40 research outputs found

    The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

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    <p>Abstract</p> <p>Background</p> <p>Most evolutionary developmental biology ("evo-devo") studies of emerging model organisms focus on small numbers of candidate genes cloned individually using degenerate PCR. However, newly available sequencing technologies such as 454 pyrosequencing have recently begun to allow for massive gene discovery in animals without sequenced genomes. Within insects, although large volumes of sequence data are available for holometabolous insects, developmental studies of basally branching hemimetabolous insects typically suffer from low rates of gene discovery.</p> <p>Results</p> <p>We used 454 pyrosequencing to sequence over 500 million bases of cDNA from the ovaries and embryos of the milkweed bug <it>Oncopeltus fasciatus</it>, which lacks a sequenced genome. This indirectly developing insect occupies an important phylogenetic position, branching basal to Diptera (including fruit flies) and Hymenoptera (including honeybees), and is an experimentally tractable model for short-germ development. 2,087,410 reads from both normalized and non-normalized cDNA assembled into 21,097 sequences (isotigs) and 112,531 singletons. The assembled sequences fell into 16,617 unique gene models, and included predictions of splicing isoforms, which we examined experimentally. Discovery of new genes plateaued after assembly of ~1.5 million reads, suggesting that we have sequenced nearly all transcripts present in the cDNA sampled. Many transcripts have been assembled at close to full length, and there is a net gain of sequence data for over half of the pre-existing <it>O. fasciatus </it>accessions for developmental genes in GenBank. We identified 10,775 unique genes, including members of all major conserved metazoan signaling pathways and genes involved in several major categories of early developmental processes. We also specifically address the effects of cDNA normalization on gene discovery in <it>de novo </it>transcriptome analyses.</p> <p>Conclusions</p> <p>Our sequencing, assembly and annotation framework provide a simple and effective way to achieve high-throughput gene discovery for organisms lacking a sequenced genome. These data will have applications to the study of the evolution of arthropod genes and genetic pathways, and to the wider evolution, development and genomics communities working with emerging model organisms.</p> <p>[The sequence data from this study have been submitted to GenBank under study accession number SRP002610 (<url>http://www.ncbi.nlm.nih.gov/sra?term=SRP002610</url>). Custom scripts generated are available at <url>http://www.extavourlab.com/protocols/index.html</url>. Seven Additional files are available.]</p

    Multidimensional Aspects of Social Networks: Implications for CPS Recurrence

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    This study examines the social network characteristics of 670 mothers reported to and investigated by the child protection system (CPS) in Milwaukee County, Wisconsin in 2016. Specifically, having a recurrent CPS investigation within one year of an index investigation that did not result in an ongoing CPS case is assessed as a function of positive social network ties, negative social network ties, and perceived neighborhood support. Few studies have explored these aspects of social networks comparatively and simultaneously in relation to CPS outcomes, or within this population. We used cluster analysis to identify particular combinations of network characteristics among mothers with recent investigations and then examined whether different cluster types are predictive of recurrent CPS involvement within one year. Clusters differed on the perceived levels of both positive and negative interpersonal ties as well as perceived neighborhood support and were associated with different levels of known child maltreatment risk factors. Clusters with lower levels of perceived neighborhood support were more likely to be associated with future CPS investigations, but this association becomes statistically insignificant when controlling for mothers’ depressive symptoms. The results of this study suggest that a more multi-faceted view of social networks can be helpful to understand the social contexts of mothers as they experience contact with CPS and raises questions about how these contexts interact with parental mental health in relation to CPS recurrence
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