but our method allowed for removal of all redundant contigs. To our knowledge, this is the first reported improvement in accurate detection of DEGs via comparative RNA-Seq analysis that involved preparation of a non-redundant reference sequence. This method could be used to rapidly and cost-effectively detect useful genes in unsequenced plants.

Isolation of an Adoxophyes orana granulovirus (AdorGV) occlusion body morphology mutant: biological activity, genome sequence and relationship to other isolates of AdorGV.

A granulovirus (GV) producing occlusion bodies (OBs) with an unusual appearance was isolated from Adoxophyes spp. larvae in the field. Ultrastructural observations revealed that its OBs were significantly larger and cuboidal in shape, rather than the standard ovo-cylindrical shape typical of GVs. N-terminal amino acid sequence analysis of the OB matrix protein from this virus suggested that this new isolate was a variant of Adoxophyes orana granulovirus (AdorGV). Bioassays of this GV (termed AdorGV-M) and an English isolate of AdorGV (termed AdorGV-E) indicated that the two isolates were equally pathogenic against larvae of Adoxophyes honmai. However, AdorGV-M retained more infectivity towards larvae after irradiation with UV light than did AdorGV-E. Sequencing and analysis of the AdorGV-M genome revealed little sequence divergence between this isolate and AdorGV-E. Comparison of selected genes among the two AdorGV isolates and other Japanese AdorGV isolates revealed differences that may account for the unusual OB morphology of AdorGV-M.

The bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice.

Plants are constantly exposed to threats from pathogenic microbes and thus developed an innate immune system to protect themselves. On the other hand, many plants also have the ability to establish endosymbiosis with beneficial microbes such as arbuscular mycorrhizal (AM) fungi or rhizobial bacteria, which improves the growth of host plants. How plants evolved these systems managing such opposite plant-microbe interactions is unclear. We show here that knockout (KO) mutants of OsCERK1, a rice receptor kinase essential for chitin signaling, were impaired not only for chitin-triggered defense responses but also for AM symbiosis, indicating the bifunctionality of OsCERK1 in defense and symbiosis. On the other hand, a KO mutant of OsCEBiP, which forms a receptor complex with OsCERK1 and is essential for chitin-triggered immunity, established mycorrhizal symbiosis normally. Therefore, OsCERK1 but not chitin-triggered immunity is required for AM symbiosis. Furthermore, experiments with chimeric receptors showed that the kinase domains of OsCERK1 and homologs from non-leguminous, mycorrhizal plants could trigger nodulation signaling in legume-rhizobium interactions as the kinase domain of Nod factor receptor1 (NFR1), which is essential for triggering the nodulation program in leguminous plants, did. Because leguminous plants are believed to have developed the rhizobial symbiosis on the basis of AM symbiosis, our results suggest that the symbiotic function of ancestral CERK1 in AM symbiosis enabled the molecular evolution to leguminous NFR1 and resulted in the establishment of legume-rhizobia symbiosis. These results also suggest that OsCERK1 and homologs serve as a molecular switch that activates defense or symbiotic responses depending on the infecting microbes.

Evaluation of genomic prediction considering non-additive genetic effects on fatty acid traits of Japanese Black cattle.

Genomic prediction was conducted using 2494 Japanese Black cattle from Hiroshima Prefecture and both single-nucleotide polymorphism information and phenotype data on monounsaturated fatty acid (MUFA) and oleic acid (C18:1) analyzed with gas chromatography. We compared the prediction accuracy for four models (A, additive genetic effects; AD, as for A with dominance genetic effects; ADR, as for AD with the runs of homozygosity (ROH) effects calculated by ROH-based relationship matrix; and ADF, as for AD with the ROH-based inbreeding coefficient of the linear regression). Bayesian methods were used to estimate variance components. The narrow-sense heritability estimates for MUFA and C18:1 were 0.52-0.53 and 0.57, respectively; the corresponding proportions of dominance genetic variance were 0.04-0.07 and 0.04-0.05, and the proportion of ROH variance was 0.02. The deviance information criterion values showed slight differences among the models, and the models provided similar prediction accuracy.

Reaction-norm animal model analysis of average daily gain heat tolerance in purebred Duroc pigs.

The present study aimed to genetically improve growth performance under high-heat environments by specifically designing a reaction-norm animal model (RNAM) for purebred Duroc pigs in Japan. A total of 54,750 records of average daily gain (ADG) measured for pigs reared at four farms in different prefectures were analyzed. Estimated maximum daily temperatures at the respective farm locations were used to calculate the average cumulative thermal load (TL). The TL values served as an indicator of high-heat environments for pigs. The plausible cumulative period length and threshold temperature for calculating TL were determined to be 8 weeks until just before shipping and 25°C, respectively. Variance components were estimated via RNAM analysis using TL as a linear covariate. The estimated additive genetic variances under both responsive and non-responsive to TL were found to be significant. Moreover, the estimated heritability of ADG ranged from 0.38 to 0.73 for TL values of 0-8. These results suggest that the RNAM developed holds the potential for improving the genetic ability of growth under high-heat environments in pigs.

Intraindividual and interindividual variabilities in endogenous cortisol 6ß-hydroxylation clearance as an index for in vivo CYP3A phenotyping in humans.

