BiocPkgTools: Toolkit for mining the package ecosystem.

The Bioconductor project, a large collection of open source software for the comprehension of large-scale biological data, continues to grow with new packages added each week, motivating the development of software tools focused on exposing package metadata to developers and users. The resulting BiocPkgTools package facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches. The BiocPkgTools package has been incorporated into the Bioconductor project, installs using standard procedures, and runs on any system supporting R.

Orchestrating a community-developed computational workshop and accompanying training materials.

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and analytical methods. Here, we detail the process we used to produce high-quality, community-authored educational materials that are available for public consumption and reuse.

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis.

Background: Cervicitis is an inflammatory condition of the cervix associated with upper genital tract infection and reproductive complications. Although cervicitis can be caused by several known pathogens, the etiology frequently remains obscure. Here we investigate vaginal bacteria associated with bacterial vaginosis as potential causes of cervicitis.

Metabolic signatures of bacterial vaginosis.

Unlabelled: Bacterial vaginosis (BV) is characterized by shifts in the vaginal microbiota from Lactobacillus dominant to a microbiota with diverse anaerobic bacteria. Few studies have linked specific metabolites with bacteria found in the human vagina. Here, we report dramatic differences in metabolite compositions and concentrations associated with BV using a global metabolomics approach.

More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis.

Bacterial vaginosis (BV) is a highly prevalent condition associated with adverse health outcomes. Gram stain analysis of vaginal fluid is the standard for confirming the diagnosis of BV, wherein abundances of key bacterial morphotypes are assessed. These Lactobacillus, Gardnerella, Bacteroides, and Mobiluncus morphotypes were originally linked to particular bacterial species through cultivation studies, but no studies have systematically investigated associations between uncultivated bacteria detected by molecular methods and Gram stain findings.

Software for computing and annotating genomic ranges.

We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors.

Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

Background: Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV.

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

Recent studies have demonstrated that MyoD initiates a feed-forward regulation of skeletal muscle gene expression, predicting that MyoD binds directly to many genes expressed during differentiation. We have used chromatin immunoprecipitation and high-throughput sequencing to identify genome-wide binding of MyoD in several skeletal muscle cell types. As anticipated, MyoD preferentially binds to a VCASCTG sequence that resembles the in vitro-selected site for a MyoD:E-protein heterodimer, and MyoD binding increases during differentiation at many of the regulatory regions of genes expressed in skeletal muscle.

The effect of self-fertilization, inbreeding depression, and population size on autopolyploid establishment.

The minority cytotype exclusion principle describes how random mating between diploid and autotetraploid cytotypes hinders establishment of the rare cytotype. We present deterministic and stochastic models to ascertain how selfing, inbreeding depression, unreduced gamete production, and finite population size affect minority cytotype exclusion and the establishment of autotetraploids. Results demonstrate that higher selfing rates and lower inbreeding depression in autotetraploids facilitate establishment of autotetraploid populations.

Self-fertilization and the escape from pollen limitation in variable pollination environments.

Seed production in many plants is pollen limited, likely because of unpredictable variation in the pollinator environment. One way for plants to escape the consequences of pollinator variability is to evolve mating systems, such as autonomous selfing, that assure reproduction without relying on pollinators. We explore this hypothesis through the construction and analysis of heuristic models of plant population dynamics in seed- or site-limited populations.

Plant population dynamics, pollinator foraging, and the selection of self-fertilization.

Many flowering plants rely on pollinators, self-fertilization, or both for reproduction. We model the consequences of these features for plant population dynamics and mating system evolution. Our mating systems-based population dynamics model includes an Allee effect.

Explaining phenotypic selection on plant attractive characters: male function, gender balance or ecological context?

It is widely agreed that the flowers of hermaphrodite plants evolve in response to selection acting simultaneously through male and female sexual functions, but we know very little about the pattern of gender-specific selection. We review three current hypotheses for gender-specific selection by viewing them within a single phenotypic selection framework. We compile data from phenotypic selection and manipulative studies and evaluate the fit between empirical data and the hypotheses.

