DNA-binding specificities of human transcription factors.

Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.

Mechanical and genetic control of ascidian endoderm invagination during gastrulation.

Gastrulation is a near universal developmental process of animal embryogenesis, during which dramatic morphogenetic events take place: the mesodermal and endodermal tissues are internalized, the ectoderm spreads to cover the embryo surface, and the animal body plan and germ layers are established. Morphogenesis during gastrulation has long been considered the result of spatio-temporally localised forces driven by the transcriptional programme of the embryo. Recent work has shown that tissue rheological properties, which define the mechanical response of tissues to internally-generated or external forces, are also important dynamic regulators of gastrulation. Here, we first introduce how embryonic mechanics can be represented, before outlining current knowledge of the mechanical and genetic control of gastrulation in ascidians, invertebrate marine chordates which develop with invariant cell lineages and a solid-like rheological behaviour until the neurula stages. We discuss the potential of these organisms for the experimental and computational whole-embryo characterisation of the mechanisms shaping gastrulation, and how they may inform the more complex tissue internalization strategies used by other model organisms.

A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination.

Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin network. First, endoderm precursors constrict their apex. Second, they shorten apico-basally, while retaining small apical surfaces, thereby causing invagination. The mechanisms that prevent endoderm cell division, trigger the transition between step 1 and step 2, and drive apico-basal shortening have remained elusive. Here, we demonstrate a conserved role for Nodal and Eph signalling during invagination in two distantly related ascidian species, Phallusia mammillata and Ciona intestinalis Specifically, we show that the transition to step 2 is triggered by Nodal relayed by Eph signalling. In addition, our results indicate that Eph signalling lengthens the endodermal cell cycle, independently of Nodal. Finally, we find that both Nodal and Eph signals are dispensable for endoderm fate specification. These results illustrate commonalities as well as differences in the action of Nodal during ascidian and vertebrate gastrulation.

How do distracting events influence children's arithmetic performance?

To understand how distraction influences children's arithmetic performance, we examined effects of irrelevant sounds on children's performance while they solve arithmetic problems. Third and fifth graders were asked to verify true/false, one-digit addition problems (e.g., 9 + 4 = 12. True? False?) under silence and sound conditions. The sounds began when the problems started to appear on the screen (Experiment 1; N = 76) or slightly after (Experiment 2; N = 92) and continued until participants responded. The results showed that (a) children solved arithmetic problems more quickly in the sound condition than in the silence condition when the sounds started with problem display (phasic arousal effects); (b) children were slower on the arithmetic problem verification task when the sounds was played slightly after the problems started to appear on the screen (distraction effects); (c) phasic arousal effects were found only in third graders, whereas distraction effects were found in both grades, although their magnitudes were smaller in fifth graders; (d) distraction effects increased with increasing latencies in third graders but did not change across the entire latency distribution in fifth graders; and (e) distraction effects on current trials were smaller after sound trials than after silence trials in both age groups (sequential modulations of distraction effects). These findings have important implications for furthering our understanding of effects of irrelevant sounds on arithmetic performance as well as cognitive processes involved in children's arithmetic.

How Distracting Events Influence Young and Older adults' Arithmetic Performance?

In this study, I investigated the role of distraction on arithmetic performance and whether this role changes with aging during adulthood. Young and older adults were asked to verify one-digit addition problems (Expt. 1) or to estimate the results of two-digit multiplication problems (Expt. 2). In both experiments, true and false simple problems (Expt. 1) or easier and harder complex problems (Expt. 2) were displayed superimposed or not on irrelevant, emotionally neutral pictures (e.g. mushrooms). In both simple and complex arithmetic, young and older adults obtained poorer arithmetic performance under distraction relative to no-distraction conditions. Most interesting, deleterious effects of irrelevant stimuli on arithmetic performance were larger in older than in young adults. Moreover, magnitude of distraction effects increased with longer solution latencies in young (but not in older) adults while solving complex arithmetic problems. These findings have important implications for furthering our understanding of the role of distraction on cognitive performance in general, and arithmetic performance in particular, as well as age-related differences in this role.

Protein kinases and protein phosphatases encoded in the Ciona robusta genome.

Protein kinases (PKs) and protein phosphatases (PPs) regulate the phosphorylation of proteins that are involved in a variety of biological processes. To study such biological processes systematically, it is important to know the whole repertoire of PKs and PPs encoded in a genome. In the present study, we surveyed the genome of an ascidian (Ciona robusta or Ciona intestinalis type A) to comprehensively identify the genes that encoded PKs and PPs. Because ascidians belong to the sister group of vertebrates, a comparison of the whole repertoire of PKs and PPs of ascidians with those of vertebrates may help to delineate the complements of these proteins that were present in the last common ancestor of these two groups of animals. Our results show that the repertory of PPs was much more expanded in vertebrates than the repertory of PKs. We also showed that approximately 75% of PKs and PPs were expressed during development from eggs to larvae. Thus, the present study provides catalogs for PKs and PPs encoded in the ascidian genome. These catalogs will be useful for systematic studies of biological processes that involve phosphorylation and for evolutionary studies of the origin of vertebrates.

