The role of vertebrate conserved non-coding elements in hindbrain development and evolution

Vertebrate conserved non-coding elements (CNEs) act as cis-regulatory modules of developmental genes. To assess their roles in coordinating gene expression during embryogenesis, CNEs were subjected to motif searches. Using reporter gene assays in zebrafish (Danio rerio) embryos, Pbx-Hox (TGATNNAT) motifs are demonstrated to be poor predictors of hindbrain enhancer activity. Hindbrain enhancer CNEs are distinguished from hindbrain negative CNEs accurately by virtue of co-occurring Pbx-Hox (TGA TDDA TKD) and Meis/Pknox (CTGTCA) motifs. The grammar of these motifs was investigated using a bioinformatic pipeline for the detection of multiple conserved motifs, revealing no patterns in their relative organisation aside from spatial co-occurrence. These motifs were then used to identify additional conserved hindbrain enhancers with high efficacy (89%). Substitutions targeted to either motif abrogate expression by the enhancer or generate ectopic reporter gene expression, suggesting that motif co-occurrence is required for efficient and segment-specific hindbrain activation. Pbx-Hox and Meis/Pknox motifs are enriched in gnathostome CNE sets but are not detected in invertebrate chordate CNEs. Furthermore the presence (or absence) of the hindbrain syntax correlates with the conservation (or lack thereof) of segment-restricted enhancer activity in orthologous CNEs from the sea lamprey. A library of zebrafish hindbrain regulatory elements is made available. The heterogeneity of function and the loose grammar of motifs are consistent with combinatorial factor binding; a model of CNEs as exceptionally well- conserved billboard enhancers is presented (inflexible billboard model). The implications of these data for models of the evolution of the vertebrate hindbrain are discussed. Several components of the hindbrain gene regulatory network are shared- derived characters of gnathostomes, suggesting the establishment and elaboration of the conserved regulatory code controlling hindbrain development on the vertebrate and gnathostome stems, respectively

Computational genomics of regulatory elements and regulatory territories

Whole genome comparison of metazoan genomes reveals extremely high level of noncoding conservation over tens to hundreds of base pairs across distant species. These sequences are termed as conserved noncoding elements (CNEs). Arrays of conserved noncoding elements that span the loci of developmental regulatory genes and their span defines regulatory genomic blocks (GRBs). CNEs are currently known to be involved in transcriptional regulation and development as long-range enhancers. However, no molecular mechanism can yet explain their exceptional degree of conservation. As a first step towards the genome-wide study of these elements, I developed two R/Bioconductor packages CNEr and TFBSTools, to detect and analyse regulatory elements. Next, I designed a novel CNE detection pipeline for duplicated regions in the ameiotic Adineta vaga genome. Identification of CNEs in this genome suggests that the principal function of CNEs is regulation of developmental gene expression rather than copy number sensing. In addition, I performed a de novo genome annotation of European common carp Cyprinus carpio. This genome stands as an ideal candidate for comparative study of zebrafish genome. Its analysis revealed a wealth of previously undetected fish regulatory elements and their unexpectedly high level of conservation between the two genomes. Finally, I presented a computational method for the identification of GRB boundaries and prediction of the corresponding target genes under long-range regulation. The predicted target genes are implicated in developmental, transcriptional regulation and axon guidance. The disruption of regulation of these target genes is likely to cause complex diseases, including cancer. The GRB boundaries and predicted target genes are valuable resource for investigating developmental regulation and interpreting genome-wide association studies.Open Acces

A STATE OF KNOWLEDGE ON ALGEBRA IN THE UNITED STATES’ ELEMENTARY SCHOOL

https://doi.org/10.1590/CC245630Em 1905, um estudo sobre a reestruturação do ensino elementar estadunidense é publicado na revista Educational Review, apontando a necessidade de uma álgebra neste nível escolar. Um estado do conhecimento histórico acerca desse tema na revista foi realizado, com base na perspectiva das humanidades digitais, utilizando o software IRaMuTeQ. A álgebra foi o foco na busca por publicações, a partir da seleção e da análise dos textos com o software. Observou-se um movimento a favor de um ensino centrado em equações e sistemas lineares, aplicados a problemas complexos de aritmética

Annual reports of the selectmen, treasurer and town clerk of the town of Weare together with the report of the school board for the year ending January 31, 1931.

