Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis

Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs

Optical cavity with a double-layered cholesteric liquid crystal mirror and its prospective application to solid state laser

The authors have fabricated an optical cavity with silver (Ag) and double-layered cholesteric liquid crystal (CLC) mirrors facing each other. This CLC mirror consists of left-handed CLC and right-handed CLC films for high light reflection irrespective of polarization states. A single-mode lasing was observed in dye-doped CLC sandwiched between Ag and double-layered CLC mirrors. The authors also fabricated a flexible solid state device with a spin-coated dye molecular film sandwiched between Ag and double-layered CLC mirrors. Amplified spontaneous emission was observed from the solid state device, suggesting a possible structure for a flexible and tunable solid state laser.open

Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis

Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs

Development of a cadmium telluride pixel detector for astrophysical applications

We are developing imaging Cadmium Telluride (CdTe) pixel detectors optimized for astrophysical hard X-ray applications. Our hybrid detector consist of a CdTe crystal 1mm thick and 2cm × 2cm in area with segmented anode contacts directly bonded to a custom low-noise application specific integrated circuit (ASIC). The CdTe sensor, fabricated by ACRORAD (Okinawa, Japan), has Schottky blocking contacts on a 605 micron pitch in a 32 × 32 array, providing low leakage current and enabling readout of the anode side. The detector is bonded using epoxy-gold stud interconnects to a custom low noise, low power ASIC circuit developed by Caltech's Space Radiation Laboratory. We have achieved very good energy resolution over a wide energy range (0.62keV FWHM @ 60keV, 10.8keV FWHM @ 662keV). We observe polarization effects at room temperature, but they are suppressed if we operate the detector at or below 0°C degree. These detectors have potential application for future missions such as the International X-ray Observatory (IXO)

Friend of Prmt1, FOP is a novel component of the nuclear SMN complex isolated using biotin affinity purification

SMN (survival motor neuron protein) complexes are essential for the biogenesis of uridine-rich small nuclear ribonucleoproteins (UsnRNPs). During the biogenesis, the SMN complexes bound to UsnRNPs are transported from the cytoplasm to the nucleus, and moved to Cajal body (bodies)/Gems (Cajal/Gems) where the SMN complexes- UsnRNPs are subjected to additional chemical modifications and dissociated to the SMN complexes and the mature UsnRNPs. Although the mature UsnRNPs are assembled into spliceosome with newly transcribed pre-mRNA in the perichromatin fibrils at the chromatin, the role of the dissociated nuclear SMN complexes remains undetermined. In this study, we identified Friend of Prmt1 (FOP; chromatin target of Prmt1, CHTOP; C1orf77) as a novel component of the nuclear SMN complexes by the biotin affinity purification, coupled with the mass spectrometry-based protein identification. FOP was associated with SMN, Gemines 2, 3, 4, 6, and 8, unrip, and fragile X mental retardation 1 protein (FMR1), as well as with U5and U6 snRNAs in the nucleus, but not with Sm proteins, Gemin5, coilin, and U1 and U2snRNAs. Using the quantitative proteomic method with SILAC coupled with RNA interference, we also showed that FOP is required for the association of the SMN complexes with hnRNPs, histone proteins, and various RNA-binding proteins. It is reported that FOP localizes mainly in the nuclear speckles, binds chromatin, and plays a role in mRNA transcriptional regulation. Our present data suggest that the nuclear SMN complex containing FOP participates in the process of mRNA post-transcriptional regulation

Factors associated with kindergarten teachers’ willingness to continue working

The turnover rate among kindergarten teachers in advanced countries is extremely high. As such, there is an urgent need to determine the reasons for this turnover and to identify ways to prevent it. The current study investigates the individual and environmental factors that impact kindergarten teachers’ willingness to continue working.A total of 600 kindergarten teachers in Japan participated in this study. Participants responded to questionnaires regarding their willingness to continue working, mental health, work engagement, and the availability of social support. Multiple logistic regression analysis was used to analyze participants’ data, with willingness to continue working for 5 or more years as the dependent variable. Additionally, Spearman rank correlation was used to examine the correlations between factors associated with willingness to continue working.Factors such as older age, living with a spouse, caring for younger children (up to 2 years old) at work, good mental health, and higher work engagement were significantly associated with teachers’ higher willingness to continue working. Factors such as marriage, health and family problems, overtime work, issues with workplace childcare, and education policy, working time/day problems, human relations, and difficulties taking care of children were correlated with teachers’ lack of willingness to continue working.The findings of this cross-sectional study suggest that welfare benefits and individual support systems could be key elements to encourage kindergarten teachers to continue working and could lead to their improved job satisfaction and mental health. Balanced work conditions and workers’ high agreement with their workplace\u27s overall childcare or educational policies may lead to lower turnover. Some programs – such as relationship counselling – could have a positive impact on teachers’ mental health and job satisfaction

Significant impact of biochemical recurrence on overall mortality in patients with high-risk prostate cancer after carbon-ion radiotherapy combined with androgen deprivation therapy

BACKGROUNDWhether biochemical recurrence (BR) is a significant predictive factor of mortality after definitive radiation therapy for prostate cancer remains unknown. The aim of the current study was to investigate the relation between BR and overall mortality (OAM) in high-risk prostate cancer patients who were treated with carbon-ion radiotherapy (CIRT) and had long-term follow-up in 2 prospective trials.METHODSIn the 2 phase 2 clinical trials, which involved 466 prostate cancer patients who received 63.0 to 66.0 Gy of CIRT (relative biological effect) in 20 fractions between 2000 and 2007, 324 patients who were deemed to be at high risk on the basis of the modified D\u27Amico classification criteria and received CIRT along with androgen-deprivation therapy (ADT) were examined. The OAM rate was adjusted for the ADT duration, and multivariate analyses using a Cox proportional hazards model were performed for OAM with BR as a time-dependent covariate.RESULTSThe median follow-up period was 107.4 months, and the 5- and 10-year OAM rates after adjustments for the ADT duration were 7.0% (95% confidence interval [CI], 4.0%-9.4%) and 23.9% (95% CI, 16.4%-26.2%), respectively. A multivariate analysis revealed that the presence of BR (hazard ratio, 2.82; 95% Cl, 1.57-5.08; P = .001) was one of the predictive factors for OAM. On the other hand, the duration of ADT had no impact on OAM.CONCLUSIONSBR after CIRT combined with ADT is an independent predictive factor for OAM in high-risk prostate cancer patients. The results of this study could be applied to other high-dose radiation therapies

Sex-inducing effects toward planarians widely present among parasitic flatworms

Summary Various parasitic flatworms infect vertebrates for sexual reproduction, often causing devastating diseases in their hosts. Consequently, flatworms are of great socioeconomic and biomedical importance. Although the cessation of parasitic flatworm sexual reproduction is a major target of anti-parasitic drug design, little is known regarding bioactive compounds controlling flatworm sexual maturation. Using the planarian Dugesia ryukyuensis, we observed that sex-inducing substances found in planarians are also widespread in parasitic flatworms, such as monogeneans and flukes (but not in tapeworms). Reverse-phase HPLC analysis revealed the sex-inducing substance(s) eluting around the tryptophan retention time in the fluke Calicophoron calicophorum, consistent with previous studies on the planarian Bipalium nobile, suggesting that the substance(s) is likely conserved among flatworms. Moreover, six of the 18 ovary-inducing substances identified via transcriptome and metabolome analyses are involved in purine metabolism. Our findings provide a basis for understanding and modifying the life cycles of various parasitic flatworms.journal articl

Development of a cadmium telluride pixel detector for astrophysical applications

We are developing imaging Cadmium Telluride (CdTe) pixel detectors optimized for astrophysical hard X-ray applications. Our hybrid detector consist of a CdTe crystal 1mm thick and 2cm × 2cm in area with segmented anode contacts directly bonded to a custom low-noise application specific integrated circuit (ASIC). The CdTe sensor, fabricated by ACRORAD (Okinawa, Japan), has Schottky blocking contacts on a 605 micron pitch in a 32 × 32 array, providing low leakage current and enabling readout of the anode side. The detector is bonded using epoxy-gold stud interconnects to a custom low noise, low power ASIC circuit developed by Caltech's Space Radiation Laboratory. We have achieved very good energy resolution over a wide energy range (0.62keV FWHM @ 60keV, 10.8keV FWHM @ 662keV). We observe polarization effects at room temperature, but they are suppressed if we operate the detector at or below 0°C degree. These detectors have potential application for future missions such as the International X-ray Observatory (IXO)