Characterization Of The Integrative Precursor Protein-dna Complex Of Bacteriophage Mu

Bacteriophage Mu integrates and replicates its genome via DNA transposition. Mu transposition during integration is non-replicative (conservative) and generates simple insertions. Transposition during the lytic cycle is replicative and amplifies the Mu genome by cointegrate production. Mu therefore, must choose between these two pathways. Infecting Mu-DNA is found associated with a coinjected, 64-kDa virion protein bound noncovalently to its ends. Characterization of the protein-DNA complex is reported here.;Antiserum was prepared against the virion 64-kDa protein and used to probe an expression library of cloned Mu DNA sequences. The Mu {dollar}N{dollar} gene was mapped to the overproducing clones by physical and genetic techniques. Partial proteolysis of the N protein produced in vitro and the 64-kDa protein isolated from the protein-DNA complex showed them to be identical. The Mu {dollar}N{dollar} gene was sequenced and a region of homology to many site specific DNA binding proteins was observed.;The transposition end product produced in vitro by the N protein-Mu DNA complex isolated from Mu infected cells was examined by neutral and alkaline agarose gel electrophoresis. The protein-DNA complex was found to form an identical strand transferred end product as the mini-Mu control plasmid. The implication of these findings for Mu integration is that in vivo, the strand transferred product is probably processed by a second nick following the initial strand transfer reaction of transposition

amIcompositional: Simple Tests for Compositional Behaviour of High Throughput Data with Common Transformations

Compositional approaches are beginning to permeate high throughput biomedical sciences in the areas of microbiome, genomics, transcriptomics and proteomics. Yet non-compositional approaches are still commonly observed. Non-compositional approaches are particularly problematic in network analysis based on correlation, ordination and exploratory data analysis based on distance, and differential abundance analysis based on normalization. Here we describe the aIc R package, a simple tool that answers the fundamental question: does the dataset or normalization exhibit compositional artefacts that will skew interpretations when analyzing high throughput biomedical data? The aIc R package includes options for several of the most widely used normalizations and filtering methods. The R package includes tests for subcompositional dominance and coherence along with perturbation and scale invariance. Exploratory analysis is facilitated by an R Shiny app that makes the process simple for those not wishing to use an R console. This simple approach will allow research groups to acknowledge and account for potential artefacts in data analysis resulting in more robust and reliable inferences

Research priorities in the field of posttraumatic pain and disability: Results of a transdisciplinary consensus-generating workshop

© Copyright 2016 David M.Walton et al. Background. Chronic or persistent pain and disability following noncatastrophic \u27musculoskeletal\u27 (MSK) trauma is a pervasive public health problem. Recent intervention trials have provided little evidence of benefit from several specific treatments for preventing chronic problems. Such findings may appear to argue against formal targeted intervention for MSK traumas. However, these negative findings may reflect a lack of understanding of the causal mechanisms underlying the transition from acute to chronic pain, rendering informed and objective treatment decisions difficult. The Canadian Institutes of Health Research (CIHR) Institute ofMusculoskeletalHealth and Arthritis (IMHA) has recently identified better understanding of causalmechanisms as one of three priority foci of their most recent strategic plan. Objectives. A 2-day invitation-only active participation workshop was held inMarch 2015 that included 30 academics, clinicians, and consumers with the purpose of identifying consensus research priorities in the field of trauma-relatedMSK pain and disability, prediction, and prevention. Methods. Conversations were recorded, explored thematically, and member-checked for accuracy. Results. From the discussions, 13 themes were generated that ranged from a focus on identifying causal mechanisms and models to challenges with funding and patient engagement. Discussion. Novel priorities included the inclusion of consumer groups in research from the early conceptualization and design stages and interdisciplinary longitudinal studies that include evaluation of integrated phenotypes and mechanisms

Solar radiation and functional traits explain the decline of forest primary productivity along a tropical elevation gradient

One of the major challenges in ecology is to understand how ecosystems respond to changes in environmental conditions, and how taxonomic and functional diversity mediate these changes. In this study, we use a trait-spectra and individual-based model, to analyse variation in forest primary productivity along a 3.3 km elevation gradient in the Amazon-Andes. The model accurately predicted the magnitude and trends in forest productivity with elevation, with solar radiation and plant functional traits (leaf dry mass per area, leaf nitrogen and phosphorus concentration, and wood density) collectively accounting for productivity variation. Remarkably, explicit representation of temperature variation with elevation was not required to achieve accurate predictions of forest productivity, as trait variation driven by species turnover appears to capture the effect of temperature. Our semi-mechanistic model suggests that spatial variation in traits can potentially be used to estimate spatial variation in productivity at the landscape scale.N.F. and Y.M were funded by a European Research Council (ERC) Advanced Investigator grant GEM-TRAIT (321131) to Y.M. The field campaign was funded by grants to Y.M. and PM from the UK Natural Environment Research Council (Grants NE/ J023418/1, NE/J023531/1, NE/F002149/1) and the Gordon and Betty Moore Foundation to Y.M, G.P.A and O.L.P. with additional support from European Research Council Advanced Investigator grants GEM-TRAIT (321131) and TFORCES (291585) to Y.M. and O.L.P. under the European Union’s Seventh Framework Programme (FP7/2007-2013) and the U.S. National Science Foundation grant to G.P.A. (DEB-1146206). B.J.E. was supported by an Oxford Martin School Visiting Fellowship and NSF grant DEB 1457804. Y.M. was also supported by the Jackson Foundation; O.K.A. and P.M. acknowledge the support of the Australian Research Council (CE140100008, DP0986823, DP130101252, FT110100457). S.D. was partially supported by a Visiting Professorship Grant from the Leverhulme Trust, UK

Research Priorities in the Field of Posttraumatic Pain and Disability: Results of a Transdisciplinary Consensus-Generating Workshop

Background. Chronic or persistent pain and disability following noncatastrophic “musculoskeletal” (MSK) trauma is a pervasive public health problem. Recent intervention trials have provided little evidence of benefit from several specific treatments for preventing chronic problems. Such findings may appear to argue against formal targeted intervention for MSK traumas. However, these negative findings may reflect a lack of understanding of the causal mechanisms underlying the transition from acute to chronic pain, rendering informed and objective treatment decisions difficult. The Canadian Institutes of Health Research (CIHR) Institute of Musculoskeletal Health and Arthritis (IMHA) has recently identified better understanding of causal mechanisms as one of three priority foci of their most recent strategic plan. Objectives. A 2-day invitation-only active participation workshop was held in March 2015 that included 30 academics, clinicians, and consumers with the purpose of identifying consensus research priorities in the field of trauma-related MSK pain and disability, prediction, and prevention. Methods. Conversations were recorded, explored thematically, and member-checked for accuracy. Results. From the discussions, 13 themes were generated that ranged from a focus on identifying causal mechanisms and models to challenges with funding and patient engagement. Discussion. Novel priorities included the inclusion of consumer groups in research from the early conceptualization and design stages and interdisciplinary longitudinal studies that include evaluation of integrated phenotypes and mechanisms