Showing papers by "University of Auckland published in 2007"
TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.
Abstract: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/
under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
11,916 citations
TL;DR: This paper provided a conceptual analysis of feedback and reviewed the evidence related to its impact on learning and achievement, and suggested ways in which feedback can be used to enhance its effectiveness in classrooms.
Abstract: Feedback is one of the most powerful influences on learning and achievement, but this impact can be either positive or negative. Its power is frequently mentioned in articles about learning and teaching, but surprisingly few recent studies have systematically investigated its meaning. This article provides a conceptual analysis of feedback and reviews the evidence related to its impact on learning and achievement. This evidence shows that although feedback is among the major influences, the type of feedback and the way it is given can be differentially effective. A model of feedback is then proposed that identifies the particular properties and circumstances that make it effective, and some typically thorny issues are discussed, including the timing of feedback and the effects of positive and negative feedback. Finally, this analysis is used to suggest ways in which feedback can be used to enhance its effectiveness in classrooms.
7,222 citations
TL;DR: The designed methodology effectively satisfies the three objectives of design science research methodology and has the potential to help aid the acceptance of DS research in the IS discipline.
Abstract: The paper motivates, presents, demonstrates in use, and evaluates a methodology for conducting design science (DS) research in information systems (IS). DS is of importance in a discipline oriented to the creation of successful artifacts. Several researchers have pioneered DS research in IS, yet over the past 15 years, little DS research has been done within the discipline. The lack of a methodology to serve as a commonly accepted framework for DS research and of a template for its presentation may have contributed to its slow adoption. The design science research methodology (DSRM) presented here incorporates principles, practices, and procedures required to carry out such research and meets three objectives: it is consistent with prior literature, it provides a nominal process model for doing DS research, and it provides a mental model for presenting and evaluating DS research in IS. The DS process includes six steps: problem identification and motivation, definition of the objectives for a solution, design and development, demonstration, evaluation, and communication. We demonstrate and evaluate the methodology by presenting four case studies in terms of the DSRM, including cases that present the design of a database to support health assessment methods, a software reuse measure, an Internet video telephony application, and an IS planning method. The designed methodology effectively satisfies the three objectives and has the potential to help aid the acceptance of DS research in the IS discipline.
5,420 citations
TL;DR: This work presents a new method and software for inference of haplotypes phase and missing data that can accurately phase data from whole-genome association studies, and presents the first comparison of haplotype-inference methods for real and simulated data sets with thousands of genotyped individuals.
Abstract: Whole-genome association studies present many new statistical and computational challenges due to the large quantity of data obtained. One of these challenges is haplotype inference; methods for haplotype inference designed for small data sets from candidate-gene studies do not scale well to the large number of individuals genotyped in whole-genome association studies. We present a new method and software for inference of haplotype phase and missing data that can accurately phase data from whole-genome association studies, and we present the first comparison of haplotype-inference methods for real and simulated data sets with thousands of genotyped individuals. We find that our method outperforms existing methods in terms of both speed and accuracy for large data sets with thousands of individuals and densely spaced genetic markers, and we use our method to phase a real data set of 3,002 individuals genotyped for 490,032 markers in 3.1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available.
2,849 citations
TL;DR: Treatment with zoledronic acid reduced the risk of morphometric vertebral fracture by 70% during a 3-year period, as compared with placebo.
Abstract: Background A single infusion of intravenous zoledronic acid decreases bone turnover and improves bone density at 12 months in postmenopausal women with osteoporosis. We assessed the effects of annual infusions of zoledronic acid on fracture risk during a 3-year period. Methods In this double-blind, placebo-controlled trial, 3889 patients (mean age, 73 years) were randomly assigned to receive a single 15-minute infusion of zoledronic acid (5 mg) and 3876 were assigned to receive placebo at baseline, at 12 months, and at 24 months; the patients were followed until 36 months. Primary end points were new vertebral fracture (in patients not taking concomitant osteoporosis medications) and hip fracture (in all patients). Secondary end points included bone mineral density, bone turnover markers, and safety outcomes. Results Treatment with zoledronic acid reduced the risk of morphometric vertebral fracture by 70% during a 3-year period, as compared with placebo (3.3% in the zoledronic-acid group vs. 10.9% in the ...
2,451 citations
TL;DR: This paper argued that the chi-square exact-fit test is the only substantive test of fit for structural equation model, but, its sensitivity to discrepancies from expected values at increasing sample sizes can be highly problematic if those discrepancies are considered trivial from an explanatory-theory perspective.
