Leech Segmental Repeats Develop Normally in the Absence of Signals from either Anterior or Posterior Segments

AbstractWe have investigated whether the development of segmental repeats is autonomous in the embryo of the leech Helobdella robusta. The segmental tissues of the germinal band arise from progeny of five stem cells called teloblasts. Asymmetric divisions of the teloblasts form chains of segment founder cells (called primary blast cells) that divide in a stereotypical manner to produce differentiated descendants. Using two distinct techniques, we have looked for potential interactions between neighboring blast cell clones along the anterior–posterior axis. In one technique, we prevented the birth of primary blast cells by injection of DNase I into the teloblast, thereby depriving the last blast cell produced before the ablation of its normal posterior neighbors. We also ablated single blast cells with a laser microbeam, which allowed us to assess potential signals acting on either more anterior or more posterior primary blast cell clones. Our results suggest that interactions along the anterior–posterior axis between neighboring primary blast cell clones are not required for development of normal segmental organization within the blast cell clone. We also examined the possibility that blast cells receive redundant signals from both anterior and posterior neighboring clones and that either is sufficient for normal development. Using double blast cell laser ablations to isolate a primary blast cell clone by removal of both its anterior and its posterior neighbor, we found that the isolated clone still develops normally. These results reveal that the fundamental segmental repeat in the leech embryo, the primary blast cell clone, can develop normally in the apparent absence of signals from adjacent repeats along the anterior–posterior axis

Expression of FoxA and GATA transcription factors correlates with regionalized gut development in two lophotrochozoan marine worms: Chaetopterus (Annelida) and Themiste lageniformis (Sipuncula)

<p>Abstract</p> <p>Background</p> <p>A through gut is present in almost all metazoans, and most likely represents an ancient innovation that enabled bilaterian animals to exploit a wide range of habitats. Molecular developmental studies indicate that <it>Fox </it>and <it>GATA </it>regulatory genes specify tissue regions along the gut tube in a broad diversity of taxa, although little is known about gut regionalization within the Lophotrochozoa. In this study, we isolated <it>FoxA </it>and <it>GATA456 </it>orthologs and used whole mount <it>in situ </it>hybridization during larval gut formation in two marine worms: the segmented, polychaete annelid <it>Chaetopterus</it>, which develops a planktotrophic larva with a tripartite gut, and the non-segmented sipunculan <it>Themiste lageniformis</it>, which develops a lecithotrophic larva with a U-shaped gut.</p> <p>Results</p> <p><it>FoxA </it>and <it>GATA456 </it>transcripts are predominantly restricted to gut tissue, and together show regional expression spanning most of the alimentary canal in each of these lophotrochozoans, although neither <it>FoxA </it>nor <it>GATA456 </it>is expressed in the posterior intestine of <it>Chaetopterus</it>. In both species, <it>FoxA </it>is expressed at the blastula stage, transiently in presumptive endoderm before formation of a definitive gut tube, and throughout early larval development in discrete foregut and hindgut domains. <it>GATA456 </it>genes are expressed during endoderm formation, and in endoderm and mesoderm associated with the midgut in each species. Several species-specific differences were detected, including an overlap of <it>FoxA </it>and <it>GATA456 </it>expression in the intestinal system of <it>Themiste</it>, which is instead complimentary in <it>Chaetopterus</it>. Other differences include additional discrete expression domains of <it>FoxA </it>in ectodermal trunk cells in <it>Themiste </it>but not <it>Chaetopterus</it>, and expression of <it>GATA456 </it>in anterior ectoderm and midgut cells unique to <it>Chaetopterus</it>.</p> <p>Conclusions</p> <p>This study of gene expression in a sipunculan contributes new comparative developmental insights from lophotrochozoans, and shows that <it>FoxA </it>and <it>GATA456 </it>transcription factors are part of an ancient patterning mechanism that was deployed during early evolution of the metazoan through gut. The common utilization of <it>FoxA </it>and <it>GATA456 </it>throughout gut formation by species with contrasting life history modes indicates that both genes are core components of a gut-specific gene regulatory network in spiralians. Despite a highly conserved pattern of early development, and probably similar ontogenic origins of gut tissue, there are molecular differences in gut regionalization between lophotrochozoan species.</p

Expression of the pair-rule gene homologs runt, Pax3/7, even-skipped-1 and even-skipped-2 during larval and juvenile development of the polychaete annelid Capitella teleta does not support a role in segmentation

