Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse

Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

The role of mother's and child's self-regulation on bidirectional links between harsh parenting and child externalizing problems

The authors examined task-based (i.e., executive function), surveyed (i.e., effortful control), and physiological (i.e., resting cardiac respiratory sinus arrhythmia [RSA]) measures of child and maternal regulation as distinct moderators of longitudinal bidirectional links between child externalizing (EXT) behaviors and harsh parenting (HP) from 6 to 9 years. The sample size was 299 (50.9% female; 1% Asian, 4% multiple races; 14% Black; 78% White), and participants were recruited in the United States (a rural college town in Virginia and a midsized city in North Carolina). Higher child EXT at 6 years predicted higher HP at 7-8 years, which predicted higher EXT at 9 years. Also, this path was moderated by 6-year child effortful control, 6-year resting RSA, and 9-year executive function. In contrast, there was no moderating effect of any measure of maternal regulation. Findings suggest it is important to consider child self-regulation when examining bidirectionality in parent and child effects for HP and child EXT. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).

Compliance-Adjusted Estimates of Aspirin Effects Among Older Persons in the ASPREE Randomized Trial

The Aspirin in Reducing Events in the Elderly (ASPREE) Trial recruited 19,114 participants across Australia and the United States during 2010-2014. Participants were randomized to receive either 100 mg of aspirin daily or matching placebo, with disability-free survival as the primary outcome. During a median 4.7 years of follow-up, 37% of participants in the aspirin group permanently ceased taking their study medication and 10% commenced open-label aspirin use. In the placebo group, 35% and 11% ceased using study medication and commenced open-label aspirin use, respectively. In order to estimate compliance-adjusted effects of aspirin, we applied rank-preserving structural failure time models. The results for disability-free survival and most secondary endpoints were similar in intention-to-treat and compliance-adjusted analyses. For major hemorrhage, cancer mortality, and all-cause mortality, compliance-adjusted effects of aspirin indicated greater risks than were seen in intention-to-treat analyses. These findings were robust in a range of sensitivity analyses. In accordance with the original trial analyses, compliance-adjusted results showed an absence of benefit with aspirin for primary prevention in older people, along with an elevated risk of clinically significant bleeding.

Developmental patterns of children's shyness: Relations with physiological, emotional, and regulatory responses to being treated unfairly

The dysregulation of social fear has been widely studied in children's shyness, but we know little about how shy children regulate during unfair treatment. We first characterized developmental patterns of children's shyness (N = 304, ngirls  = 153; 74% White, 26% Other) across 2 (Mage  = 2.07), 3 (Mage  = 3.08), 4 (Mage  = 4.08), and 6 (Mage  = 6.58) years of age. Data collection occurred from 2007 to 2014. At age 6, the high stable group had higher cardiac vagal withdrawal and lower expressed sadness and approach-related regulatory strategy than the low stable group when being treated unfairly. Although shy children may be more physiologically impacted by being treated unfairly, they may mask their sadness to signal appeasement.

Biochemical pathways represented by Gene Ontology-Causal Activity Models identify distinct phenotypes resulting from mutations in pathways

Gene inactivation can affect the process(es) in which that gene acts and causally downstream ones, yielding diverse mutant phenotypes. Identifying the genetic pathways resulting in a given phenotype helps us understand how individual genes interact in a functional network. Computable representations of biological pathways include detailed process descriptions in the Reactome Knowledgebase and causal activity flows between molecular functions in Gene Ontology-Causal Activity Models (GO-CAMs). A computational process has been developed to convert Reactome pathways to GO-CAMs. Laboratory mice are widely used models of normal and pathological human processes. We have converted human Reactome GO-CAMs to orthologous mouse GO-CAMs, as a resource to transfer pathway knowledge between humans and model organisms. These mouse GO-CAMs allowed us to define sets of genes that function in a causally connected way. To demonstrate that individual variant genes from connected pathways result in similar but distinguishable phenotypes, we used the genes in our pathway models to cross-query mouse phenotype annotations in the Mouse Genome Database (MGD). Using GO-CAM representations of 2 related but distinct pathways, gluconeogenesis and glycolysis, we show that individual causal paths in gene networks give rise to discrete phenotypic outcomes resulting from perturbations of glycolytic and gluconeogenic genes. The accurate and detailed descriptions of gene interactions recovered in this analysis of well-studied processes suggest that this strategy can be applied to less well-understood processes in less well-studied model systems to predict phenotypic outcomes of novel gene variants and to identify potential gene targets in altered processes.

Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting from Mutations in Pathways

Gene inactivation can affect the process(es) in which that gene acts and causally downstream ones, yielding diverse mutant phenotypes. Identifying the genetic pathways resulting in a given phenotype helps us understand how individual genes interact in a functional network. Computable representations of biological pathways include detailed process descriptions in the Reactome Knowledgebase, and causal activity flows between molecular functions in Gene Ontology-Causal Activity Models (GO-CAMs). A computational process has been developed to convert Reactome pathways to GO-CAMs. Laboratory mice are widely used models of normal and pathological human processes. We have converted human Reactome GO-CAMs to orthologous mouse GO-CAMs, as a resource to transfer pathway knowledge between humans and model organisms. These mouse GO-CAMs allowed us to define sets of genes that function in a connected and well-defined way. To test whether individual genes from well-defined pathways result in similar and distinguishable phenotypes, we used the genes in our pathway models to cross-query mouse phenotype annotations in the Mouse Genome Database (MGD). Using GO-CAM representations of two related but distinct pathways, gluconeogenesis and glycolysis, we can identify causal paths in gene networks that give rise to discrete phenotypic outcomes for perturbations of glycolysis and gluconeogenesis. The accurate and detailed descriptions of gene interactions recovered in this analysis of well-studied processes suggest that this strategy can be applied to less well-understood processes in less well-studied model systems to predict phenotypic outcomes of novel gene variants and to identify potential gene targets in altered processes.

Changes in children's anger, sadness, and persistence across blocked goals: Implications for self-regulation

The current study took a person-centered approach to examine the heterogeneity of changes in children's emotions and persistence during a goal-blocking task and examined how different profiles of emotions and persistence related to children's self-regulation. Children's anger, sadness, and persistence were rated in a goal-blocking task in toddlerhood (T1; N = 140, 72 boys, M_age  = 2.67 years, 90.7% White) and preschool (T2). Children's self-regulation, specifically sustained attention and engagement, was assessed at T1, T2, and early school-age (T3) from 2005 to 2012. Growth mixture modeling revealed two classes of children at T1 and three classes at T2 with different patterns of anger, sadness, and persistence. Children's classification at T2, but not T1, significantly predicted their sustained attention and engagement both concurrently and longitudinally.

Longitudinal bidirectional relations between children’s negative affectivity and maternal emotion expressivity

Although children’s negative affectivity is a temperamental characteristic that is biologically based, it is framed within and shaped by their emotional environments which are partly created by maternal emotion expressivity in the family. Children, in turn, play a role in shaping their family emotional context, which could lead to changes in mothers’ emotion expressivity in the family. However, these theorized longitudinal bidirectional relations between child negative affectivity and maternal positive and negative expressivity have not been studied from toddlerhood to early school-age. The current study utilized a cross-lagged panel model to examine the reciprocal relations between children’s negative affectivity and maternal expressivity within the family over the course of early childhood. Participants were 140 mother–child dyads (72 boys, mean age = 2.67 years, primarily White). Mothers reported the positive and negative expressivity in the family and children’s negative affectivity in toddlerhood (T1), preschool (T2), and school-age (T3). Maternal negative expressivity and child negative affectivity at T1 were significantly correlated. Maternal negative expressivity at T1 significantly predicted child negative affectivity at T3. Children’s negative affectivity at T2 significantly predicted mothers’ negative expressivity at T3. Mothers’ positive expressivity was not related to children’s negative affectivity at any of the three time points. The findings demonstrate the reciprocal relations between children’s negative affectivity and maternal negative expressivity in the family, suggesting the importance of the interplay between child temperament and maternal expressivity within the family emotional context.

