Characterization of Gene Expression Profiles of Normal Canine Retina and Brain Using a Retinal cDNA Microarray

Purpose: Construction of a canine retinal custom cDNA microarray for comprehensive retinal gene expression profiling and application for the identification of genes that are preferentially expressed in the retina and brain lobes using a brain pool reference tissue. Methods: A cDNA microarray was constructed utilizing clones obtained from a normalized canine retinal expressed sequence tag library. Gene expression profiles were analyzed for normal retina, as well as the cortex of the frontal, occipital, and temporal brain regions. Each sample was studied against a reference sample of pooled brain RNA. Data from a quantified scanned image were normalized using the loess subgrid procedure. Retina-enriched genes were identified using the Significance Analysis of Microarrays (SAM) algorithm, and confirmed by northern blot analyses for selected genes. Differences between biological samples were displayed using principal component analysis (PCA). Results: Expression profiles for each tissue set were analyzed against the common reference of pooled brain. Changes in expression between the sample and the reference were higher in the retina (27.9%) than the individual brain tissues (2-6.6%). Furthermore, all individual retinal samples were clearly separated from any of the hybridizations using brain tissue in the PCA. The accuracy of observed changes in expression has been confirmed by northern blot analysis using five randomly chosen genes that represented a wide range of different expression levels between retina and brain. Conclusions: We have established an accurate and robust microarray system suitable for the investigation of expression patterns in the retina and brain. Characterization of the gene expression profiles in normal retina will facilitate the understanding of the processes that underline differences between normal and diseased retinas

Patient perceptions of virtual reality for pain relief in labor: A qualitative study

IntroductionLabor represents the most common reason for hospitalization, and most patients will use some form of pain management during their labor. While some studies have suggested that virtual reality (VR) may be an effective option for managing pain, more study is necessary to understand the patient experience of VR. The aim of this study is to characterize the effect of VR on patient perceptions of coping in labor and their descriptions of the VR experience.MethodologyA nested prospective, descriptive study within a randomized controlled trial of VR in laboring patients. We included nulliparous, term patients, having contractions at least every 5 min, a pain score on the Wong-Baker pain scale of 4–7, and who had been randomized to receive the 30 min virtual reality intervention in the trial. Subjects completed a childbirth self-efficacy inventory prior to the intervention. After the intervention, they completed a modified childbirth self-efficacy inventory related to VR and underwent a structured interview. Self-efficacy scores were compared using t-tests and qualitative, thematic analysis was performed using Dedoose.ResultsTwenty-one subjects received the VR intervention. Twenty subjects completed the post-intervention survey and structured interview; one declined due to discomfort. Subjects noted a significant increase in perceived degree to which VR could improve their self-efficacy in managing pain during labor. Thematic analysis revealed that subjects described the VR experience as allowing them to connect with their breathing, feeling more relaxed, and being distracted from pain. In total, 70% believed VR reduced their pain, 60% felt it reduced their anxiety, and 100% would recommend VR availability for laboring patients.ConclusionVR can improve patient self-efficacy for managing pain in labor. Future studies should focus on the content of the visualizations, optimized user experience and design, and effectiveness with ongoing exposure to VR content in labor

The organizational social context of mental health services and clinician attitudes toward evidence-based practice: a United States national study.

UnlabelledABSTBACKGROUND: Evidence-based practices have not been routinely adopted in community mental health organizations despite the support of scientific evidence and in some cases even legislative or regulatory action. We examined the association of clinician attitudes toward evidence-based practice with organizational culture, climate, and other characteristics in a nationally representative sample of mental health organizations in the United States.MethodsIn-person, group-administered surveys were conducted with a sample of 1,112 mental health service providers in a nationwide sample of 100 mental health service institutions in 26 states in the United States. The study examines these associations with a two-level Hierarchical Linear Modeling (HLM) analysis of responses to the Evidence-Based Practice Attitude Scale (EBPAS) at the individual clinician level as a function of the Organizational Social Context (OSC) measure at the organizational level, controlling for other organization and clinician characteristics.ResultsWe found that more proficient organizational cultures and more engaged and less stressful organizational climates were associated with positive clinician attitudes toward adopting evidence-based practice.ConclusionsThe findings suggest that organizational intervention strategies for improving the organizational social context of mental health services may contribute to the success of evidence-based practice dissemination and implementation efforts by influencing clinician attitudes

A new spin-anisotropic harmonic honeycomb iridate

The physics of Mott insulators underlies diverse phenomena ranging from high temperature superconductivity to exotic magnetism. Although both the electron spin and the structure of the local orbitals play a key role in this physics, in most systems these are connected only indirectly --- via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) open a further dimension to this problem by introducing strong spin-orbit interactions, such that the Mott physics has a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin-anisotropic interactions, coupling the spin orientation to a given spatial direction of exchange and leading to strongly frustrated magnetism. The potential for new physics emerging from such interactions has driven much scientific excitement, most recently in the search for a new quantum spin liquid, first discussed by Kitaev \cite{kitaev_anyons_2006}. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb, but in a three-dimensional framework. The temperature dependence of the magnetic susceptibility exhibits a striking reordering of the magnetic anisotropy, giving evidence for highly spin-anisotropic exchange interactions. Furthermore, the basic structural units of this material suggest the possibility of a new family of structures, the `harmonic honeycomb' iridates. This compound thus provides a unique and exciting glimpse into the physics of a new class of strongly spin-orbit coupled Mott insulators.Comment: 12 pages including bibliography, 5 figure