This study was designed to evaluate the in vivo activity of cytochrome P450 3A (CYP3A) in 49 healthy Japanese subjects aged 22-58 years using endogenous cortisol 6ß-hydroxylation clearance [CLm(6ß)], a novel biomarker for CYP3A phenotyping. CLm(6ß) in the 49 healthy subjects was 2.40 ± 0.79 ml/min with an approximately 4-fold interindividual variability of CYP3A activity. The mean clearance in the 24 women was 2.50 ± 0.89 ml/min; the value in the women was higher than in the 25 men (2.30 ± 0.69 ml/min) by approximately 9%. We also measured the change of CLm(6ß) in 14 healthy subjects in the morning at 10:00-12:00 every 2 or 3 days over a period of 36-53 days and observed a 1.5-fold to 3.4-fold day-to-day intraindividual variability in the CYP3A activity. The mean value for CLm(6ß) in each subject for 36-53 days was 2.54 ± 0.76 ml/min (n = 14). We also evaluated the CLm(6ß) every 2 hours from 8:00-20:00 in 26 healthy subjects. The within-day intraindividual clearance variability was 1.1-fold to 2.5-fold (2.45 ± 0.91 ml/min, n = 26). No characteristic diurnal rhythms were observed in the in vivo activity of CYP3A.

Gut microbiota of Parkinson's disease in an appendectomy cohort: a preliminary study.

In patients with Parkinson's disease (PD), α-synuclein pathology is thought to spread to the brain via the dorsal motor nucleus of the vagus nerve. The link between the gut microbiome and PD has been explored in various studies. The appendix might play an important role in immunity by maintaining the microbiota as a reservoir. In recent times, appendectomy has been linked to a lower risk of PD, possibly owing to the role of the appendix in altering the gut microbiome. We aimed to elucidate whether the gut microbiota affects PD development in the appendectomy cohort. We analyzed the fecal microbial composition in patients with PD and healthy controls with and without a history of appendectomy. The abundance of microbes from the family Enterobacteriaceae was higher in feces samples from patients with Parkinson's disease compared to that in samples collected from healthy controls. Furthermore, there was a significant phylogenetic difference between patients with PD and healthy controls who had undergone appendectomy. There was a significant phylogenetic difference between patients with PD and HCs who had undergone APP. These results suggest the correlation between gut microbiota and PD in patients who have undergone APP.

Annual Increase of Acute Inpatients with Both Cancer and Cardiovascular Diseases in Japan 2011-2015: Analysis From National Database of Health Insurance Claims and Specific Health Checkups of Japan.

BACKGROUND: Patients with cancer were able to live longer due to improvements in cancer treatment. Additionally, cardiovascular disease (CVD) is the second leading cause of mortality in cancer survivors. However, epidemiological data on onco-CVD have not been sufficiently provided. We aimed to investigate the clinical characteristics of cancer in CVD patients using the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB). METHOD AND RESULTS: The NDB sampling dataset used in this study was randomly sampled 10% from the whole Diagnosis Procedure Combination (DPC) records from every January, April, July, and October from 2011 to 2015. The significance of the increase trend in the percentage of records in each disease group to the total number of all DPC records from 2011 to 2015 was checked with Chi-square test with a Bonferroni correction. The percentage of records in cancer with the CVD group to the total number of all DPC records significantly increased over time, and their average age also increased since 2011. Their proportion over 75 years was approximately 56 % in 2015. There was no difference in the cancer sites. However, the prevalence of heart failure dramatically elevated. CONCLUSION: We were able to assess the increase in cancer among CVD patients using DPC inpatient records obtained from the NDB. Both cardiologists and oncologists should be more aware of this phenomenon.

Evaluating the performance of genomic prediction accounting for effects of single nucleotide polymorphism markers in reproductive traits of Japanese Black cattle.

We examined the prediction accuracies of genomic best linear unbiased prediction (GBLUP), various weighted GBLUP according to the degrees of marker effects (WGBLUP) and machine learning (ML) methods, and compared them with traditional BLUP for age at first calving (AFC), calving difficulty (CD), and gestation length in Japanese Black cattle. For WGBLUP, firstly, BayesC and FarmCPU were used to estimate marker effects. Then, we constructed three weighted genomic relationship matrices from information of estimated marker effects in the first step: absolute value of the estimated marker-effect WGBLUP, estimated marker-variance WGBLUP, and genomic-feature WGBLUP. For ML, we applied Gaussian kernel, random forest, extreme gradient boost, and support vector regression. We collected a total of 2583 animals having both phenotypic records and genotypes with 30,105 markers and 16,406 pedigree records. For AFC, prediction accuracies of WGBLUP methods using FarmCPU exceeded BLUP by 25.7%-39.5%. For CD, estimated marker-variance WGBLUP using BayesC achieved the highest prediction accuracy. Among ML methods, extreme gradient boost, support vector regression, and Gaussian kernel increased prediction accuracies by 28.4%, 19.0%, and 36.4% for AFC, CD, and gestation length compared with BLUP, respectively. Thus, prediction performance could be improved using suitable WGBLUP and ML methods according to target reproductive traits for the population used.

Combined actions of bacteriophage-encoded genes in Wolbachia-induced male lethality.

Some Wolbachia endosymbionts induce male killing, whereby male offspring of infected females are killed during development; however, the origin and diversity of the underlying mechanisms remain unclear. In this study, we identified a 76 kbp prophage region specific to male-killing Wolbachia hosted by the moth Homona magnanima. The prophage encoded a homolog of the male-killing gene oscar in Ostrinia moths and the wmk gene that induces various toxicities in Drosophila melanogaster. Upon overexpressing these genes in D. melanogaster, wmk-1 and wmk-3 killed all males and most females, whereas Hm-oscar, wmk-2, and wmk-4 had no impact on insect survival. Strikingly, co-expression of tandemly arrayed wmk-3 and wmk-4 killed 90% of males and restored 70% of females, suggesting their conjugated functions for male-specific lethality. While the male-killing gene in the native host remains unknown, our findings highlight the role of bacteriophages in male-killing evolution and differences in male-killing mechanisms among insects.