34,149 research outputs found
Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains
No full textInternational audienceCite as: Robinson-Rechavi, M. 2017. Combining molecular information on chromatin organisation wit eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains. Peer Community in Evolutionary Biology, 100035. In this manuscript [1], Francisco J. Novo proposes candidate non-coding genomic elements regulating neurodevelopmental genes. What is very nice about this study is the way in which public molecular data, including physical interaction data, is used to leverage recent advances in our understanding to molecular mechanisms of gene regulation in an evolutionary context. More specifically, evolutionarily conserved non coding sequences are combined with enhancers from the FANTOM5 project, DNAse hypersensitive sites, chromatin segmentation, ChIP-seq of transcription factors and of p300, gene expression and eQTLs from GTEx, and physical interactions from several Hi-C datasets. The candidate regulatory regions thus identified are linked to candidate regulated genes, and the author shows their potential implication in brain development
Competing models of socially constructed economic man : differentiating Defoe's Crusoe from the Robinson of neoclassical economics
No full textDaniel Defoe’s Robinson Crusoe has seldom been read as an explicitly political text. When it has, it appears that the central character was designed to warn the early eighteenth-century reader against political challenges to the existing economic order. Insofar as Defoe’s Crusoe stands for "economic man", he is a reflection of historically-produced assumptions about the need for social conformity, not the embodiment of any genuinely essential economic characteristics. This insight is used to compare Defoe’s conception of economic man with that of the neoclassical Robinson Crusoe economy. On the most important of the ostensibly generic principles espoused by neoclassical theorists, their "Robinson" has no parallels with Defoe’s Crusoe. Despite the shared name, two quite distinct social constructions serve two equally distinct pedagogical purposes. Defoe’s Crusoe extols the virtues of passive middle-class sobriety for effective social organisation; the neoclassical Robinson champions the establishment of markets for the sake of productive efficiency
Twofoldness/threefoldness: Marc Lüders' photopicturen
No full textMy essay 'Twofoldness/Threefoldness: Marc Lüders' Photopicturen' used as the text accompanying Marc Lüders' exhibition - 'Marc Lüders/Twofoldness' at the Levy Gallery, Hamburg in November 2018
Claude Cosandey, Marc Robinson - Hydrologie continentale
No full textHugonie Gérard. Claude Cosandey, Marc Robinson - Hydrologie continentale . In: L'information géographique, volume 65, n°1, 2001. p. 94
Ernest Thompson Seton: an unforgettable personality, by Edgar M. Robinson
No full textThis piece, titled “Ernest Thomas Seton: an unforgettable personality”, gives a first hand interpretation of who Ernest Thompson Seton (it is believed that whoever put the cover on this document spelled his name wrong) was through the eyes of Edgar Robinson. Robinson explains what a strong relationship the two of them had and what a strong mentor Seton was to Robinson. Ernest Thompson Seton was an author and illustrator of more than 50 works, and was largely responsible for the American Indian influence in the Boy Scouts of America that offered young people knowledge of an outdoor life based on Native American Indian customs, legends and beliefs. Seton was Chief Scout of the Boy Scouts of America from 1910 to 1915. Edgar M. Robinson was a 1901 graduate from the YMCA Training School, now Springfield college, where he later returned to serve on the faculty as the Honorary Director of Boys Work Courses and the Adviser in Methods and Principles in Work with Boys from 1927-1937.For biographical information on Edgar M. Robinson, see: https://springfield.as.atlas-sys.com/agents/people/554
For more information on Ernest Thompson Seton, see: https://springfield.as.atlas-sys.com/agents/people/553On the bottom of page number 1 there is a rip, which prevents part of the bottom two lines from being read. On that back of page number one appear the numbers "46757" written in pencil
Robinson Crusoe
No full textDaniel Defoe (c. 1660-1731) was an English merchant, author, and political pamphleteer best known for the classic adventure novel Robinson Crusoe.Cover Page -- Title Page -- Contents -- Chapter I-Start in Life -- Chapter II-Slavery and Escape -- Chapter III-Wrecked on a Desert Island -- Chapter IV-First Weeks on the Island -- Chapter V-Builds a House-The Journal -- Chapter VI-Ill and Conscience-Stricken -- Chapter VII-Agricultural Experience -- Chapter VIII-Surveys his Position -- Chapter IX-A Boat -- Chapter X-Tames Goats -- Chapter XI-Finds Print of Man's Foot on the Sand -- Chapter XII-A Cave Retreat -- Chapter XIII-Wreck of a Spanish Ship -- Chapter XIV-A Dream Realised -- Chapter XV-Friday's Education -- Chapter XVI-Rescue of Prisoners from Cannibals -- Chapter XVII-Visit of Mutineers -- Chapter XVIII-The Ship Recovered -- Chapter XIX-Return to England -- Chapter XX-Fight between Friday and a Bear -- Copyright PageDaniel Defoe (c. 1660-1731) was an English merchant, author, and political pamphleteer best known for the classic adventure novel Robinson Crusoe.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
Early events in the evolution of spider silk genes.
No full textSilk spinning is essential to spider ecology and has had a key role in the expansive diversification of spiders. Silk is composed primarily of proteins called spidroins, which are encoded by a multi-gene family. Spidroins have been studied extensively in the derived clade, Orbiculariae (orb-weavers), from the suborder Araneomorphae ('true spiders'). Orbicularians produce a suite of different silks, and underlying this repertoire is a history of duplication and spidroin gene divergence. A second class of silk proteins, Egg Case Proteins (ECPs), is known only from the orbicularian species, Lactrodectus hesperus (Western black widow). In L. hesperus, ECPs bond with tubuliform spidroins to form egg case silk fibers. Because most of the phylogenetic diversity of spiders has not been sampled for their silk genes, there is limited understanding of spidroin gene family history and the prevalence of ECPs. Silk genes have not been reported from the suborder Mesothelae (segmented spiders), which diverged from all other spiders >380 million years ago, and sampling from Mygalomorphae (tarantulas, trapdoor spiders) and basal araneomorph lineages is sparse. In comparison to orbicularians, mesotheles and mygalomorphs have a simpler silk biology and thus are hypothesized to have less diversity of silk genes. Here, we present cDNAs synthesized from the silk glands of six mygalomorph species, a mesothele, and a non-orbicularian araneomorph, and uncover a surprisingly rich silk gene diversity. In particular, we find ECP homologs in the mesothele, suggesting that ECPs were present in the common ancestor of extant spiders, and originally were not specialized to complex with tubuliform spidroins. Furthermore, gene-tree/species-tree reconciliation analysis reveals that numerous spidroin gene duplications occurred after the split between Mesothelae and Opisthothelae (Mygalomorphae plus Araneomorphae). We use the spidroin gene tree to reconstruct the evolution of amino acid compositions of spidroins that perform different ecological functions
Gene expression variability and evolutionary outcomes after whole-genome duplication in fishes
No full textVariation within natural populations is fundamental to evolution, as it provides the raw material for natural selection. However, despite its central role, the study of variation and variability (the tendency of a trait to vary) has often been overlooked in evolutionary biology. Gene expression, a dynamic process that determines where, when, and how much of a gene product is formed, is a crucial intermediary between genotype and phenotype, making its variability a key yet understudied aspect of evolutionary processes. This thesis explores the evolutionary implications of gene expression variability in two main studies. Using bulk organ transcriptomic data from outbred individuals of three ray-finned fishes, I investigate (1) how variability reflects constraints on regulatory evolution, and (2) how variability reflects evolvability, based on patterns of duplication gene retention and functional divergence after whole-genome duplication (WGD).
The first study examines inter-individual gene expression variability measured in multiple organs in spotted gar (Lepisosteus oculatus), zebrafish (Danio rerio), and Northern pike (Esox lucius). I find that highly variable genes evolve under weaker purifying selection at the coding sequence, showing that intra-species variability in gene expression is linked to inter-species protein sequence divergence. The key finding is that the variability of a gene is largely determined by its primary organ of expression rather than being independently regulated in each organ. Notably, genes that are most expressed in the brain (brain-biased) are lowly variable across non-nervous organs, suggesting stabilizing selection on regulatory evolution. This suggests that organ-specific selective pressures shape gene regulatory evolution and thus variability.
The second study focuses on how gene expression variability influences the retention and functional divergence of WGD paralogs (ohnologs). Here, I use spotted gar and Northern pike as outgroups to the teleost and salmonid WGDs, respectively, to approximate the ancestral expression pattern pre-duplication. First, results suggest that genes retained in duplicate post-WGD tend to have higher variability preceding duplication, particularly organ-biased genes which evolve under weaker selective constraints relative to broadly expressed genes. Second, by characterizing the expression divergence patterns of teleost ohnolog pairs in zebrafish and relating it to variability in spotted gar, I show that variability is linked to functional divergence of lowly constrained ohnolog pairs. This suggests that variability can facilitate the evolution of gene function post-duplication. These results highlight the interplay between selective constraints and expression evolvability in shaping the evolutionary fates of ohnologs.
Lastly, I provide a perspective on approaches to classify the evolutionary outcomes of duplicate genes using transcriptomic data. This is a challenging task which involves translating conceptual models of post-duplication fates (e.g., subfunctionalization and neofunctionalization, among others) into appropriate empirical tests with suitable metrics and inclusion criteria. I discuss simplifying assumptions (heuristics) in using gene expression as a proxy for function, differences in the verbal and graphical descriptions of conceptual models (semantics), metrics, and other methodological considerations. I also highlight important factors to consider to improve comparability across studies and to advance our knowledge of gene function evolution
Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods
No full textGene expression studies often use bulk RNA sequencing of mixed cell populations because single cell or sorted cell sequencing may be prohibitively expensive. However, mixed cell studies may miss expression patterns that are restricted to specific cell populations. Computational deconvolution can be used to estimate cell fractions from bulk expression data and infer average cell-type expression in a set of samples (e.g., cases or controls), but imputing sample-level cell-type expression is required for more detailed analyses, such as relating expression to quantitative traits, and is less commonly addressed. Here, we assessed the accuracy of imputing sample-level cell-type expression using a real dataset where mixed peripheral blood mononuclear cells (PBMC) and sorted (CD4, CD8, CD14, CD19) RNA sequencing data were generated from the same subjects (N=158), and pseudobulk datasets synthesised from eQTLgen single cell RNA-seq data. We compared three domain-specific methods, CIBERSORTx, bMIND and debCAM/ swCAM, and two cross-domain machine learning methods, multiple response LASSO and ridge, that had not been used for this task before. We also assessed the methods according to their ability to recover differential gene expression (DGE) results. LASSO/ ridge showed higher sensitivity but lower specificity for recovering DGE signals seen in observed data compared to deconvolution methods, although LASSO/ridge had higher area under curves than deconvolution methods. Machine learning methods have the potential to outperform domain-specific methods when suitable training data are available
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy
No full textAbstract
Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.
Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee.
Availability: download section of the Bgee website http://bgee.unil.ch/
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p
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