Effects of natural rates of geitonogamy on fruit set in Asclepias speciosa (Apocynaceae): evidence favoring the plant's dilemma.

The role of geitonogamy in the evolution of inflorescence design is not well understood. The plant's dilemma hypothesis proposes that evolution of larger inflorescences is driven by selection for greater pollinator attraction, but constrained by higher rates of geitonogamy experienced by larger inflorescences. Here we investigate the role of geitonogamy on fruit set in natural populations of Asclepias speciosa.

Coevolution in temporally variable environments.

Many potentially mutualistic interactions are conditional, with selection that varies between mutualism and antagonism over space and time. We develop a genetic model of temporally variable coevolution that incorporates stochastic fluctuations between mutualism and antagonism. We use this model to determine conditions necessary for the coevolution of matching traits between a host and a conditional mutualist.

Patterns and mechanisms of selection on a family-diagnostic trait: evidence from experimental manipulation and lifetime fitness selection gradients.

Plant traits that show little variation across higher taxa are often used as diagnostic traits, but the reason for the stasis of such traits remains unclear. Wild radish, Raphanus raphanistrum, exhibits tetradynamous stamens (four long and two short, producing a dimorphism in anther height within each flower), as do the vast majority of the more than 3,000 species in the Brassicaceae. Here we examine the hypothesis that selection maintains the stasis of dimorphic anther height by investigating the effects of this trait on pollen removal, seed siring success, and seed set in R.

Evolution of a small-muscle polymorphism in lines of house mice selected for high activity levels.

To study the correlated evolution of locomotor behavior and exercise physiology, we conducted an artificial selection experiment. From the outbred Hsd:ICR strain of Mus domesticus, we began eight separate lines, each consisting of 10 breeding pairs. In four of the lines, we used within-family selection to increase voluntary wheel running.

ATTRACTIVE STRUCTURES AND THE STABILITY OF HERMAPHRODITIC SEX EXPRESSION IN FLOWERING PLANTS.

Plant attributes serving both male and female sex functions are thought to favor hermaphroditic breeding systems over systems where sex expression is separated between individuals. Morphological features used by plants to attract biotic pollinators can be considered in this light, because such "attractive" structures are prerequisite for both pollen donation and receipt. A model involving allocation of a limiting resource between attractive structures benefiting both sex functions, structures benefiting male function only, and structures benefiting female function only, is constructed and analyzed using the evolutionary stable strategy (ESS) approach.

THE DISSOLUTION OF A COMPLEX GENETIC POLYMORPHISM: THE EVOLUTION OF SELF-FERTILIZATION IN TRISTYLOUS EICHHORNIA PANICULATA (PONTEDERIACEAE).

Eichhornia paniculata (Pontederiaceae) displays a wide range of outcrossing levels as a result of the dissolution of the tristylous genetic polymorphism and the evolution of semihomostyly. Population surveys, comparison of fitness components of the style morphs, and computer simulations were used to investigate the breakdown of tristyly and the selective mechanisms responsible for the evolution of self-fertilization. Of 110 populations surveyed in northeast Brazil and Jamaica, 53% were trimorphic, 25% were dimorphic, and 22% were monomorphic for style morph.

HISTORICAL FACTORS AND ANISOPLETHIC POPULATION STRUCTURE IN TRISTYLOUS PONTEDERIA CORDATA: A REASSESSMENT.

Theoretical models of floral-morph frequencies in tristylous species predict a single equilibrium with all three morphs represented in equal proportions (isoplethy). North American populations of Pontederia cordata exhibit considerable heterogeneity of morph frequencies between populations, with the short-styled morph often in excess of isoplethic expectations and the long-styled morph commonly underrepresented. In a previous study, it was proposed that anisoplethic population structure in P.