2,113 citations
TL;DR: A dramaturgical model based on Goffman's seminal work on social life is proposed as a useful way of conceptualizing the qualitative interview and guidelines for the conduct of qualitative interviews are suggested.
1,865 citations
TL;DR: It is submitted that mental time travel is not an encapsulated cognitive system, but instead comprises several subsidiary mechanisms that allow prediction of future situations and should be considered in addition to direct evidence of future-directed action.
Abstract: In a dynamic world, mechanisms allowing prediction of future situations can provide a selective advantage. We suggest that memory systems differ in the degree of flexibility they offer for anticipatory behavior and put forward a corresponding taxonomy of prospection. The adaptive advantage of any memory system can only lie in what it contributes for future survival. The most flexible is episodic memory, which we suggest is part of a more general faculty of mental time travel that allows us not only to go back in time, but also to foresee, plan, and shape virtually any specific future event. We review comparative studies and find that, in spite of increased research in the area, there is as yet no convincing evidence for mental time travel in nonhuman animals. We submit that mental time travel is not an encapsulated cognitive system, but instead comprises several subsidiary mechanisms. A theater metaphor serves as an analogy for the kind of mechanisms required for effective mental time travel. We propose that future research should consider these mechanisms in addition to direct evidence of future-directed action. We maintain that the emergence of mental time travel in evolution was a crucial step towards our current success.
1,623 citations
TL;DR: A worldwide goal for stroke is proposed: a 2% reduction each year over and above that which may happen as a result of better case management and treatment, which would result in 6.4 million fewer deaths from stroke from 2005 to 2015.
Abstract: Summary Stroke caused an estimated 5·7 million deaths in 2005, and 87% of these deaths were in low-income and middle-income countries. Without intervention, the number of global deaths is projected to rise to 6·5 million in 2015 and to 7·8 million in 2030. The rising burden of stroke, especially in low-income and middle-income countries, leads us to propose a worldwide goal for stroke: a 2% reduction each year over and above that which may happen as a result of better case management and treatment. The experience of high-income countries indicates that sustained interventions can achieve at least the required 4% annual average decline in stroke mortality for people age 60–69 years. Achieving this goal for stroke would result in 6·4 million fewer deaths from stroke from 2005 to 2015. More of these deaths will be averted in low-income and middle-income countries than in high-income countries.
1,339 citations
McGill University1, University of Groningen2, University of Oslo3, University of Michigan4, University of Auckland5, University of St Andrews6, University of Arizona7, University of California, Merced8, University of Alberta9, University of California, Santa Barbara10, Pontifical Catholic University of Chile11, University of Chile12, Michigan State University13, Arizona State University14
TL;DR: Theoretical, empirical and statistical developments in the study of Species abundance distributions are reviewed and it is optimistic that SADs can provide significant insights into basic and applied ecological science.
Abstract: Species abundance distributions (SADs) follow one of ecologys oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.
1,237 citations
TL;DR: Findings indicate that international differences in asthma symptom prevalence have reduced, particularly in the 13–14 year age group, with decreases in prevalence in English speaking countries and Western Europe and increases inPrevalence in regions where prevalence was previously low.
Abstract: BACKGROUND: Phase I of the International Study of Asthma and Allergies in Childhood (ISAAC) was designed to allow worldwide comparisons of the prevalence of asthma symptoms. In phase III the phase I survey was repeated in order to assess changes over time. METHODS: The phase I survey was repeated after an interval of 5-10 years in 106 centres in 56 countries in children aged 13-14 years (n = 304,679) and in 66 centres in 37 countries in children aged 6-7 years (n = 193,404). RESULTS: The mean symptom prevalence of current wheeze in the last 12 months changed slightly from 13.2% to 13.7% in the 13-14 year age group (mean increase of 0.06% per year) and from 11.1% to 11.6% in the 6-7 year age group (mean increase of 0.13% per year). There was also little change in the mean symptom prevalence of severe asthma or the symptom prevalence measured with the asthma video questionnaire. However, the time trends in asthma symptom prevalence showed different regional patterns. In Western Europe, current wheeze decreased by 0.07% per year in children aged 13-14 years but increased by 0.20% per year in children aged 6-7 years. The corresponding findings per year for the other regions in children aged 13-14 years and 6-7 years, respectively, were: Oceania (-0.39% and -0.21%); Latin America (+0.32% and +0.07%); Northern and Eastern Europe (+0.26% and +0.05%); Africa (+0.16% and +0.10%); North America (+0.12% and +0.32%); Eastern Mediterranean (-0.10% and +0.79%); Asia-Pacific (+0.07% and -0.06%); and the Indian subcontinent (+0.02% and +0.06%). There was a particularly marked reduction in current asthma symptom prevalence in English language countries (-0.51% and -0.09%). Similar patterns were observed for symptoms of severe asthma. However, the percentage of children reported to have had asthma at some time in their lives increased by 0.28% per year in the 13-14 year age group and by 0.18% per year in the 6-7 year age group. CONCLUSIONS: These findings indicate that international differences in asthma symptom prevalence have reduced, particularly in the 13-14 year age group, with decreases in prevalence in English speaking countries and Western Europe and increases in prevalence in regions where prevalence was previously low. Although there was little change in the overall prevalence of current wheeze, the percentage of children reported to have had asthma increased significantly, possibly reflecting greater awareness of this condition and/or changes in diagnostic practice. The increases in asthma symptom prevalence in Africa, Latin America and parts of Asia indicate that the global burden of asthma is continuing to rise, but the global prevalence differences are lessening.
