Duplication events downstream of IRX1 cause North Carolina macular dystrophy at the MCDR3 locus

Autosomal dominant North Carolina macular dystrophy (NCMD) is believed to represent a failure of macular development. The disorder has been linked to two loci, MCDR1 (chromosome 6q16) and MCDR3 (chromosome 5p15-p13). Recently, non-coding variants upstream of PRDM13 (MCDR1) and a duplication including IRX1 (MCDR3) have been identified. However, the underlying disease-causing mechanism remains uncertain. Through a combination of sequencing studies on eighteen NCMD families, we report two novel overlapping duplications at the MCDR3 locus, in a gene desert downstream of IRX1 and upstream of ADAMTS16. One duplication of 43 kb was identified in nine families (with evidence for a shared ancestral haplotype), and another one of 45 kb was found in a single family. Three families carry the previously reported V2 variant (MCDR1), while five remain unsolved. The MCDR3 locus is thus refined to a shared region of 39 kb that contains DNAse hypersensitive sites active at a restricted time window during retinal development. Publicly available data confirmed expression of IRX1 and ADAMTS16 in human fetal retina, with IRX1 preferentially expressed in fetal macula. These findings represent a major advance in our understanding of the molecular genetics of NCMD and provide insights into the genetic pathways involved in human macular development

A Chemical Genetic Screen for Modulators of Asymmetrical 2,2′-Dimeric Naphthoquinones Cytotoxicity in Yeast

BACKGROUND: Dimeric naphthoquinones (BiQ) were originally synthesized as a new class of HIV integrase inhibitors but have shown integrase-independent cytotoxicity in acute lymphoblastic leukemia cell lines suggesting their use as potential anti-neoplastic agents. The mechanism of this cytotoxicity is unknown. In order to gain insight into the mode of action of binaphthoquinones we performed a systematic high-throughput screen in a yeast isogenic deletion mutant array for enhanced or suppressed growth in the presence of binaphthoquinones. METHODOLOGY/PRINCIPAL FINDINGS: Exposure of wild type yeast strains to various BiQs demonstrated inhibition of yeast growth with IC(50)s in the microM range. Drug sensitivity and resistance screens were performed by exposing arrays of a haploid yeast deletion mutant library to BiQs at concentrations near their IC(50). Sensitivity screens identified yeast with deletions affecting mitochondrial function and cellular respiration as having increased sensitivity to BiQs. Corresponding to this, wild type yeast grown in the absence of a fermentable carbon source were particularly sensitive to BiQs, and treatment with BiQs was shown to disrupt the mitochondrial membrane potential and lead to the generation of reactive oxygen species (ROS). Furthermore, baseline ROS production in BiQ sensitive mutant strains was increased compared to wild type and could be further augmented by the presence of BiQ. Screens for resistance to BiQ action identified the mitochondrial external NAD(P)H dehydrogenase, NDE1, as critical to BiQ toxicity and over-expression of this gene resulted in increased ROS production and increased sensitivity of wild type yeast to BiQ. CONCLUSIONS/SIGNIFICANCE: In yeast, binaphthoquinone cytotoxicity is likely mediated through NAD(P)H:quonine oxidoreductases leading to ROS production and dysfunctional mitochondria. Further studies are required to validate this mechanism in mammalian cells

Tracing the wider impacts of biomedical research: A literature search to develop a novel citation categorisation technique

There is an increasing need both to understand the translation of biomedical research into improved healthcare and to assess the range of wider impacts from health research such as improved health policies, health practices and healthcare. Conducting such assessments is complex and new methods are being sought. Our new approach involves several steps. First, we developed a qualitative citation analysis technique to apply to biomedical research in order to assess the contribution that individual papers made to further research. Second, using this method, we then proposed to trace the citations to the original research through a series of generations of citing papers. Third, we aimed eventually to assess the wider impacts of the various generations. This article describes our comprehensive literature search to inform the new technique. We searched various databases, specific bibliometrics journals and the bibliographies of key papers. After excluding irrelevant papers we reviewed those remaining for either general or specific details that could inform development of our new technique. Various characteristics of citations were identified that had been found to predict their importance to the citing paper including the citation’s location; number of citation occasions and whether the author(s) of the cited paper were named within the citing paper. We combined these objective characteristics with subjective approaches also identified from the literature search to develop a citation categorisation technique that would allow us to achieve the first of the steps above, i.e., being able routinely to assess the contribution that individual papers make to further research.Medical Research Council as part of the MRC-NIHR Methodology Research Programme, and Professor Martin Buxton

Comparison of Synchrotron X-Ray Microanalysis With Electron and Proton Microscopy for Individual Particle Analysis

This paper is concerned with the evaluation of the use of synchrotron/radiation induced x-ray fluorescences ({mu}-SRXRF) as implemented at two existing X-ray microprobes for the analysis of individual particles. As representative environmental particulates, National Institutes of Science and Technology (NIST) K227, K309, K441 and K961 glass microspheres were analyzed using two types of X-ray micro probes: the white light microprobe at beamline X26A of the monochromatic (15 keV) X-ray microprobe at station 7.6 of the SRS. For reference, the particles were also analyzed with microanalytical techniques more commonly employed for individual particles analysis such as EPMA and micro-PIXE

Software survey: VOSviewer, a computer program for bibliometric mapping

We present VOSviewer, a freely available computer program that we have developed for constructing and viewing bibliometric maps. Unlike most computer programs that are used for bibliometric mapping, VOSviewer pays special attention to the graphical representation of bibliometric maps. The functionality of VOSviewer is especially useful for displaying large bibliometric maps in an easy-to-interpret way. The paper consists of three parts. In the first part, an overview of VOSviewer's functionality for displaying bibliometric maps is provided. In the second part, the technical implementation of specific parts of the program is discussed. Finally, in the third part, VOSviewer's ability to handle large maps is demonstrated by using the program to construct and display a co-citation map of 5,000 major scientific journals

Predation on an Upper Trophic Marine Predator, the Steller Sea Lion: Evaluating High Juvenile Mortality in a Density Dependent Conceptual Framework

The endangered western stock of the Steller sea lion (Eumetopias jubatus) – the largest of the eared seals – has declined by 80% from population levels encountered four decades ago. Current overall trends from the Gulf of Alaska to the Aleutian Islands appear neutral with strong regional heterogeneities. A published inferential model has been used to hypothesize a continuous decline in natality and depressed juvenile survival during the height of the decline in the mid-late 1980's, followed by the recent recovery of juvenile survival to pre-decline rates. However, these hypotheses have not been tested by direct means, and causes underlying past and present population trajectories remain unresolved and controversial. We determined post-weaning juvenile survival and causes of mortality using data received post-mortem via satellite from telemetry transmitters implanted into 36 juvenile Steller sea lions from 2005 through 2011. Data show high post-weaning mortality by predation in the eastern Gulf of Alaska region. To evaluate the impact of such high levels of predation, we developed a conceptual framework to integrate density dependent with density independent effects on vital rates and population trajectories. Our data and model do not support the hypothesized recent recovery of juvenile survival rates and reduced natality. Instead, our data demonstrate continued low juvenile survival in the Prince William Sound and Kenai Fjords region of the Gulf of Alaska. Our results on contemporary predation rates combined with the density dependent conceptual framework suggest predation on juvenile sea lions as the largest impediment to recovery of the species in the eastern Gulf of Alaska region. The framework also highlights the necessity for demographic models based on age-structured census data to incorporate the differential impact of predation on multiple vital rates