<p>Abstract</p> <p>Background</p> <p>Annelids and arthropods each possess a segmented body. Whether this similarity represents an evolutionary convergence or inheritance from a common segmented ancestor is the subject of ongoing investigation.</p> <p>Methods</p> <p>To investigate whether annelids and arthropods share molecular components that control segmentation, we isolated orthologs of the <it>Drosophila melanogaster </it>pair-rule genes, <it>runt</it>, <it>paired </it>(<it>Pax3/7</it>) and <it>eve</it>, from the polychaete annelid <it>Capitella teleta </it>and used whole mount <it>in situ </it>hybridization to characterize their expression patterns.</p> <p>Results</p> <p>When segments first appear, expression of the single <it>C. teleta runt </it>ortholog is only detected in the brain. Later, <it>Ct-runt </it>is expressed in the ventral nerve cord, foregut and hindgut. Analysis of <it>Pax </it>genes in the <it>C. teleta </it>genome reveals the presence of a single <it>Pax3/7 </it>ortholog. <it>Ct-Pax3/7 </it>is initially detected in the mid-body prior to segmentation, but is restricted to two longitudinal bands in the ventral ectoderm. Each of the two <it>C. teleta eve </it>orthologs has a unique and complex expression pattern, although there is partial overlap in several tissues. Prior to and during segment formation, <it>Ct-eve1 </it>and <it>Ct-eve2 </it>are both expressed in the bilaterial pair of mesoteloblasts, while <it>Ct-eve1 </it>is expressed in the descendant mesodermal band cells. At later stages, <it>Ct-eve2 </it>is expressed in the central and peripheral nervous system, and in mesoderm along the dorsal midline. In late stage larvae and adults, <it>Ct-eve1 </it>and <it>Ct-eve2 </it>are expressed in the posterior growth zone.</p> <p>Conclusions</p> <p><it>C. teleta eve, Pax3/7 </it>and <it>runt </it>homologs all have distinct expression patterns and share expression domains with homologs from other bilaterians. None of the pair-rule orthologs examined in <it>C. teleta </it>exhibit segmental or pair-rule stripes of expression in the ectoderm or mesoderm, consistent with an independent origin of segmentation between annelids and arthropods.</p

A comprehensive fate map by intracellular injection of identified blastomeres in the marine polychaete Capitella teleta

<p>Abstract</p> <p>Background</p> <p>The polychaete annelid <it>Capitella teleta </it>(formerly <it>Capitella </it>sp. I) develops by spiral cleavage and has been the focus of several recent developmental studies aided by a fully sequenced genome. Fate mapping in polychaetes has lagged behind other spiralian taxa, because of technical limitations.</p> <p>Results</p> <p>To generate a modern fate map for <it>C. teleta</it>, we injected 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) into individual identified blastomeres through fourth-quartet micromere formation. Confocal laser scanning microscopy at single-cell resolution was used to characterize blastomere fates during larval stages. Our results corroborate previous observations from classic studies, and show a number of similarities with other spiralian fate maps, including unique and stereotypic fates for individual blastomeres, presence of four discrete body domains arising from the A, B, C and D cell quadrants, generation of anterior ectoderm from first quartet micromeres, and contributions to trunk ectoderm and ventral nerve cord by the 2d somatoblast. Of particular interest are several instances in which the <it>C. teleta </it>fate map deviates from other spiralian fate maps. For example, we identified four to seven distinct origins of mesoderm, all ectomesodermal. In addition, the left and right mesodermal bands arise from 3d and 3c, respectively, whereas 4d generates a small number of trunk muscle cells, the primordial germ cells and the anus. We identified a complex set of blastomere contributions to the posterior gut in <it>C. teleta</it>, which establishes the most complete map of posterior gut territories to date.</p> <p>Conclusions</p> <p>Our detailed cellular descriptions reveal previously underappreciated complexity in the ontogenetic contributions to several spiralian larval tissues, including the mesoderm, nervous system and gut. The formation of the mesodermal bands by 3c and 3d is in stark contrast to other spiralians, in which 4d generates the mesodermal bands. The results of this study provide a framework for future phylogenetic comparisons and functional analyses of cell-fate specification.</p

Expression and phylogenetic analysis of the zic gene family in the evolution and development of metazoans

<p>Abstract</p> <p>Background</p> <p><it>zic </it>genes are members of the <it>gli/glis/nkl/zic </it>super-family of C2H2 zinc finger (ZF) transcription factors. Homologs of the <it>zic </it>family have been implicated in patterning neural and mesodermal tissues in bilaterians. Prior to this study, the origin of the metazoan <it>zic </it>gene family was unknown and expression of <it>zic </it>gene homologs during the development of early branching metazoans had not been investigated.</p> <p>Results</p> <p>Phylogenetic analyses of novel <it>zic </it>candidate genes identified a definitive <it>zic </it>homolog in the placozoan <it>Trichoplax adhaerens</it>, two <it>gli/glis/nkl-</it>like genes in the ctenophore <it>Mnemiopsis leidyi</it>, confirmed the presence of three <it>gli/glis/nkl</it>-like genes in Porifera, and confirmed the five previously identified <it>zic </it>genes in the cnidarian <it>Nematostella vectensis</it>. In the cnidarian <it>N. vectensis</it>, <it>zic </it>homologs are expressed in ectoderm and the gastrodermis (a bifunctional endomesoderm), in presumptive and developing tentacles, and in oral and sensory apical tuft ectoderm. The <it>Capitella teleta zic </it>homolog (<it>Ct-zic</it>) is detectable in a subset of the developing nervous system, the foregut, and the mesoderm associated with the segmentally repeated chaetae. Lastly, expression of <it>gli </it>and <it>glis </it>homologs in <it>Mnemiopsis</it>. <it>leidyi </it>is detected exclusively in neural cells in floor of the apical organ.</p> <p>Conclusions</p> <p>Based on our analyses, we propose that the <it>zic </it>gene family arose in the common ancestor of the Placozoa, Cnidaria and Bilateria from a <it>gli/glis/nkl</it>-like gene and that both ZOC and ZF-NC domains evolved prior to cnidarian-bilaterian divergence. We also conclude that <it>zic </it>expression in neural ectoderm and developing neurons is pervasive throughout the Metazoa and likely evolved from neural expression of an ancestral <it>gli/glis/nkl/zic </it>gene. <it>zic </it>expression in bilaterian mesoderm may be related to the expression in the gastrodermis of a cnidarian-bilaterian common ancestor.</p