TL;DR: AAV-GAD gene therapy of the subthalamic nucleus is safe and well tolerated by patients with advanced Parkinson's disease, suggesting that in-vivo gene therapy in the adult brain might be safe for various neurodegenerative diseases.
TL;DR: In this article, the authors reported the transcript levels of the anthocyanin biosynthetic genes in a red-fleshed apple compared with a white-fleshhed cultivar.
Abstract: Anthocyanin concentration is an important determinant of the colour of many fruits. In apple (Malus x domestica), centuries of breeding have produced numerous varieties in which levels of anthocyanin pigment vary widely and change in response to environmental and developmental stimuli. The apple fruit cortex is usually colourless, although germplasm does exist where the cortex is highly pigmented due to the accumulation of either anthocyanins or carotenoids. From studies in a diverse array of plant species, it is apparent that anthocyanin biosynthesis is controlled at the level of transcription. Here we report the transcript levels of the anthocyanin biosynthetic genes in a red-fleshed apple compared with a white-fleshed cultivar. We also describe an apple MYB transcription factor, MdMYB10, that is similar in sequence to known anthocyanin regulators in other species. We further show that this transcription factor can induce anthocyanin accumulation in both heterologous and homologous systems, generating pigmented patches in transient assays in tobacco leaves and highly pigmented apple plants following stable transformation with constitutively expressed MdMYB10. Efficient induction of anthocyanin biosynthesis in transient assays by MdMYB10 was dependent on the co-expression of two distinct bHLH proteins from apple, MdbHLH3 and MdbHLH33. The strong correlation between the expression of MdMYB10 and apple anthocyanin levels during fruit development suggests that this transcription factor is responsible for controlling anthocyanin biosynthesis in apple fruit; in the red-fleshed cultivar and in the skin of other varieties, there is an induction of MdMYB10 expression concurrent with colour formation during development. Characterization of MdMYB10 has implications for the development of new varieties through classical breeding or a biotechnological approach.
TL;DR: In this article, the authors present a detailed analysis of the performance of the Large Hadron Collider (CMS) at 14 TeV and compare it with the state-of-the-art analytical tools.
Abstract: CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider (LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking--through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start-up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb−1 or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, Bs production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb−1 to 30 fb−1. The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z0 boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing ET, B-mesons and τ's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model
TL;DR: The presence of a human RMS is demonstrated, which is unexpectedly organized around a lateral ventricular extension reaching the OB, and the neuroblasts in it are illustrated.
Abstract: The rostral migratory stream (RMS) is the main pathway by which newly born subventricular zone cells reach the olfactory bulb (OB) in rodents. However, the RMS in the adult human brain has been elusive. We demonstrate the presence of a human RMS, which is unexpectedly organized around a lateral ventricular extension reaching the OB, and illustrate the neuroblasts in it. The RMS ensheathing the lateral olfactory ventricular extension, as seen by magnetic resonance imaging, cell-specific markers, and electron microscopy, contains progenitor cells with migratory characteristics and cells that incorporate 5-bromo-2'-deoxyuridine and become mature neurons in the OB.
TL;DR: It is proposed that the DOHaD phenomenon can be considered as a subset of the broader processes of developmental plasticity by which organisms adapt to their environment during their life course, allowing genotypic variation to be preserved through transient environmental changes.