This is an annual report containing vital statistics for a town/city in the state of New Hampshire

Real-time simulation model of the HL-20 lifting body

A proposed manned spacecraft design, designated the HL-20, has been under investigation at Langley Research Center. Included in that investigation are flight control design and flying qualities studies utilizing a man-in-the-loop real-time simulator. This report documents the current real-time simulation model of the HL-20 lifting body vehicle, known as version 2.0, presently in use at NASA Langley Research Center. Included are data on vehicle aerodynamics, inertias, geometries, guidance and control laws, and cockpit displays and controllers. In addition, trim case and dynamic check case data is provided. The intent of this document is to provide the reader with sufficient information to develop and validate an equivalent simulation of the HL-20 for use in real-time or analytical studies

Novel role for SOX2 in the development of the zebrafish epithalamus

The sex determining region Y-box 2 (sox2) gene is one of the most important transcription factors during development, particularly the development of the central nervous system (CNS). It is expressed in embryonic stem cells and later in neural stem cells, where it modulates their maintenance and differentiation. In humans, heterozygous mutations are associated with eye malformations, including anophthalmia and severe microphthalmia. Also, a subset of patients has extra-ocular phenotypes, such as hearing loss, seizures and pituitary hypoplasia. Although the roles of sox2 in embryonic stem cells and eye development are well studied, the function of sox2 in brain development and disease is still elusive. The aim of this project was to characterize a novel role for sox2 in the development of zebrafish epithalamus, which was identified from an in silico screen previously performed in our laboratory. The zebrafish epithalamus, located in the dorsal diencephalon, consists of three main structures: the pineal gland, the parapineal organ and the habenular nuclei. The pineal gland, also known as epiphysis, is a photoreceptive (in zebrafish) and neuroendocrine organ that detects light and rhythmically produces melatonin in order to regulate the circadian rhythms. The parapineal organ is located to the left side of the pineal gland and is important for the elaboration of the asymmetries observed between the left and right habenular nuclei. Finally, the bilateral habenulae are part of the dorsal diencephalic conduction system that links the forebrain with the mid- and hindbrain. The left and right habenulae show both molecular and neuroanatomical asymmetries, including differences in neuropil organization, in levels of gene expression and in the morphology and connectivity of their neurons’ projections. The relatively simple architecture of the pineal gland and the asymmetric character of the habenulae provide a useful tool for studying cell-fate determination, cell migration and establishment of brain asymmetries. In this study, we used zebrafish as a model to dissect the novel functions of sox2 in the development of the epithalamus. We showed that sox2 works synergistically with Notch pathway to negatively regulate neurogenesis within the pineal gland. The pineal gland consists of only two cell types: the photoreceptors and the projection neurons. Previous studies showed that the Notch and BMP pathways are important for the proper specification of these cells. Here, we show that sox2 normally inhibits the photoreceptor cell fate, whereas it has no effect on the number of projection neurons. Therefore, sox2 complements Notch and BMP pathways in cell-fate determination within the pineal gland. In addition, downregulation of sox2 results in abnormal parapineal organ development and disruption of the asymmetric architecture of the habenulae. A subset of sox2 morphant embryos develops right-sided parapineal organs, which is consistent with abnormal bilateral expression of the Nodal gene, pitx2 (paired-like homeodomain transcription factor 2). Also, timelapse experiments showed that migration of the parapineal cells is defective, resulting in scattered cells. The aberrant parapineal development leads to disorganization of the habenular nuclei, as shown by the abnormal neuropil arrangement and the expression of the asymmetric marker kctd12.1 (potassium channel tetramerisation domain containing 12.1)

2種の多型メダカ集団におけるゲノム・エピゲノム比較解析

学位の種別: 課程博士審査委員会委員 : （主査）東京大学教授 久保 健雄, 東京大学教授 岡 良隆, 東京大学教授 武田 洋幸, 東京大学准教授 入江 直樹, 東京大学准教授 近藤 真理子University of Tokyo(東京大学

Environmental dynamics at orbital altitudes

The influence of real satellite aerodynamics on the determination of upper atmospheric density was investigated. A method of analysis of satellite drag data is presented which includes the effect of satellite lift and the variation in aerodynamic properties around the orbit. The studies indicate that satellite lift may be responsible for the observed orbit precession rather than a super rotation of the upper atmosphere. The influence of simplifying assumptions concerning the aerodynamics of objects in falling sphere analysis were evaluated and an improved method of analysis was developed. Wind tunnel data was used to develop more accurate drag coefficient relationships for studying altitudes between 80 and 120 Km. The improved drag coefficient relationships revealed a considerable error in previous falling sphere drag interpretation. These data were reanalyzed using the more accurate relationships. Theoretical investigations of the drag coefficient in the very low speed ratio region were also conducted