Influence of emotional stimuli on metacognition: A study in arithmetic.

We investigate the role of negative emotional stimuli on direct and indirect metacognition, and document age-related differences in this role during adulthood. Participants were presented with negative or neutral pictures while asked to select which of two available strategies was the better strategy to find approximate estimates of two-digit multiplication problems. Following each strategy selection, participants provided either a direct (confidence judgment; Expt. 1) or an indirect (opt-out judgment; Expt. 2) evaluation of their strategy choice. Negative emotional stimuli decreased metacognitive accuracy for arithmetic strategy selection, but only when indirect metacognitive measures were collected. No differences were found when direct metacognitive judgments were requested. The effects of emotional stimuli on indirect metacognition and lack of effects on direct metacognition were found in both young and older adults. These findings have important implications for our understanding of the mechanisms underlying the effects of emotion on metacognition in young and older adults.

ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.

ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

Effects of prior-task failure on arithmetic performance: A study in young and older adults.

Effects of prior-task failure (i.e., decreased performance on a target task following failure on a prior task) were tested in young and older adults. Young and older participants (N=120) accomplished a computational estimation task (i.e., providing the best estimates to arithmetic problems) before and after accomplishing a dot comparison task in a control or in a failure condition. Both groups decreased their performance on the target computational estimation following failure on the prior dot comparison task. Also, prior-task failure led young and older adults to select the better strategy less often and to use the easier strategy more often. Our findings show, for the first time, impaired performance after experiencing failure in both young and older adults. We discuss implications of these findings for further our understanding of effects of task transitions (i.e., prior-task success and failure) on cognitive performance.

Age-related differences in how negative emotions influence arithmetic performance.

In this study, we investigated the role of negative emotions on arithmetic and whether this role changes with aging during adulthood. Young and older adults were asked to verify one-digit addition problems (Experiment 1) and to estimate the results of two-digit multiplication problems (Experiment 2). In both experiments, easier and harder problems were displayed superimposed on emotionally neutral (e.g. mushrooms) or emotionally negative (e.g. a corpse) pictures. In both simple and complex arithmetic, young and older adults obtained poorer arithmetic performance under negative emotion conditions, especially while solving harder problems. Most interesting, deleterious effects of negative emotions on arithmetic performance were larger in young than in older adults. These findings have important implications for further our understanding of the role of negative emotions in the domain of arithmetic and age-related differences in this role.

Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.

Transcriptional regulation of the Ciona Gsx gene in the neural plate.

The ascidian neural plate consists of a defined number of identifiable cells organized in a grid of rows and columns, representing a useful model to investigate the molecular mechanisms controlling neural patterning in chordates. Distinct anterior brain lineages are specified via unique combinatorial inputs of signalling pathways with Nodal and Delta-Notch signals patterning along the medial-lateral axis and FGF/MEK/ERK signals patterning along the anterior-posterior axis of the neural plate. The Ciona Gsx gene is specifically expressed in the a9.33 cells in the row III/column 2 position of anterior brain lineages, characterised by a combinatorial input of Nodal-OFF, Notch-ON and FGF-ON. Here, we identify the minimal cis-regulatory element (CRE) of 376 bp, which can recapitulate the early activation of Gsx. We show that this minimal CRE responds in the same way as the endogenous Gsx gene to manipulation of FGF- and Notch-signalling pathways and to overexpression of Snail, a mediator of Nodal signals, and Six3/6, which is required to demarcate the anterior boundary of Gsx expression at the late neurula stage. We reveal that sequences proximal to the transcription start site include a temporal regulatory element required for the precise transcriptional onset of gene expression. We conclude that sufficient spatial and temporal information for Gsx expression is integrated in 376 bp of non-coding cis-regulatory sequences.

A genome database for a Japanese population of the larvacean Oikopleura dioica.

The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Age-Related Changes in Verbal Working Memory Strategies.

Background/Study context: Maintenance in verbal working memory is thought to rely on two main systems: a phonological and a semantic system. The three objectives of the present study were to clarify how these systems are organized and interact, to examine whether their involvement in maintenance changes with aging, and to identify which underlying mechanism accounts for both age-related changes in the available set of mechanisms and immediate recall.Methods: To address these issues, we examined age-related changes in strategic aspects of maintenance of information in working memory. We collected trial-by-trial verbal reports of which strategy young and older adults used while accomplishing a verbal complex span task. In addition, individuals' speed of articulation was collected.Results: Results support the existence of separable systems (i.e., phonological and semantic systems) that participants combine to cope with increasing memory loads. We also found age-related differences (e.g., older individuals used more strategies than young individuals and used available strategies unequally often) and invariance (e.g., both age groups used strategies based on phonological and semantic processing) in strategic aspects of working memory maintenance. Importantly, articulation speed accounted for effects of both memory load and age on strategy distributions as well as for age-related differences in immediate recall.Conclusion: Our findings suggest that young and older adults' use of common and different sets of maintenance mechanisms stems for the constraints of the phonological loop in working memory, especially the speed of articulation, which slowed down with aging.