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Advances in Behavioral Remote Data Collection in the Home Setting: Assessing the Mother-Infant Relationship and Infant's Adaptive Behavior via Virtual Visits

Psychological science is struggling with moving forward in the midst of the COVID-19 pandemic, especially due to the halting of behavioral data collection in the laboratory. Safety barriers to assessing psychological behavior in person increased the need for remote data collection in natural settings. In response to these challenges, researchers, including our team, have utilized this time to advance remote behavioral methodology. In this article, we provide an overview of our group’s strategies for remote data collection methodology and examples from our research in collecting behavioral data in the context of psychological functioning. Then, we describe the design and development of our strategies for remote data collection of mother-infant interactions, with the goal being to assess maternal sensitivity and intrusiveness, as well as infants’ adaptive behaviors in several developmental domains. During these virtual visits over Zoom, mother-infant dyads watched a book-reading video and were asked to participate in peek-a-boo, toy play, and toy removal tasks. After the behavioral tasks, a semi-structured interview (Vineland Adaptive Behavior Scale – VABS III) was conducted to assess the infant’s adaptive behavior in communication, socialization, daily living skills, and motor domains. We delineate the specific strategies we applied to integrate laboratory tasks and a semi-structured interview into remote data collection in home settings with mothers and infants. We also elaborate on issues encountered during remote data collection and how we resolved these challenges. Lastly, to inform protocols for future remote data collection, we address considerations and recommendations, as well as benefits and future directions for behavioral researchers in developmental psychology research.

Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource

Recombinase alleles and transgenes can be used to facilitate spatio-temporal specificity of gene disruption or transgene expression. However, the versatility of this in vivo recombination system relies on having detailed and accurate characterization of recombinase expression and activity to enable selection of the appropriate allele or transgene. The CrePortal (http://www.informatics.jax.org/home/recombinase) leverages the informatics infrastructure of Mouse Genome Informatics to integrate data from the scientific literature, direct data submissions from the scientific community at-large, and from major projects developing new recombinase lines and characterizing recombinase expression and specificity patterns. Searching the CrePortal by recombinase activity or specific recombinase gene driver provides users with a recombinase alleles and transgenes activity tissue summary and matrix comparison of gene expression and recombinase activity with links to generation details, a recombinase activity grid, and associated phenotype annotations. Future improvements will add cell type-based activity annotations. The CrePortal provides a comprehensive presentation of recombinase allele and transgene data to assist researchers in selection of the recombinase allele or transgene based on where and when recombination is desired.

The mouse Gene Expression Database (GXD): 2019 update

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD's gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities.

Mouse Genome Database (MGD) 2019

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN's FANTOM 5 initiative.

Parenting and Children's Executive Function Stability Across the Transition to School

When children transition to school between the ages of 4 and 6 years, they must learn to control their attention and behavior to be successful. Concurrently, executive function (EF) is an important skill undergoing significant development in childhood. To understand changes occurring during this period, we examined the role of parenting in the development of children's EF from 4 to 6 years old. Participants were mother and child dyads (N = 151). Children completed cognitive tasks to assess overall EF at age 4 and age 6. At both time points, mothers and children completed interaction tasks which were videotaped and coded to assess various parenting dimensions. Results indicated that children with high EF at age 4 were more likely to have high EF at age 6. In addition, results suggested that higher levels of positive parenting across the transition to school promote stability of individual differences in EF.

Context of Maternal Intrusiveness During Infancy and Associations with Preschool Executive Function

The relation between maternal behavior and neurocognitive development is complex and may depend on the task context. We examined 5-month-old infant frontal EEG, maternal intrusiveness (MI) evaluated during two play contexts at 5 and 10 months, and a battery of executive function (EF) tasks completed at 48 months to evaluate if MI during infancy and infant neural function interacted to predict later cognition. Infant frontal EEG was a predictor of 4-year EF. MI during structured play at both 5 and 10 months predicted preschool EF, and MI during unstructured did not have a main effect on EF but showed a potential moderating effect of infant EEG on later EF. The pattern changed between ages, with MI during structured play at 5 months showing a positive association with age 4 EF, whereas MI during structured play at 10 months had a negative association with age 4 EF. We demonstrate differences in the context of maternal behavior used to predict childhood EF, highlighting the importance of considering parenting context in EF development.

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the key community mouse database which supports basic, translational and computational research by providing integrated data on the genetics, genomics, and biology of the laboratory mouse. MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology and disease. We report here on recent enhancements to this resource, including improved access to mouse disease model and human phenotype data and enhanced relationships of mouse models to human disease.

Infant frontal EEG asymmetry moderates the association between maternal behavior and toddler negative affectivity

Relatively little work has examined potential interactions between child intrinsic factors and extrinsic environmental factors in the development of negative affect in early life. This work is important because high levels of early negative affectivity have been associated with difficulties in later childhood adjustment. We examined associations between infant frontal electroencephalogram (EEG), maternal parenting behaviors, and children's negative affect across the first two years of life. Infant baseline frontal EEG asymmetry was measured at 5 months; maternal sensitivity and intrusiveness were observed during mother-child interaction at 5 and 24 months; and mothers provided reports of toddler negative affect at 24 months. Results indicated that maternal sensitive behaviors at 5 months were associated with less negative affect at 24 months, but only for infants with left frontal EEG asymmetry. Similarly, maternal sensitive behaviors at 24 months were associated with less toddler negative affect at 24 months, but only for infants with left frontal EEG asymmetry. In contrast, maternal intrusive behaviors at 5- and 24-months were associated with greater toddler negative affect, but only for infants with right frontal EEG asymmetry at 5-months. Findings suggest that levels of negative affect in toddlers may be at least partially a result of interactions between children's own early neurophysiological functioning and maternal behavior during everyday interactions with children in the first two years of life.

Patterns of parental emotion-related discourse and links with children's problem behaviors: A person-centered approach

Research demonstrates that parents' emotion-related discourse during reminiscing shapes children's psychosocial outcomes, yet little is known about how different forms of parental emotion-related discourse work in combination. The present study takes a person-centered approach to better understand the relation of multiple forms of parental emotion discourse during reminiscing with problem behaviors in early childhood, as well as child influences on parents' emotion discourse during reminiscing. Specifically, we simultaneously examine three forms of parents' emotion-related discourse (emotion coaching and dismissing, emotion explanations, and elaboration) using cluster analysis to determine parents' patterns of these three discourse forms during discussion about past events. Parents and their preschool-aged children (n = 154) completed a parent-child reminiscing task. Transcripts were coded for emotion coaching and dismissing, emotion explanations, and elaboration. Parents reported on children's internalizing and externalizing behaviors, temperament, and gender, and children completed a language assessment. Cluster analyses revealed three parental discourse patterns: elaboration/negative emotion emphasis, positive and negative emotion emphasis, and low emotion discourse. Children's receptive language was associated with parents' membership in the low emotion discourse cluster. Children's temperament and gender were unrelated to parental emotion-related discourse patterns. Parents in the positive and negative emotion emphasis cluster had children with fewer internalizing behaviors compared to both other clusters, and parents in the elaboration/negative emotion emphasis cluster had children with more internalizing behaviors compared to both other clusters. Findings support the utility of a person-centered approach in providing a holistic view of parents' use of multiple emotion socialization strategies during reminiscing. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Intergenerational transmission of maternal emotion regulation to child emotion regulation: Moderated mediation of maternal positive and negative emotions

Research on maternal socialization of child emotion regulation often involves measures of general parenting, yet little research has considered how maternal emotion regulation and emotion expressivity relate to children's ability to regulate their emotions. Because emotion regulation can be viewed as intergenerational, mothers who display higher levels of positive emotions and lower levels of negative emotions may create a more optimal emotional climate for children to learn and practice emotion regulation, aiding in the intergenerational transmission of optimal emotion regulation. We tested a mediation model where maternal positive expressivity was hypothesized to mediate the relation of maternal emotion regulation to child emotion regulation. We also examined maternal negative expressivity as a moderator of the association of maternal positive expressivity to child emotion regulation. Maternal emotion regulation, measured as the use of reappraisal, and maternal expressivity were self-reported when children were 4-5 years old (T1). Child emotion regulation, measured as effortful control, was observed at T1. When children were 8-9 years old (T2), a summary score of child emotion regulation was computed from observed and teacher-reported effortful control. Higher levels of maternal reappraisal were related to more maternal positive expressivity, which in turn was associated with better child emotion regulation (T2), controlling for prior levels of child regulation (T1), only when maternal negative expressivity was low. This longitudinal moderated mediation pathway suggests that adaptive emotion regulation strategies used by mothers can be transmitted to children through maternal emotional expressions, specifically the interplay of positive and negative emotions. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Maternal behaviors in toddlerhood as predictors of children's private speech in preschool

Private speech is an important strategy reflecting children's self-regulation, and thus understanding how parenting may support private speech can inform intervention work on improving self-regulation. The current study longitudinally investigated how sensitive parenting and directive parenting in toddlerhood interacted to predict preschoolers' private speech in an emotion-eliciting task. In toddlerhood, maternal parenting behaviors were observed during two freeplay sessions. Preschoolers' social and private speech were transcribed and coded during a frustration task. Whereas parenting did not relate to other forms of private speech, preschoolers' facilitative task-relevant private speech was predicted by the interaction of mothers' sensitive and directive behaviors. When sensitivity was high, parents who were less directive had children who used more facilitative task-relevant private speech. These findings highlight that children's regulation may be supported through the combination of high sensitivity and low directiveness when parents and children are engaged in unstructured play together.

Disease Ontology: improving and unifying disease annotations across species

Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integrating relevant model organism and/or human data often apply disparate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained. The Mouse Genome Database (MGD, http://www.informatics.jax.org), Rat Genome Database (RGD, http://rgd.mcw.edu) and Disease Ontology (DO, http://www.disease-ontology.org) projects are collaborating to augment DO, aligning and incorporating disease terms used by MGD and RGD, and improving DO as a tool for unifying disease annotations across species. Coordinated assessment of MGD's and RGD's disease term annotations identified new terms that enhance DO's representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO's domain coverage and utility for annotating many types of data generated from experimental and clinical investigations. The extension of anatomy-based DO classification structure of disease improves accessibility of terms and facilitates application of DO for computational research. A consistent representation of disease associations across data types from cellular to whole organism, generated from clinical and model organism studies, will promote the integration, mining and comparative analysis of these data. The coordinated enrichment of the DO and adoption of DO by MGD and RGD demonstrates DO's usability across human data, MGD, RGD and the rest of the model organism database community.

Summary: Analyzing diverse disease data requires a comprehensive, robust disease ontology to integrate annotations and retrieve accurate, interpretable results. MGD, RGD and DO are working in collaboration to achieve this goal.

The Vertical Dust Profile over Gale Crater, Mars

We create a vertically coarse, but complete, vertical profile of dust mixing ratio from the surface to the upper atmosphere over Gale Crater, Mars, using the frequent joint atmospheric observations of the orbiting Mars Climate Sounder (MCS) and the Mars Science Laboratory (MSL) Curiosity rover. Using these data and an estimate of planetary boundary layer (PBL) depth from the MarsWRF general circulation model, we divide the vertical column into three regions. The first region is the Gale Crater PBL, the second is the MCS-sampled region, and the third is between these first two. We solve for a well-mixed dust mixing ratio within this third (middle) layer of atmosphere to complete the profile. We identify a unique seasonal cycle of dust within each atmospheric layer. Within the Gale PBL, dust mixing ratio maximizes near southern hemisphere summer solstice (L_s = 270°) and minimizes near winter solstice (L_s = 90-100°) with a smooth sinusoidal transition between them. However, the layer above Gale Crater and below the MCS-sampled region more closely follows the global opacity cycle and has a maximum in opacity near L_s = 240° and exhibits a local minimum (associated with the "solsticial pause" in dust storm activity) near L_s = 270°. With knowledge of the complete vertical dust profile, we can also assess the frequency of high-altitude dust layers over Gale. We determine that 36% of MCS profiles near Gale Crater contain an "absolute" high-altitude dust layer wherein the dust mixing ratio is the maximum in the entire vertical column.

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.

Parenting, anger, and effortful control as predictors of child externalizing behavior

Externalizing behaviors observed in early childhood have been found to be stable, particularly for boys, but little research has investigated the antecedents of these behaviors, especially how the antecedents may differentially relate to externalizing behaviors in boys and girls. The goal of this study was to explore predictors of externalizing behaviors concurrently in toddlerhood and longitudinally to preschool. When children ( n = 140) were 30–36 months old, maternal supportive and controlling behaviors were observed, and children’s effortful control and anger were measured through observations and maternal report. Mothers reported on children’s externalizing behavior during toddlerhood and approximately 2 years later ( n = 116). Although mean level differences were not found between boys and girls, effortful control was differentially related to externalizing behaviors in toddlerhood. Higher levels of effortful control were associated with less externalizing behaviors for boys but not for girls. Additionally, anger was positively related to externalizing behaviors. Few associations were found for maternal behaviors, which emphasizes the importance of child characteristics in externalizing behaviors. Our findings emphasize how future research should continue to examine relations of early antecedents to concurrent and later externalizing behaviors even if mean level sex differences are not found.

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research

The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.

The Human Phenotype Ontology in 2017

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge. Here, we report on recent enhancements made to the resource and new features.

Infant frontal electroencephalogram asymmetry and negative emotional reactivity as predictors of toddlerhood effortful control

Given the importance of children's self-regulation, relations were examined between two fundamental components of self-regulation, specifically temperamentally based reactivity and regulation. Infant negative emotional reactivity and regulation, measured via frontal electroencephalogram (EEG) asymmetry, were examined as potential precursors to understanding toddlerhood regulation, conceptualized as effortful control. Our longitudinal design allowed for examination of two perspectives on the interplay of reactivity and regulation, namely that (a) early negative affectivity interferes with the development of later regulation and (b) regulation is necessary to modulate negative affectivity and, thus, would buffer the effects of negative affectivity on later regulation. Mother-child dyads participated in a three-wave longitudinal study. Baseline frontal EEG asymmetry was assessed at 10months (T1). Mothers rated children's negative reactivity at both 10 and 24months (T2). Children's effortful control, measured at 30-36months (T3), was a composite score of maternal ratings and observed behavior during a snack delay. Negative affectivity was related to effortful control; however, significant interactions between negative affect and frontal EEG asymmetry were found. Higher levels of negative affectivity at both T1 and T2 were associated with lower levels of effortful control at T3, but only for toddlers who also had right frontal EEG asymmetry. Negative affectivity was not associated with effortful control for the left frontal EEG asymmetry group. Our moderation findings highlight the complex relations of negative affect and frontal EEG asymmetry in understanding children's development of self-regulation, specifically effortful control. The interaction between early reactivity and physiological regulation indicates that both may be important precursors of effortful control.

The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources

The availability of and access to quality genetically defined, health-status known mouse resources is critical for biomedical research. By ensuring that mice used in research experiments are biologically, genetically, and health-status equivalent, we enable knowledge transfer, hypothesis building based on multiple data streams, and experimental reproducibility based on common mouse resources (reagents). Major repositories for mouse resources have developed over time and each has significant unique resources to offer. Here we (a) describe The International Mouse Strain Resource that offers users a combined catalog of worldwide mouse resources (live, cryopreserved, embryonic stem cells), with direct access to repository sites holding resources of interest and (b) discuss the commitment to nomenclature standards among resources that remain a challenge in unifying mouse resource catalogs.