Genomic sequence analysis and characterization of Sneathia amnii sp. nov

Background Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. BecauseSneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms. Results Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated Leptotrichia amnionii . As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified. Conclusions Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health

Erosion rate maps highlight spatio-temporal patterns of uplift and quantify sediment export of the Northern Andes

Erosion rates are widely used to assess tectonic uplift and sediment export from mountain ranges. However, the scarcity of erosion rate measurements often hinders detailed tectonic interpretations. Here, we present 25 new cosmogenic nuclide-derived erosion rates from the Northern Andes of Colombia to study spatio-temporal patterns of uplift along the Central and Eastern Cordillera. Specifically, we combine new and published erosion rate data with precipitation-corrected normalized channel steepness measurements to construct high-resolution erosion rate maps. We find that erosion rates in the southern Central Cordillera are relatively uniform and average ∼0.3 mm/a. In the northern Central Cordillera rapidly eroding canyons dissect slowly eroding, low-relief surfaces uplifting since 8.3+ 3.7 - 2.6 Ma, based on a block uplift model. We interpret that persistent steep slab subduction has led to an erosional steady-state in the southern Central Cordillera, whereas in the northern Central Cordillera, Late Miocene slab flattening caused an acceleration in uplift, to which the landscape has not yet equilibrated. The Eastern Cordillera also displays pronounced erosional disequilibrium, with a slowly eroding central plateau rimmed by faster eroding western and eastern flanks. Our maps suggest Late Miocene topographic growth of the Eastern Cordillera, with deformation focused along the eastern flank, which is also supported by balanced cross-sections and thermochronologic data. Spatial gradients in predicted erosion rates along the eastern flank of the Eastern Cordillera suggest transient basin-ward migration of thrusts. Finally, sediment fluxes based on our erosion maps, suggest that the Eastern Cordillera exports nearly four times more sediment than the Central Cordillera. Our analysis shows that accounting for spatial variations in erosion parameters and climate reveals important variations in tectonic forcing that would otherwise be obscured in traditional river profile analyses. Moreover, given relationships between tectonic and topographic evolution, we hypothesize that spatio-temporal variations in slab dip are the primary driver of the dynamic landscape evolution of the Northern Andes, with potentially superposed effects from inherited Mesozoic rift structures

Arf4 is required for Mammalian development but dispensable for ciliary assembly

The primary cilium is a sensory organelle, defects in which cause a wide range of human diseases including retinal degeneration, polycystic kidney disease and birth defects. The sensory functions of cilia require specific receptors to be targeted to the ciliary subdomain of the plasma membrane. Arf4 has been proposed to sort cargo destined for the cilium at the Golgi complex and deemed a key regulator of ciliary protein trafficking. In this work, we show that Arf4 binds to the ciliary targeting sequence (CTS) of fibrocystin. Knockdown of Arf4 indicates that it is not absolutely required for trafficking of the fibrocystin CTS to cilia as steady-state CTS levels are unaffected. However, we did observe a delay in delivery of newly synthesized CTS from the Golgi complex to the cilium when Arf4 was reduced. Arf4 mutant mice are embryonic lethal and die at mid-gestation shortly after node formation. Nodal cilia appeared normal and functioned properly to break left-right symmetry in Arf4 mutant embryos. At this stage of development Arf4 expression is highest in the visceral endoderm but we did not detect cilia on these cells. In the visceral endoderm, the lack of Arf4 caused defects in cell structure and apical protein localization. This work suggests that while Arf4 is not required for ciliary assembly, it is important for the efficient transport of fibrocystin to cilia, and also plays critical roles in non-ciliary processes

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; FranciaFil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; ChinaFil: Maumus, Florian.Fil: Rivarola, Maximo Lisandro.Fil: Bhavsar, Jaysheel.Fil: Creasy, Todd.Fil: O'Brien, Kimberly.Fil: Sengamalay, Naomi A..Fil: Tallon, Luke J..Fil: Smith, Andrew D..Fil: Rayko, Edda.Fil: Ahmed, Ikhlak.Fil: Crom, Stéphane Le.Fil: Farrant, Gregory K..Fil: Sgro, Jean-Yves.Fil: Olson, Sue A..Fil: Bondurant, Sandra Splinter.Fil: Allen, Andrew.Fil: Rabinowicz, Pablo D..Fil: Sussman, Michael R..Fil: Bowler, Chris.Fil: Tirichine, Leïla