Abstract: Biomedical science has little considered the relevance of life history theory and evolutionary and ecological developmental biology to clinical medicine. However, the observations that early life influences can alter later disease risk--the "developmental origins of health and disease" (DOHaD) paradigm--have led to a recognition that these perspectives can inform our understanding of human biology. We propose that the DOHaD phenomenon can be considered as a subset of the broader processes of developmental plasticity by which organisms adapt to their environment during their life course. Such adaptive processes allow genotypic variation to be preserved through transient environmental changes. Cues for plasticity operate particularly during early development; they may affect a single organ or system, but generally they induce integrated adjustments in the mature phenotype, a process underpinned by epigenetic mechanisms and influenced by prediction of the mature environment. In mammals, an adverse intrauterine environment results in an integrated suite of responses, suggesting the involvement of a few key regulatory genes, that resets the developmental trajectory in expectation of poor postnatal conditions. Mismatch between the anticipated and the actual mature environment exposes the organism to risk of adverse consequences-the greater the mismatch, the greater the risk. For humans, prediction is inaccurate for many individuals because of changes in the postnatal environment toward energy-dense nutrition and low energy expenditure, contributing to the epidemic of chronic noncommunicable disease. This view of human disease from the perspectives of life history biology and evolutionary theory offers new approaches to prevention, diagnosis and intervention.
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TL;DR: In this article, a nonlinear time varying factor model is proposed to represent the behavior of economies in transition allowing for a wide range of possible time paths and individual heterogeneity, and a simple regression based convergence test is developed, whose asymptotic properties are analyzed under both null and local alternatives.
Abstract: A new panel data model is proposed to represent the behavior of economies in transition allowing for a wide range of possible time paths and individual heterogeneity. The model has both common and individual specific components and is formulated as a nonlinear time varying factor model. When applied to a micro panel, the decomposition provides flexibility in idiosyncratic behavior over time and across section, while retaining some commonality across the panel by means of an unknown common growth component. This commonality means that when the heterogeneous time varying idiosyncratic components converge over time to a constant, a form of panel convergence holds, analogous to the concept of conditional sigma convergence. The paper provides a framework of asymptotic representations for the factor components which enables the development of econometric procedures of estimation and testing. In particular, a simple regression based convergence test is developed, whose asymptotic properties are analyzed under both null and local alternatives, and a new method of clustering panels into club convergence groups is constructed. These econometric methods are applied to analyze convergence in cost of living indices among 19 US. metropolitan cities.
TL;DR: In this article, a nonlinear time varying factor model is proposed to represent the behavior of economies in transition, allowing for a wide range of possible time paths and individual heterogeneity, and a framework of asymptotic representations for the factor components that enables the development of econometric procedures of estimation and testing.
Abstract: A new panel data model is proposed to represent the behavior of economies in transition, allowing for a wide range of possible time paths and individual heterogeneity. The model has both common and individual specific components, and is formulated as a nonlinear time varying factor model. When applied to a micro panel, the decomposition provides flexibility in idiosyncratic behavior over time and across section, while retaining some commonality across the panel by means of an unknown common growth component. This commonality means that when the heterogeneous time varying idiosyncratic components converge over time to a constant, a form of panel convergence holds, analogous to the concept of conditional sigma convergence. The paper provides a framework of asymptotic representations for the factor components that enables the development of econometric procedures of estimation and testing. In particular, a simple regression based convergence test is developed, whose asymptotic properties are analyzed under both null and local alternatives, and a new method of clustering panels into club convergence groups is constructed. These econometric methods are applied to analyze convergence in cost of living indices among 19 U.S. metropolitan cities.
TL;DR: In this article, the influence of brand image and reputation on customers' perceptions of product and service quality, customer value, and customer loyalty in a business market where there are three manufacturers marketing their brands directly to a large number of small firms.
University of Toronto1, University of Zurich2, Harvard University3, Queen Mary University of London4, Tufts University5, University of California, San Diego6, Boston University7, Medical University of South Carolina8, University of Helsinki9, University of Queensland10, Queensland Health11, University of California, Riverside12, University of Auckland13, University of Saskatchewan14, Ruhr University Bochum15
TL;DR: There is now strong evidence that increasing vitamin D intake will lower risk of falling and lower fracture risk in older men and women and regulatory agencies in the United States and abroad should review the evidence and reassess their dietary recommendations.
TL;DR: In this article, a study was conducted using Buchi mini spray dryer B-191 to produce spray-dried watermelon powders using two different maltodextrin concentrations (3% and 5%) as the encapsulating agent and four different inlet temperatures (145°C, 155¼C, 165 ¼C and 175¼°C).
Abstract: A study was conducted using Buchi mini spray dryer B-191 to produce spray-dried watermelon powders using two different maltodextrin concentrations (3% and 5%) as the encapsulating agent and four different inlet temperatures (145 °C, 155 °C, 165 °C and 175 °C). The spray-dried watermelon powders were analysed for moisture content, dissolution, water activity, colour, lycopene and β-carotene. Results demonstrated that as inlet temperature increased, the moisture content and dissolution decreased. However, there were no significant changes in the water activities of the spray-dried powders for all the inlet temperatures investigated. Colormetric analyses showed that the L * , a * , b * , hue and chroma values changed with the inlet temperatures. The results were well correlated to the lycopene and β-carotene contents of the spray-dried powders.
University Health Network1, University of Oxford2, University of Auckland3, Canadian Institutes of Health Research4, Medical Research Council5, University of Sydney6, Indian Council of Medical Research7, National Institutes of Health8, Emory University9, Isfahan University of Medical Sciences10, PepsiCo11, John Radcliffe Hospital12
TL;DR: The top 20 policy and research priorities for conditions such as diabetes, stroke and heart disease are revealed.
Abstract: The top 20 policy and research priorities for conditions such as diabetes, stroke and heart disease.
TL;DR: In this article, the authors examined the relationship between high-performance work system (HPWS) practices and employee attitudes using a randomly selected, national population sample, and found clear evidence for a positive relationship between HPWS practices and the attitudinal variables of job satisfaction, trust in management, and organizational commitment.
Abstract: In order to improve our understanding of mediating variables inside the ‘black box’ of the firm's labour management, this paper examines the relationship between high-performance work system (HPWS) practices and employee attitudes. Using a randomly selected, national population sample, clear evidence was found for a positive relationship between HPWS practices and the attitudinal variables of job satisfaction, trust in management, and organizational commitment, implying that HPWS can provide win-win outcomes for employees and employers. However, the study also tests – from an employee perspective – the ‘complementarities thesis’ and finds negative interaction effects among HPWS practices. This strengthens the argument that there are likely to be limits to the positive outcomes of HPWSs for employees. Evidence of sequencing in the employee attitudinal responses to HPWSs was also found, with job satisfaction as the key mediating variable.
TL;DR: These two population-based intervention strategies could therefore substantially reduce mortality from chronic diseases, and make a major (and affordable) contribution towards achievement of the global goal to prevent and control chronic diseases.
TL;DR: The zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies, and the EF1α, Rpl13α and 18S rRNA genes are more suitable as a reference gene panel for zebra fish tissue analysis.
Abstract: The normalization of quantitative real time RT-PCR (qRT-PCR) is important to obtain accurate gene expression data. The most common method for qRT-PCR normalization is to use reference, or house- keeping genes. However, there is emerging evidence that even reference genes can be regulated under differ- ent conditions. qRT-PCR has only recently been used in terms of zebrafish gene expression studies and there is no validated set of reference genes. This study characterizes the expression of nine possible reference genes during zebrafish embryonic development and in a zebrafish tissue panel. All nine reference genes exhibited variable expression. The β-actin, EF1α and Rpl13α genes comprise a validated reference gene panel for zebrafish developmental time course studies, and the EF1α, Rpl13α and 18S rRNA genes are more suitable as a reference gene panel for zebrafish tissue analysis. Importantly, the zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies.
TL;DR: Vitamin D status, which is amenable to intervention by safely increasing sun exposure or vitamin D supplementation, was associated inversely with BP in a large sample representative of the US population.
TL;DR: It is shown that GIGANTEA (GI) is essential to establish and sustain oscillations of ZTL by a direct protein-protein interaction, which results in the high-amplitude TOC1 rhythms necessary for proper clock function.
