An Analysis of Providers’ Perceived Barriers to Contraceptive Access and Reproductive Healthcare

The field of Reproductive Healthcare covers nearly every aspect of women’s health. Even during non-reproductive years, Reproductive Healthcare is important for women because it provides medical care often essential to their lives before and after child-bearing years. Contraception is needed by many women before they wish to have children, and after they have any children they choose to have, they may again wish to use contraception or they may require help with postpartum care. One of many reasons why Reproductive Healthcare is so important is because it explains the wide array of options available when it comes to methods of contraception. Despite the large variety of methods available, women are often unable to obtain their preferred method. In order to discover why this is, several states including Vermont … created surveys asking providers to identify the biggest and most significant barriers their patients face when seeking Reproductive Healthcare. Until just recently, Rhode Island had no such data. This project is an in depth analysis of the data gathered from the provider survey distributed by the Rhode Island Department of Health. Many factors were compared in hopes of finding correlations between factors affecting reproductive health and contraception

Implementing Peer Observation of Teaching. A Formative Staff Develpment Initiative

For higher education institutions in Ireland, the call for improved efficiency and accountability to stakeholders in all areas of activity has never been more prominent than today. Reform initiatives are taking place across the sector and a key focus of this reformation is the quality assurance and quality enhancement of teaching activity, and the professional development of teaching staff. Peer observation of teaching is widely accepted as a mode of enhancing teaching practice and as a conduit for staff development. This change project centres on the implementation of a pilot of peer observation of teaching within a higher education institution and describes the process enacted when implementing the pilot project. Guided by the framework of the HSE Change Model the change process is described and its strengths and limitations acknowledged. The perceptions and experiences of participants in the pilot project are evaluated using the Jacobs Model of Evaluation. A survey of 66 teaching staff was conducted to elicit staff perceptions of peer observation of teaching. Staff volunteers participated in an education workshop and then undertook one peer observation, five acting as observers and 5 acting as observees. Their experiences were captured in focus groups interviews (n=7). The results indicate that staff would like to see peer observation of teaching introduced and that they value the formative, developmental model, as evidenced in the literature. Finally an informed basis for introducing a formative model of peer observation of teaching into the institution that consolidates the findings of this study is proposed

Molecular evolutionary analysis of nematode Zona Pellucida (ZP) modules reveals disulfide-bond reshuffling and standalone ZP-C domains

This is the author accepted manuscript. The final version is available on open access from Oxford University Press via the DOI in this recordZona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. While some biomedically-relevant ZP modules are well-studied, little is known about the protein family’s broad-scale diversity and evolution. The increasing availability of sequenced genomes from “non-model” systems provides a valuable opportunity to address this issue, and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains—which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation—can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.Royal Societ

Entangled Plants and Property: A Landscape of Gardens and Alleys

The primacy of private property, and its incumbent rights, structures who has access to space in the city and who can be displaced. This regime of property includes not only theoretical and legal underpinnings of property and space in the city, but also the narratives and normative understandings necessary to support this institution. This thesis looks towards denaturalizing private property as the only conceivable way of organizing space (Macpherson, 1978). The act of gardening has long been linked to claiming property, while domestic gardens have been characterized as both paradoxical spaces (Longhurst, 2013) and liminal zones (Blomley, 2004c). I look at the ways that supposedly rigid boundaries of property are entangled, transgressed, and blurred through everyday interactions between people and plants in the gardens and alleys of the Parc Extension neighbourhood in Montréal. This study is a personal reflection on gardening practice along the boundaries of public and private. I draw from my own gardening experience, conversations with neighbours, photographs, alley walking, and interactions with plants to make the case that lived experience in gardens is far more complex than normative understandings linked to property suggest. Further, I argue that by exploring the entanglements of property and plants in the landscape of gardens and alleys, we can find lived experiences that contradict harmful assumptions bound up in private property; assumptions that see tenants as incapable of improving property and that link tenancy, migrancy, and disorder

Long-wavelength sensitive visual pigments of the guppy (Poecilia reticulata): six opsins expressed in a single individual

BACKGROUND: The diversity of visual systems in fish has long been of interest for evolutionary biologists and neurophysiologists, and has recently begun to attract the attention of molecular evolutionary geneticists. Several recent studies on the copy number and genomic organization of visual pigment proteins, the opsins, have revealed an increased opsin diversity in fish relative to most vertebrates, brought about through recent instances of opsin duplication and divergence. However, for the subfamily of opsin genes that mediate vision at the long-wavelength end of the spectrum, the LWS opsins, it appears that most fishes possess only one or two loci, a value comparable to most other vertebrates. Here, we characterize the LWS opsins from cDNA of an individual guppy, Poecilia reticulata, a fish that is known exhibit variation in its long-wavelength sensitive visual system, mate preferences and colour patterns. RESULTS: We identified six LWS opsins expressed within a single individual. Phylogenetic analysis revealed that these opsins descend from duplication events both pre-dating and following the divergence of the guppy lineage from that of the bluefin killifish, Lucania goodei, the closest species for which comparable data exists. Numerous amino acid substitutions exist among these different LWS opsins, many at sites known to be important for visual pigment function, including spectral sensitivity and G-protein activation. Likelihood analyses using codon-based models of evolution reveal significant changes in selective constraint along two of the guppy LWS opsin lineages. CONCLUSION: The guppy displays an unusually high number of LWS opsins compared to other fish, and to vertebrates in general. Observing both substitutions at functionally important sites and the persistence of lineages across species boundaries suggests that these opsins might have functionally different roles, especially with regard to G-protein activation. The reasons why are currently unknown, but may relate to aspects of the guppy's behavioural ecology, in which both male colour patterns and the female mate preferences for these colour patterns experience strong, highly variable selection pressures

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

Background: Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results: We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs), and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA- sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in a congeneric species, the sailfin molly (Poecilia latipinna). Over 40% of reads from the sailfin molly sample aligned to the guppy transcriptome. Conclusions: We show that next-generation sequencing provided a reliable and broad reference transcriptome. This resource allowed us to identify candidate gene variants, SNPs in coding regions, and sex-specific gene expression, and permitted quantitative analysis of differential gene expression

Duplicate dmbx1 genes regulate progenitor cell cycle and differentiation during zebrafish midbrain and retinal development

Abstract Background The Dmbx1 gene is important for the development of the midbrain and hindbrain, and mouse gene targeting experiments reveal that this gene is required for mediating postnatal and adult feeding behaviours. A single Dmbx1 gene exists in terrestrial vertebrate genomes, while teleost genomes have at least two paralogs. We compared the loss of function of the zebrafish dmbx1a and dmbx1b genes in order to gain insight into the molecular mechanism by which dmbx1 regulates neurogenesis, and to begin to understand why these duplicate genes have been retained in the zebrafish genome. Results Using gene knockdown experiments we examined the function of the dmbx1 gene paralogs in zebrafish, dmbx1a and dmbx1b in regulating neurogenesis in the developing retina and midbrain. Dose-dependent loss of dmbx1a and dmbx1b function causes a significant reduction in growth of the midbrain and retina that is evident between 48-72 hpf. We show that this phenotype is not due to patterning defects or persistent cell death, but rather a deficit in progenitor cell cycle exit and differentiation. Analyses of the morphant retina or anterior hindbrain indicate that paralogous function is partially diverged since loss of dmbx1a is more severe than loss of dmbx1b. Molecular evolutionary analyses of the Dmbx1 genes suggest that while this gene family is conservative in its evolution, there was a dramatic change in selective constraint after the duplication event that gave rise to the dmbx1a and dmbx1b gene families in teleost fish, suggestive of positive selection. Interestingly, in contrast to zebrafish dmbx1a, over expression of the mouse Dmbx1 gene does not functionally compensate for the zebrafish dmbx1a knockdown phenotype, while over expression of the dmbx1b gene only partially compensates for the dmbx1a knockdown phenotype. Conclusion Our data suggest that both zebrafish dmbx1a and dmbx1b genes are retained in the fish genome due to their requirement during midbrain and retinal neurogenesis, although their function is partially diverged. At the cellular level, Dmbx1 regulates cell cycle exit and differentiation of progenitor cells. The unexpected observation of putative post-duplication positive selection of teleost Dmbx1 genes, especially dmbx1a, and the differences in functionality between the mouse and zebrafish genes suggests that the teleost Dmbx1 genes may have evolved a diverged function in the regulation of neurogenesis

Convergent evolution of small molecule pheromones in pristionchus nematodes

This is the final version. Available from eLife Sciences Publications via the DOI in this recordData availability: All data generated during this study are included in the manuscript and supporting files. Source data files have been provided.The small molecules that mediate chemical communication between nematodes—so-called “nematode-derived-modular-metabolites” (NDMMs)—are of major interest due to their ability to regulate development, behavior, and life-history. Pristionchus pacificus nematodes produce an impressive diversity of structurally complex NDMMs, some of which act as primer pheromones capable of triggering irreversible developmental switches. Many of these NDMMs have only ever been found in P. pacificus but no attempts had been made to study their evolution by profiling closely related species. This study was designed to bring a comparative perspective to the biochemical study of NDMMs via the systematic MS/MS and NMR-based analysis of exo-metabolomes from over 30 Pristionchus species. We identified 36 novel compounds and found evidence for the convergent evolution of complex NDMMs in separate branches of the Pristionchus phylogeny. Our results demonstrate that biochemical innovation is a recurrent process in Pristionchus nematodes, a pattern likely typical across the animal kingdom.Max Planck Societ

Improved reference genome uncovers novel sex-linked regions in the Guppy (Poecilia reticulata)

This is the author accepted manuscript. The final version is available on open access from Oxford University Press via the DOI in this recordData availability: Population genomics data are available on ENA: Study: PRJEB10680 PCR-free data are available on ENA: Study PRJEB36450 Genome assembly is available on ENA ID: PRJEB36704; ERP119926 All scripts and pipelines are available on github: https://github.com/bfrasercommits/guppy_genomeTheory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.Max Planck SocietyEuropean Research Council (ERC)Natural Environment Research Council (NERC