A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

<p>Abstract</p> <p>Background</p> <p>High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (~400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool.</p> <p>Results</p> <p>We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip^®Rice Genome Array, using the rice cultivars with full genome sequence, <it>japonica </it>cultivar Nipponbare and <it>indica </it>cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated.</p> <p>Conclusions</p> <p>The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50%) in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of <it>Oryza sativa</it>) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.</p

ホンコン ノ ネンショウシャ ニホンゴ ガクシュウシャ ニ カンスル イチ コウサツ -ホゴシャ ノ イシキ ヲ チュウシン ニ-

香港において、年少の日本語学習者が存在感を増しつつある。本論は、年少の日本語学習者に大きな影響を与えると思われる保護者を対象にインタビューを実施し、保護者が年少者に日本語を学習させる際の意識を考察する。全体的な傾向として、日本への親近感・好印象が、統合的動機へと結びつく。同時に、保護者の意識の中にある子どもの就職や旅行など具体的な目標が、道具的動機へと結びつく。加えて、統合的でも道具的でもない「学びそのものへの積極性」から生じる学習動機が存在する。香港においては、「学ぶこと」を肯定する意識が非常に強く、英語と中国語の習得が前提付けられた多言語社会にありながらも、日本語が第三の言語として学ばれるのである。Recently, the presence of young learners of Japanese has become increasingly significant in Hong Kong. Using interviews, this paper investigates the attitudes of the parents of young learners. Overall, the parents\u27 sense of familiarity and positive impressions towards Japan lead to integrative motivations. Also, definite purposes such as getting a job or traveling serve as instrumental motivation. Aside from integrative and instrumental motivations, the parents can encourage their children to study Japanese because "learning something" is beneficial and meaningful in its own right. Although people in this multilingual society are destined to learn English and Chinese, "learning" is so highly valued in the context of Hong Kong that they still can be motivated to study Japanese as a third language

Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system

半数体生物の性染色体上の性決定遺伝子を解明 --コケがもつ現生生物最古の起源の性染色体--. 京都大学プレスリリース. 2021-11-08.Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply to sex chromosomes in organisms where sex is determined in the haploid phase of the life cycle: both sex chromosomes, female U and male V, are expected to maintain their gene functions, even though both are non-recombining. This is in contrast to the X-Y (or Z-W) asymmetry and Y (W) chromosome degeneration in XY (ZW) systems of diploids. Here, we provide evidence that sex chromosomes diverged early during the evolution of haploid liverworts and identify the sex determinant on the Marchantia polymorpha U chromosome. This gene, Feminizer, encodes a member of the plant-specific BASIC PENTACYSTEINE transcription factor family. It triggers female differentiation via regulation of the autosomal sex-determining locus of FEMALE GAMETOPHYTE MYB and SUPPRESSOR OF FEMINIZATION. Phylogenetic analyses of Feminizer and other sex chromosome genes indicate dimorphic sex chromosomes had already been established 430 mya in the ancestral liverwort. Feminizer also plays a role in reproductive induction that is shared with its gametolog on the V chromosome, suggesting an ancestral function, distinct from sex determination, was retained by the gametologs. This implies ancestral functions can be preserved after the acquisition of a sex determination mechanism during the evolution of a dominant haploid sex chromosome system

離乳期の低栄養による小腸糖質消化吸収関連遺伝子の食事に対する応答性の変化

第3回日本DOHaD研究会学術集会　抄録集　【ポスター発表

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology