Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Association of Japanese Breakfast Intake with Macro- and Micronutrients and Morning Chronotype

(1) Background: Dietary intake may have a remarkable effect on sleep because skipping breakfast and having a late dinner affects many sleep parameters. Breakfast is the most important meal of the day for children and adults to maintain morning chronotype. We examine whether breakfast style is associated with nutrient intake and sleep factors. (2) Methods: This cross-sectional analysis, with a large sample size of 2671 (766 men and 1805 women aged 20–60 years after data brush-up), was based on data obtained from an online survey. Correlation analysis was performed using Spearman’s rank correlation test. The Kruskal–Wallis’s test followed by post hoc Dunn’s multiple comparison test was used to evaluate the interaction between sleep factors and breakfast categories. Multiple regression analyses were performed to identify variables associated with multiple confounding factors. Dietary data were analyzed using approximately one-month average dietary records from the application. The basic characteristics of the participants (age, sex, and BMI) and other lifestyle-related factors (sleep and physical activity) were obtained accordingly. Sleep parameters including the timing of weekday sleep onset, weekday wake-up, weekend (free day) sleep onset, weekend wake-up, sleep, and midpoints of sleep phase were calculated for each participant. We categorized participants’ breakfast types into five groups: (1) Japanese meal, where breakfast may contain Japanese ingredients such as rice; (2) Western meal, where breakfast may contain bread; (3) alternating eating patterns of Japanese and Western meals; (4) cereals and supplements, where breakfast may contain cereals or supplements and energy bars; and (5) skipped breakfast (no breakfast). (3) Results: The midpoint values of the sleep phase on weekends adjusted for sleep debt on work days (MSFsc) related to chronotype were higher in women, suggesting that they may prefer eveningness. Participants with obesity, young age, and low physical activity preferred eveningness with longer sleep durations. Intake of Japanese-style breakfast was significantly associated with early wake-up time on both weekdays and weekends. Cereal-style breakfast intake was significantly associated with late wake-up on both weekdays and weekends. Intake of macronutrients such as protein, fat, carbohydrate, and sodium at breakfast time was positively and strongly associated with the intake of Japanese breakfast, whereas macronutrients were negatively associated with the intake of cereal breakfast. Among micronutrients, vitamin K was positively correlated with Japanese breakfast and negatively correlated with cereal breakfast; (4) Conclusions: Japanese-style breakfast is associated not only with morning preference but also with high intake of macro- and micronutrients

Association of Eating Pattern, Chronotype, and Social Jetlag: A Cross-Sectional Study Using Data Accumulated in a Japanese Food-Logging Mobile Health Application

Chronotype (morningness–eveningness) and social jetlag (SJL; discrepancy in the sleep pattern between the weekday and weekend) are related to eating behavior and health. The association between sleep behavior and the daily macro- and micronutrient eating pattern of each meal (breakfast, lunch, and dinner) have not been discussed well and need more evidence. Here, meal pattern datasets of Japanese participants aged 20–59 years were obtained as averages over 1 month from the data stored in the food-logging app “Asken”. We allocated three groups for each chronotype and SJL. Multiple regression analyses revealed that morning chronotype and small SJL were associated with higher total daily intake of potassium, fiber, magnesium, phosphorus, and vitamin K. Breakfast energy intake and consumption of nutrients, including protein, lipid, carbohydrate, and minerals, were higher in the morning chronotype or small SJL. Lunch intake of potassium, cholesterol, fiber, magnesium, and vitamin K was also higher in the morning chronotype or small SJL. Dinner energy intake and nutrient intake of proteins, lipids, carbohydrates, sodium, and saturated fatty acids were lower in the morning chronotype or small SJL. The current data would help to establish a detailed reference for dietary intake which considers eating patterns over a day

DL4-mediated Notch signaling is required for the development of fetal αβ and γδ T cells.

T-cell development depends upon interactions between thymocytes and thymic epithelial cells (TECs). The engagement of delta-like 4 (DL4) on TECs by Notch1 expressed by blood-borne BM-derived precursors is essential for T-cell commitment in the adult thymus. In contrast to the adult, the earliest T-cell progenitors in the embryo originate in the fetal liver and migrate to the nonvascularized fetal thymus via chemokine signals. Within the fetal thymus, some T-cell precursors undergo programmed TCRγ and TCRδ rearrangement and selection, giving rise to unique γδ T cells. Despite these fundamental differences between fetal and adult T-cell lymphopoiesis, we show here that DL4-mediated Notch signaling is essential for the development of both αβ and γδ T-cell lineages in the embryo. Deletion of the DL4 gene in fetal TECs results in an early block in αβ T-cell development and a dramatic reduction of all γδ T-cell subsets in the fetal thymus. In contrast to the adult, no dramatic deviation of T-cell precursors to alternative fates was observed in the fetal thymus in the absence of Notch signaling. Taken together, our data reveal a common requirement for DL4-mediated Notch signaling in fetal and adult thymopoiesis