Convergent Acquisition of Nonembryonic Development in Styelid Ascidians.

Asexual propagation and whole body regeneration are forms of nonembryonic development (NED) widespread across animal phyla and central in life history and evolutionary diversification of metazoans. Whereas it is challenging to reconstruct the gains or losses of NED at large phylogenetic scale, comparative studies could benefit from being conducted at more restricted taxonomic scale, in groups for which phylogenetic relationships are well established. The ascidian family of Styelidae encompasses strictly sexually reproducing solitary forms as well as colonial species that combine sexual reproduction with different forms of NED. To date, the phylogenetic relationships between colonial and solitary styelids remain controversial and so is the pattern of NED evolution. In this study, we built an original pipeline to combine eight genomes with 18 de novo assembled transcriptomes and constructed data sets of unambiguously orthologous genes. Using a phylogenomic super-matrix of 4,908 genes from these 26 tunicates we provided a robust phylogeny of this family of chordates, which supports two convergent acquisitions of NED. This result prompted us to further describe the budding process in the species Polyandrocarpa zorritensis, leading to the discovery of a novel mechanism of asexual development. Whereas the pipeline and the data sets produced can be used for further phylogenetic reconstructions in tunicates, the phylogeny provided here sets an evolutionary framework for future experimental studies on the emergence and disappearance of complex characters such as asexual propagation and whole body regeneration.

When Older Adults Outperform Young Adults: Effects of Prior-Task Success in Arithmetic.

BACKGROUND: Older adults improve their cognitive performance on a target task after succeeding in a prior task. We tested whether effects of prior-task success occur via changing older adults' ability to select the better strategy and/or to execute strategies efficiently. METHODS: Young and older participants (n = 162) accomplished a computational estimation task (i.e., providing the best estimates to arithmetic problems) after accomplishing a dot comparison task. RESULTS: Both groups increased their performance on computational estimation following success on dot comparison. Older adults improved most and outperformed young adults following prior-task success. Prior-task success led older adults to select the better strategy more often and to repeat (or not) the same strategy more often when it was appropriate. Better strategy use mediated effects of prior-task success. Individual differences in baseline performance moderated individuals' sensitivity to effects of prior-task success. CONCLUSION: Our findings further our understanding of mechanisms underlying effects of prior-task success and provide new perspectives on how social environment modulates age-related differences in cognitive performance.

Effects of working memory updating on children's arithmetic performance and strategy use: A study in computational estimation.

The current study investigated how children's working memory updating processes influence arithmetic performance and strategy use. Large samples of third and fourth graders were asked to find estimates of two-digit addition problems (e.g., 42 + 76). On each problem, children could choose between the rounding-down strategy (i.e., rounding both operands down to the closest decades) or the rounding-up strategy (i.e., rounding both operands up to the closest decades). Four tasks were used to assess updating. Analyses of strategy use revealed that children with more efficient updating showed higher levels of (a) strategy flexibility (i.e., they were less likely to use a single strategy on all or nearly all problems within a test block), (b) strategy adaptivity (i.e., they selected the better strategy overall more often and were more adaptive specifically on homogeneous and rounding-up problems), and (c) strategy performance (i.e., they tended to execute strategies more quickly, especially on homogeneous and larger problems). Finally, updating exerted a more important role for problem type effects in younger children than in older children. These findings have important implications for further understanding how working memory updating processes influence children's arithmetic performance and age-related differences therein.

A phylogenomic framework and timescale for comparative studies of tunicates.

BACKGROUND: Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species. RESULTS: Phylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~ 450-350 million years ago) among the major groups and allow one to compare their evolutionary age with respect to the major vertebrate model lineages. CONCLUSIONS: Our study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.

Negative Aging Stereotypes Disrupt both the Selection and Execution of Strategies in Older Adults.

BACKGROUND: Age-based cognitive deficits are exacerbated by stereotype threat effects (i.e., the threat of being judged as cognitively incapable due to aging). We tested whether age-based stereotype threat effects can occur via impair- ing older adults' ability to select the best strategy and/or to execute strategies efficiently. METHODS: Older adults (age range: 64.3-89.5 years) were randomly assigned to a stereotype threat or control condition before taking an episodic memory task. They encoded pairs of concrete words and of abstract words, with either a repetition or an imagery strategy, and then took a cued-recall task. Whereas participants in experiment 1 could choose between these two strategies, those of experiment 2 were forced to use either the repetition or the imagery strategy. RESULTS: Our findings showed that age-based stereotype threat disrupts both the selection and execution of the most efficient, but also most resource-demanding, imagery strategy, and that these stereotype threat effects were stronger on concrete words. CONCLUSION: Our findings have important implications to further understand age-based (and other) stereotype threat effects, and how noncognitive factors modulate age-related changes in human cognition.