Monitoring commercial conventional facilities control with the APS control system: The Metasys-to-EPICS interface

As controls needs at the Advanced Photon Source matured from an installation phase to an operational phase, the need to monitor the existing conventional facilities control system with the EPICS-based accelerator control system was realized. This existing conventional facilities control network is based on a proprietary system from Johnson Controls called Metasys. Initially read-only monitoring of the Metasys parameters will be provided; however, the ability for possible future expansion to full control is available. This paper describes a method of using commercially available hardware and existing EPICS software as a bridge between the Metasys and EPICS control systems

Beyond mystery: Putting algorithmic accountability in context

Critical algorithm scholarship has demonstrated the difficulties of attributing accountability for the actions and effects of algorithmic systems. In this commentary, we argue that we cannot stop at denouncing the lack of accountability for algorithms and their effects but must engage the broader systems and distributed agencies that algorithmic systems exist within; including standards, regulations, technologies, and social relations. To this end, we explore accountability in “the Generated Detective,” an algorithmically generated comic. Taking up the mantle of detectives ourselves, we investigate accountability in relation to this piece of experimental fiction. We problematize efforts to effect accountability through transparency by undertaking a simple operation: asking for permission to re-publish a set of the algorithmically selected and modified words and images which make the frames of the comic. Recounting this process, we demonstrate slippage between the “complication” of the algorithm and the obscurity of the legal and institutional structures in which it exists

A Catalog of Dermatology Utilities: A Measure of the Burden of Skin Diseases

Utilities are measures of quality of life that reflect the strength of individuals' preferences or values for a particular health outcome. As such, utilities represent a measure of disease burden. The aim of this article is to introduce the concept of utilities to the dermatology community and to present a catalog of dermatology utilities obtained from direct patient interviews. Our data are based on 236 total subjects from Grady Hospital (Atlanta, GA), Stanford Medical Center (Palo Alto, CA), and Parkland Hospital (Dallas, TX). The mean time trade-off utilities ranged from 0.640 for blistering disorders to 1.000 for alopecia, cosmetic, and urticaria. The mean utility across all diagnoses was 0.943. We present utilities for 17 diagnostic categories and discuss the underlying reasons for the significant disease burden that these utilities represent. We also present these dermatology categories relative to noncutaneous diseases to place the cutaneous utilities in perspective and to compare the burden of disease. We have demonstrated that skin diseases have considerable burden of disease and provided a preliminary repository of utility data for future researchers and policy makers

Identifying Unique Neighborhood Characteristics to Guide Health Planning for Stroke and Heart Attack: Fuzzy Cluster and Discriminant Analyses Approaches

Socioeconomic, demographic, and geographic factors are known determinants of stroke and myocardial infarction (MI) risk. Clustering of these factors in neighborhoods needs to be taken into consideration during planning, prioritization and implementation of health programs intended to reduce disparities. Given the complex and multidimensional nature of these factors, multivariate methods are needed to identify neighborhood clusters of these determinants so as to better understand the unique neighborhood profiles. This information is critical for evidence-based health planning and service provision. Therefore, this study used a robust multivariate approach to classify neighborhoods and identify their socio-demographic characteristics so as to provide information for evidence-based neighborhood health planning for stroke and MI.The study was performed in East Tennessee Appalachia, an area with one of the highest stroke and MI risks in USA. Robust principal component analysis was performed on neighborhood (census tract) socioeconomic and demographic characteristics, obtained from the US Census, to reduce the dimensionality and influence of outliers in the data. Fuzzy cluster analysis was used to classify neighborhoods into Peer Neighborhoods (PNs) based on their socioeconomic and demographic characteristics. Nearest neighbor discriminant analysis and decision trees were used to validate PNs and determine the characteristics important for discrimination. Stroke and MI mortality risks were compared across PNs. Four distinct PNs were identified and their unique characteristics and potential health needs described. The highest risk of stroke and MI mortality tended to occur in less affluent PNs located in urban areas, while the suburban most affluent PNs had the lowest risk.Implementation of this multivariate strategy provides health planners useful information to better understand and effectively plan for the unique neighborhood health needs and is important in guiding resource allocation, service provision, and policy decisions to address neighborhood health disparities and improve population health

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed