dictyBase--a Dictyostelium bioinformatics resource update.

dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations.

Methodological Issues and the Impact of Age Stratification on the Proportion of Participants with Low Appendicular Lean Mass When Adjusting for Height and Fat Mass Using Linear Regression: Results from the Canadian Longitudinal Study on Aging.

BACKGROUND: Using residual values calculated from models regressing appendicular lean mass on fat mass and height is one of several suggested strategies for adjusting appendicular lean mass for body size when measuring sarcopenia. However, special consideration is required when using this technique in different subgroups in order to capture the correct individuals as sarcopenic. OBJECTIVES: To provide guidance about how to conduct stratified analyses for the regression adjustment technique using age groups as an example. DESIGN: Cross-sectional study. SETTING: Data collected at baseline (2012-2015) for the Canadian Longitudinal Study on Aging. PARTICIPANTS: Community dwelling participants of European descent aged 45 to 85 years (n=25,399). MEASUREMENTS: Appendicular lean mass, height, and weight were measured. Sex-specific residuals were calculated in participants before and after stratifying participants by age group (45-54, 55-64, 65-74, 75-85 years). Cut offs corresponding to the sex-specific 20th percentile residual values in participants ≥65 years were determined first in the residuals calculated in all participants and residuals calculated in only those aged ≥65 years. For each set of cut offs, the percentage of age and sex-stratified participants with low appendicular lean mass were compared for the residuals calculated in all participants and the residuals calculated after stratifying by age. RESULTS: In 12,622 males and 12,737 females, regardless of the cut off used, the percentage of participants with low appendicular lean mass decreased with age when residuals were calculated after age stratification. When the residuals were calculated in all participants, the percentage of participants with sarcopenia increased from the youngest to the oldest age groups. CONCLUSIONS: Sex-specific residuals in all participants should be calculated prior to stratifying the sample by age group, or other stratification variables, for the purposes of developing appendicular lean mass cut offs or subgroup analyses.

dictyBase, the model organism database for Dictyostelium discoideum.

dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes.