Promoter structure and transcription initiation sites of the human death receptor 5/TRAIL-R2 gene11The nucleotide sequence of the DR5 gene promoter is in the DDBJ/EMBL/GenBank databases with the following accession number: AB054004.

AbstractThe death receptor 5 (DR5) is a receptor for tumor necrosis factor-related apoptosis-inducing ligand and is able to induce apoptosis in various tumor cells. The expression of DR5 is up-regulated at the transcriptional level by p53, genotoxic stress and so on. To investigate the structure of the DR5 gene promoter, we screened and sequenced a genomic clone containing the 5′-flanking region of the DR5 gene. RNase protection assays showed two major transcription start sites around −122 and −137 upstream of the translation initiation codon ATG. Transient transfections with serial 5′-deletion mutants identified the minimal promoter element spanning −198 to −116. Site-directed mutagenesis demonstrated that the DR5 gene promoter has no typical TATA-box, but has two Sp1 sites responsible for the basal transcription activity of the DR5 gene promoter

The Effects of Font Type on Reading Accuracy and Fluency in Japanese Children with Developmental Dyslexia

We administered rapid reading tasks in Japanese children (32 with typical development and 24 with developmental dyslexia), and investigated the effects of two different font types: Rounded-Gothic and Mincho style font. In the experiment, we used four kinds of stimuli: two scripts (paragraphs and random kana character non-words) in two font types (Rounded-Gothic and Mincho style font). In this experiment, the duration time, the number of errors and the number of self-corrections were measured during reading. Participants were asked which font type was easier to read. There was no significant difference in the duration time, the number of errors and the number of self-corrections between two types of fonts among the 56 participants. On the other hand, regarding subjective readability, the developmental dyslexia group reported that the Rounded-Gothic font was easier to read. There was a difference between objective and subjective readability. In this study, there was no difference in reading performance of Rounded-Gothic and Mincho style fonts in Japanese children with developmental dyslexia

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

BACKGROUND: Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. RESULTS: Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise F(ST )and R(ST )analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. CONCLUSION: The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species

Comparing modeling methods of genomic prediction for growth traits of a tropical timber species, Shorea macrophylla

IntroductionShorea macrophylla is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to S. macrophylla.MethodsTo build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of S. macrophylla in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for diameter at breast height and total height in the 7th year from planting (D7 and H7).Results and discussionThese traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 6 methods and their derivatives with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability for D7 and H7 with the sets of selected SNPs and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high predictive abilities for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. Predictive abilities were higher in H7 when smaller number of SNP subsets selected by GWAS p-value was used, However, D7 showed the contrary tendency, which might have originated from the difference in genetic architecture between primary and secondary growth of the species. This study suggests that GS with GWAS-based SNP selection can be used in breeding for non-cultivated tree species to improve initial growth and reduce genotyping costs for next-generation seedlings

High-Throughput Identification and Screening of Novel Methylobacterium Species Using Whole-Cell MALDI-TOF/MS Analysis

Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing

Combined effects of eating alone and living alone on unhealthy dietary behaviors, obesity and underweight in older Japanese adults: Results of the JAGES

AbstractWe examined whether eating alone is associated with dietary behaviors and body weight status, and assessed the modifying effects of cohabitation status in older Japanese people. Data from the 2010 Japan Gerontological Evaluation Study, with a self-reported questionnaire for 38,690 men and 43,674 women aged ≥65 years, were used. Eating status was classified as eating with others, sometimes eating alone, or exclusively eating alone. We calculated adjusted prevalence ratios (APRs) of unhealthy dietary behaviors, obesity, and underweight, adjusting for age, education, income, disease, and dental status using Poisson regression. Overall, 16% of men and 28% of women sometimes or exclusively ate alone. Among those who exclusively ate alone, 56% of men and 68% of women lived alone. Men who exclusively ate alone were 3.74 times more likely to skip meals than men who ate with others. Among men who exclusively ate alone, those who lived alone had a higher APR than men who lived with others. Compared with subjects who ate and lived with others, the APRs of being obese (BMI ≥ 30.0 kg/m2) among men who exclusively ate alone were 1.34 (1.01–1.78) in those who lived alone and 1.17 (0.84–1.64) in those who lived with others. These combined effects of eating and living alone were weaker in women, with a potential increase in the APRs among those who ate alone despite living with others. Men who exclusively ate alone were more likely to be underweight (BMI < 18.5 kg/m2) than men who ate with others in both cohabitation statuses. Eating alone and living alone may be jointly associated with higher prevalence of obesity, underweight and unhealthy eating behaviors in men

Transcriptomic responses of oil palm (Elaeis guineensis) stem to waterlogging at plantation in relation to precipitation seasonality

Global warming-induced climate change causes significant agricultural problems by increasing the incidence of drought and flooding events. Waterlogging is an inevitable consequence of these changes but its effects on oil palms have received little attention and are poorly understood. Recent waterlogging studies have focused on oil palm seedlings, with particular emphasis on phenology. However, the transcriptomic waterlogging response of mature oil palms remains elusive in real environments. We therefore investigated transcriptomic changes over time in adult oil palms at plantations over a two-year period with pronounced seasonal variation in precipitation. A significant transcriptional waterlogging response was observed in the oil palm stem core but not in leaf samples when gene expression was correlated with cumulative precipitation over two-day periods. Pathways and processes upregulated or enriched in the stem core response included hypoxia, ethylene signaling, and carbon metabolism. Post-waterlogging recovery in oil palms was found to be associated with responses to heat stress and carotenoid biosynthesis. Nineteen transcription factors (TFs) potentially involved in the waterlogging response of mature oil palms were also identified. These data provide new insights into the transcriptomic responses of planted oil palms to waterlogging and offer valuable guidance on the sensitivity of oil palm plantations to future climate changes