Abstract: The circadian clock is essential for coordinating the proper phasing of many important cellular processes. Robust cycling of key clock elements is required to maintain strong circadian oscillations of these clock-controlled outputs. Rhythmic expression of the Arabidopsis thaliana F-box protein ZEITLUPE (ZTL) is necessary to sustain a normal circadian period by controlling the proteasome-dependent degradation of a central clock protein, TIMING OF CAB EXPRESSION 1 (TOC1). ZTL messenger RNA is constitutively expressed, but ZTL protein levels oscillate with a threefold change in amplitude through an unknown mechanism. Here we show that GIGANTEA (GI) is essential to establish and sustain oscillations of ZTL by a direct protein-protein interaction. GI, a large plant-specific protein with a previously undefined molecular role, stabilizes ZTL in vivo. Furthermore, the ZTL-GI interaction is strongly and specifically enhanced by blue light, through the amino-terminal flavin-binding LIGHT, OXYGEN OR VOLTAGE (LOV) domain of ZTL. Mutations within this domain greatly diminish ZTL-GI interactions, leading to strongly reduced ZTL levels. Notably, a C82A mutation in the LOV domain, implicated in the flavin-dependent photochemistry, eliminates blue-light-enhanced binding of GI to ZTL. These data establish ZTL as a blue-light photoreceptor, which facilitates its own stability through a blue-light-enhanced GI interaction. Because the regulation of GI transcription is clock-controlled, consequent GI protein cycling confers a post-translational rhythm on ZTL protein. This mechanism of establishing and sustaining robust oscillations of ZTL results in the high-amplitude TOC1 rhythms necessary for proper clock function.
TL;DR: To be successful, large-scale rodent campaigns should be integrated with programs to improve the livelihoods of residents, island biosecurity, and reinvasion response programs, and applied research can further aid in minimizing impacts.
Abstract: Invasive mammals are the greatest threat to island biodiversity and invasive rodents are likely responsible for the greatest number of extinctions and ecosystem changes. Techniques for eradicating rodents from islands were developed over 2 decades ago. Since that time there has been a significant development and application of this conservation tool. We reviewed the literature on invasive rodent eradications to assess its current state and identify actions to make it more effective. Worldwide, 332 successful rodent eradications have been undertaken; we identified 35 failed eradications and 20 campaigns of unknown result. Invasive rodents have been eradicated from 284 islands (47,628 ha). With the exception of two small islands, rodenticides were used in all eradication campaigns. Brodifacoum was used in 71% of campaigns and 91% of the total area treated. The most frequent rodenticide distribution methods ( from most to least) are bait stations, hand broadcasting, and aerial broadcasting. Nevertheless, campaigns using aerial broadcast made up 76% of the total area treated. Mortality of native vertebrates due to nontarget poisoning has been documented, but affected species quickly recover to pre-eradication population levels or higher. A variety of methods have been developed to mitigate nontarget impacts, and applied research can further aid in minimizing impacts. Land managers should routinely remove invasive rodents from islands <100 ha that lack vertebrates susceptible to nontarget poisoning. For larger islands and those that require nontarget mitigation, expert consultation and greater planning effort are needed. With the exception of house mice (Mus musculus), island size may no longer be the limiting factor for rodent eradications; rather, social acceptance and funding may be the main challenges. To be successful, large-scale rodent campaigns should be integrated with programs to improve the livelihoods of residents, island biosecurity, and reinvasion response programs.
TL;DR: Imagine you are at an intersection, waiting for the traffic lights, and you are about to press the gas pedal, when suddenly a cyclist swerves into your lane and you have to rapidly prevent it from moving as planned.
Abstract: Imagine you are at an intersection, waiting for the traffic lights. They turn green, and you are about to press the gas pedal, when suddenly a cyclist swerves into your lane. Before your foot has actually moved, you have to rapidly prevent it from moving as planned. This example highlights the
TL;DR: These reporter lines will have utility in dissecting the genetic determinants of commitment to the myeloid lineage and in further defining how lysozyme-expressing cells participate during inflammation.
Abstract: How different immune cell compartments contribute to a successful immune response is central to fully understanding the mechanisms behind normal processes such as tissue repair and the pathology of inflammatory diseases. However, the ability to observe and characterize such interactions, in real-time, within a living vertebrate has proved elusive. Recently, the zebrafish has been exploited to model aspects of human disease and to study specific immune cell compartments using fluorescent reporter transgenic lines. A number of blood-specific lines have provided a means to exploit the exquisite optical clarity that this vertebrate system offers and provide a level of insight into dynamic inflammatory processes previously unavailable. We used regulatory regions of the zebrafish lysozyme C (lysC) gene to drive enhanced green fluorescent protein (EGFP) and DsRED2 expression in a manner that completely recapitulated the endogenous expression profile of lysC. Labeled cells were shown by co-expression studies and FACS analysis to represent a subset of macrophages and likely also granulocytes. Functional assays within transgenic larvae proved that these marked cells possess hallmark traits of myelomonocytic cells, including the ability to migrate to inflammatory sources and phagocytose bacteria. These reporter lines will have utility in dissecting the genetic determinants of commitment to the myeloid lineage and in further defining how lysozyme-expressing cells participate during inflammation.