Mouse Genome Database: From sequence to phenotypes and disease models

The Mouse Genome Database (MGD, www.informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements of the biomedical community. To accomplish this goal, MGD provides broad data coverage, serves as the authoritative standard for mouse nomenclature for genes, mutants, and strains, and curates and integrates many types of data from literature and electronic sources. Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO) annotations for mouse gene functions, a comprehensive catalog of mouse mutations and their phenotypes, and a curated compendium of mouse models of human diseases. Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities. genesis 53:458–473, 2015. © 2015 The Authors. Genesis Published by Wiley Periodicals, Inc.

Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis

A core part of the Mouse Genome Informatics (MGI) resource is the collection of mouse mutations and the annotation phenotypes and diseases displayed by mice carrying these mutations. These data are integrated with the rest of data in MGI and exported to numerous other resources. The use of mouse phenotype data to drive translational research into human disease has expanded rapidly with the improvements in sequencing technology. MGI has implemented many improvements in allele and phenotype data annotation, search, and display to facilitate access to these data through multiple avenues. For example, the description of alleles has been modified to include more detailed categories of allele attributes. This allows improved discrimination between mutation types. Further, connections have been created between mutations involving multiple genes and each of the genes overlapping the mutation. This allows users to readily find all mutations affecting a gene and see all genes affected by a mutation. In a similar manner, the genes expressed by transgenic or knock-in alleles are now connected to these alleles. The advanced search forms and public reports have been updated to take advantage of these improvements. These search forms and reports are used by an expanding number of researchers to identify novel human disease genes and mouse models of human disease.

Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

BACKGROUND

A vast array of data is about to emerge from the large scale high-throughput mouse knockout phenotyping projects worldwide. It is critical that this information is captured in a standardized manner, made accessible, and is fully integrated with other phenotype data sets for comprehensive querying and analysis across all phenotype data types. The volume of data generated by the high-throughput phenotyping screens is expected to grow exponentially, thus, automated methods and standards to exchange phenotype data are required.

RESULTS

The IMPC (International Mouse Phenotyping Consortium) is using the Mammalian Phenotype (MP) ontology in the automated annotation of phenodeviant data from high throughput phenotyping screens. 287 new term additions with additional hierarchy revisions were made in multiple branches of the MP ontology to accurately describe the results generated by these high throughput screens.

CONCLUSIONS

Because these large scale phenotyping data sets will be reported using the MP as the common data standard for annotation and data exchange, automated importation of these data to MGI (Mouse Genome Informatics) and other resources is possible without curatorial effort. Maximum biomedical value of these mutant mice will come from integrating primary high-throughput phenotyping data with secondary, comprehensive phenotypic analyses combined with published phenotype details on these and related mutants at MGI and other resources.

Global genetic analysis in mice unveils central role for cilia in congenital heart disease

Congenital heart disease (CHD) is the most prevalent birth defect, affecting nearly 1% of live births; the incidence of CHD is up to tenfold higher in human fetuses. A genetic contribution is strongly suggested by the association of CHD with chromosome abnormalities and high recurrence risk. Here we report findings from a recessive forward genetic screen in fetal mice, showing that cilia and cilia-transduced cell signalling have important roles in the pathogenesis of CHD. The cilium is an evolutionarily conserved organelle projecting from the cell surface with essential roles in diverse cellular processes. Using echocardiography, we ultrasound scanned 87,355 chemically mutagenized C57BL/6J fetal mice and recovered 218 CHD mouse models. Whole-exome sequencing identified 91 recessive CHD mutations in 61 genes. This included 34 cilia-related genes, 16 genes involved in cilia-transduced cell signalling, and 10 genes regulating vesicular trafficking, a pathway important for ciliogenesis and cell signalling. Surprisingly, many CHD genes encoded interacting proteins, suggesting that an interactome protein network may provide a larger genomic context for CHD pathogenesis. These findings provide novel insights into the potential Mendelian genetic contribution to CHD in the fetal population, a segment of the human population not well studied. We note that the pathways identified show overlap with CHD candidate genes recovered in CHD patients, suggesting that they may have relevance to the more complex genetics of CHD overall. These CHD mouse models and >8,000 incidental mutations have been sperm archived, creating a rich public resource for human disease modelling.

Invariant natural killer T cells in children with eosinophilic esophagitis

BACKGROUND

Eosinophilic esophagitis (EoE) is an atopic disease characterized by eosinophilic inflammation in which dietary antigens (in particular, milk) play a major role. EoE is most likely a mixed IgE and non-IgE food-mediated reaction in which overexpression of Th2 cytokines, particularly IL-13, play a major role; however, the cells responsible for IL-13 overexpression remain elusive. Th2-cytokines are secreted following the ligation of invariant natural killer T cell receptors to sphingolipids (SLs). Sphingolipids (SLs) are presented via the CD1d molecule on the INKTs surface. Cow's milk-derived SL has been shown to activate iNKTs from children with IgE-mediated food allergies to milk (FA-MA) to produce Th2 cytokines. The role of iNKTs and milk-SL in EoE pathogenesis is currently unknown.

OBJECTIVE

The aim of this study was to investigate the role of iNKTs and milk-SL in EoE.

METHODS

Peripheral blood mononuclear cells (PBMCs) from 10 children with active EoE (EoE-A), 10 children with controlled EoE (EoE-C) and 16 healthy controls (non-EoE) were measured ex vivo and then incubated with α-galactosylceramide (αGal) and milk-SL. INKTs from peripheral blood (PB) and oesophageal biopsies were studied.

RESULTS

EoE-A children had significantly fewer peripheral blood iNKTs with a greater Th2-response to αGal and milk-SM compared with iNKTs of EoE-C and non-EoE children. Additionally, EoE-A children had increased iNKT levels in oesophageal biopsies compared with EoE-C children.

CONCLUSION

Milk-SLs are able to activate peripheral blood iNKTs in EoE-A children to produce Th2 cytokines. Additionally, iNKT levels are higher at the site of active oesophageal eosinophilic inflammation.

CLINICAL RELEVANCE

This study suggests that sphingolipids (SLs) contained in milk may drive the development of EoE by promoting an iNKT-cell-mediated Th2-type cytokine response that facilitates eosinophil-mediated allergic inflammation.

Metal and nutrient dynamics on an aged intensive green roof

Runoff and rainfall quality was compared between an aged intensive green roof and an adjacent conventional roof surface. Nutrient concentrations in the runoff were generally below Environmental Quality Standard (EQS) values and the green roof exhibited NO3(-) retention. Cu, Pb and Zn concentrations were in excess of EQS values for the protection of surface water. Green roof runoff was also significantly higher in Fe and Pb than on the bare roof and in rainfall. Input-output fluxes revealed the green roof to be a potential source of Pb. High concentrations of Pb within the green roof soil and bare roof dusts provide a potential source of Pb in runoff. The origin of the Pb is likely from historic urban atmospheric deposition. Aged green roofs may therefore act as a source of legacy metal pollution. This needs to be considered when constructing green roofs with the aim of improving pollution remediation.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.

Extensive epidermal naevus in a foal

CASE REPORT

A 2-month-old Standardbred filly was presented for examination and treatment of extensive congenital skin lesions that had a linear distribution on the left front leg extending from the dorsal midline to the metacarpal region. The lesions were surgically excised under general anaesthesia. Surgical excision was curative and there were no signs of recurrence 6 weeks after surgery. The number and distribution of lesions were more extensive than in previously reported cases of congenital papillomas, which have also been described as epidermal growth abnormalities (naevi or hamartomas). Early reports of congenital papillomas suggest in-utero infection with papillomavirus may be responsible, despite a lack of histological features associated with papillomavirus infection. Papillomavirus immunohistochemistry has subsequently proven negative in tested cases.

CONCLUSIONS

The presence at birth, their appearance and the extensive distribution of lesions in this case is similar to verrucous epidermal naevus of humans. A name change from congenital papilloma to epidermal naevus is proposed for this condition in horses.