Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

BackgroundMembranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of cellular ultra-structure. In addition, components embedded within the membrane participate in cell signaling, energy transduction, and other critical cellular functions. All these processes must share the limited space in the membrane; thus it represents a notable constraint on cellular functions. Membrane- and location-based processes have not yet been reconstructed and explicitly integrated into genome-scale models.ResultsThe recent genome-scale model of metabolism and protein expression in Escherichia coli (called a ME-model) computes the complete composition of the proteome required to perform whole cell functions. Here we expand the ME-model to include (1) a reconstruction of protein translocation pathways, (2) assignment of all cellular proteins to one of four compartments (cytoplasm, inner membrane, periplasm, and outer membrane) and a translocation pathway, (3) experimentally determined translocase catalytic and porin diffusion rates, and (4) a novel membrane constraint that reflects cell morphology. Comparison of computations performed with this expanded ME-model, named iJL1678-ME, against available experimental data reveals that the model accurately describes translocation pathway expression and the functional proteome by compartmentalized mass.ConclusioniJL1678-ME enables the computation of cellular phenotypes through an integrated computation of proteome composition, abundance, and activity in four cellular compartments (cytoplasm, periplasm, inner and outer membrane). Reconstruction and validation of the model has demonstrated that the iJL1678-ME is capable of capturing the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components. iJL1678-ME takes a notable step towards the inclusion of cellular ultra-structure in genome-scale models

Exploring environmental and biological drivers of cetacean occurrence in the cross-border region of the Malin Shelf using data from a European fishery survey

Irish and Scottish waters are important habitats for cetaceans in Europe. Yet, little data is available for the region of the Malin Shelf, north of Ireland. Despite a rich species diversity, relative cetacean abundance appears low compared to hotspots documented west of Scotland and Ireland. Whether this perceived low prevalence accurately portrays an ecological discontinuity or arises from a lack of published results and low survey effort in that transborder area remains unclear. Here, we used sighting records from a multi-disciplinary fisheries survey, the Western European Shelf Pelagic Acoustic Survey (WESPAS), to explore cetacean habitat preferences over the Malin and Hebridean shelves. Northern minke whale and common dolphin occurrence was modelled within a Bayesian Additive Regression Trees (BART) framework, against selected environmental and biological variables. No correlation was observed between cetacean presence and in-situ prey biomass. Minke whales distribution was better explained by oceanography, notably proxies for frontal activity, and primary productivity. Common dolphins similarly showed preferences for shelf waters within 5-25km of fronts, but also affinities for fine substrates. Favourable habitats identified by the models were consistent with literature around the Hebrides and shed light on potentially important areas along the Islay front and north of Donegal, so far unreported due to data deficiency. Results will contribute towards informing future monitoring, strategic management and conservation efforts in this cross-border region

Adaptation and qualitative evaluation of the BETTER intervention for chronic disease prevention and screening by public health nurses in low income neighbourhoods : views of community residents

The adaptation phase is one component of a study funded as a grant proposal entitled 'Advancing Cancer Prevention Among Deprived Neighbourhoods' by the Canadian Cancer Society Research Institute grant #704042 and by the Canadian Institutes of Health Research Institute of Cancer grant OCP #145450. Aisha Lofters is supported by a CIHR New Investigator Award, as a Clinician Scientist by the Department of Family and Community Medicine, University of Toronto, and as Chair in Implementation Science at the Peter Gilgan Centre for Women’s Cancers at Women’s College Hospital in partnership with the Canadian Cancer Society. Dr. Andrew Pinto holds a Canadian Institutes of Health Research Applied Public Health Chair and is supported as a Clinician-Scientist in the Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto, and supported by the Department of Family and Community Medicine, St. Michael’s Hospital, and the Li Ka Shing Knowledge Institute, St. Michael’s Hospital. He is also the Associate Director for Clinical Research at the University of Toronto Practice-Based Research Network. Lawrence Paszat is supported by a Clinician Scientist award funded by the Ontario Ministry of Health and Long Term Care.Background The BETTER intervention is an effective comprehensive evidence-based program for chronic disease prevention and screening (CDPS) delivered by trained prevention practitioners (PPs), a new role in primary care. An adapted program, BETTER HEALTH, delivered by public health nurses as PPs for community residents in low income neighbourhoods, was recently shown to be effective in improving CDPS actions. To obtain a nuanced understanding about the CDPS needs of community residents and how the BETTER HEALTH intervention was perceived by residents, we studied how the intervention was adapted to a public health setting then conducted a post-visit qualitative evaluation by community residents through focus groups and interviews. Methods We first used the ADAPT-ITT model to adapt BETTER for a public health setting in Ontario, Canada. For the post-PP visit qualitative evaluation, we asked community residents who had received a PP visit, about steps they had taken to improve their physical and mental health and the BETTER HEALTH intervention. For both phases, we conducted focus groups and interviews; transcripts were analyzed using the constant comparative method. Results Thirty-eight community residents participated in either adaptation (n = 14, 64% female; average age 54 y) or evaluation (n = 24, 83% female; average age 60 y) phases. In both adaptation and evaluation, residents described significant challenges including poverty, social isolation, and daily stress, making chronic disease prevention a lower priority. Adaptation results indicated that residents valued learning about CDPS and would attend a confidential visit with a public health nurse who was viewed as trustworthy. Despite challenges, many recipients of BETTER HEALTH perceived they had achieved at least one personal CDPS goal post PP visit. Residents described key relational aspects of the visit including feeling valued, listened to and being understood by the PP. The PPs also provided practical suggestions to overcome barriers to meeting prevention goals. Conclusions Residents living in low income neighbourhoods faced daily stress that reduced their capacity to make preventive lifestyle changes. Key adapted features of BETTER HEALTH such as public health nurses as PPs were highly supported by residents. The intervention was perceived valuable for the community by providing access to disease prevention. Trial registration #NCT03052959, 10/02/2017.Peer reviewe

Global Law as Intercontextuality and as Interlegality

Since the 1990s the effects of globalization on law and legal developments has been a central topic of scholarly debate. To date, the debate is however marked by three substantial deficiencies which this chapter seeks to remedy through a reconceptualization of global law as a law of inter-contextuality expressed through inter-legality and materialized through a particular body of legal norms which can be characterized as connectivity norms. The first deficiency is a historical and empirical one. Both critics as well as advocates of ‘non-state law’ share the assumption that ‘law beyond the state’ and related legal norms have gained in centrality when compared with previous historical times. While global law, including both public and private global governance law as well as regional occurrences such as EU law, has undergone profound transformations since the structural transformations which followed the de-colonialization processes of the mid-twentieth century, we do not have more global law relatively to other types of law today than in previous historical times. The second deficiency is a methodological one. The vast majority of scholarship on global law is either of an analytical nature, drawing on insights from philosophy, or empirically observing the existence of global law and the degree of compliance with global legal norms at a given moment in time. While both approaches bring something to the table they remain static approaches incapable of explaining and evaluating the transformation of global law over time. The third deficiency is a conceptual-theoretical one. In most instances, global law is understood as a unitary law producing singular legal norms with a planetary reach, or, alternatively, a radical pluralist perspective is adopted dismissing the existence of singular global norms. Both of these approaches however misapprehend the structural characteristics, function and societal effects of global law. Instead a third positon between unitary and radical pluralist perspectives can be adopted through an understanding of global law and its related legal norms as a de-centred kind of inter-contextual law characterised by inter-legality

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

Temperate phages drive genomic diversification in bacterial pathogens. Phage-derived sequences are more common in pathogenic than non-pathogenic taxa, and are associated with changes in pathogen virulence. High abundance and mobilisation of temperate phages within hosts suggests that temperate phages could promote within-host evolution of bacterial pathogens. However,their role in pathogen evolution has not been experimentally tested. We experimentally evolved replicate populations of Pseudomonas aeruginosa with or without a community of three temperate phages active in cystic fibrosis (CF) lung infections, including the transposable phage, ɸ4, which is closely related to phage D3112. Populations grew as free-floating biofilms in artificial sputum medium, mimicking sputum of CF lungs where P. aeruginosa is an important pathogen and undergoes evolutionary adaptation and diversification during chronic infection. While bacterial populations adapted to the biofilm environment in both treatments, population genomic analysis revealed that phages altered both the trajectory and mode of evolution. Populations evolving with phages exhibited a greater degree of parallel evolution and faster selective sweeps than populations without phages. Phage ɸ4, integrated randomly into the bacterial chromosome but integrations into motility-associated genes and regulators of quorum sensing systems essential for virulence were selected in parallel, strongly suggesting that these insertional inactivation mutations were adaptive. Temperate phages, and in particular transposable phages, are therefore likely to facilitate adaptive evolution of bacterial pathogens within hosts

Swift XRT Observations of the Afterglow of GRB 050319

Swift discovered the high redshift GRB 050319 with the Burst Alert Telescope and began observing with its narrow field instruments only 225 s after the burst onset. The afterglow X-ray emission was monitored by the XRT up to 28 days after the burst. The light curve shows a decay with three different phases, each characterized by a distinct slope: an initial steep decay with a power law index of ~ 5.5, a second phase characterized by a flat decay slope of \~ 0.54, and a third phase with a decay slope of ~ 1.14. During the first phase the spectral energy distribution is softer than in the following two phases and the photon index is consistent with the GRB prompt spectrum. The extrapolation of the BAT light curve to the XRT band suggests that the initial fast decaying phase of the XRT afterglow might be the low energy tail of the prompt emission. The second break in the afterglow light curve occurs about 27000 s after the burst. The spectral energy distribution before and after the second break does not change and it can be tentatively interpreted as a jet break or the end of a delayed or continuous energy injection phase.Comment: 15 pages, 2 figures. Accepted for publication in Ap

Strengthening and stretching for rheumatoid arthritis of the hand (SARAH):Design of a randomised controlled trial of a hand and upper limb exercise intervention-ISRCTN89936343

Background: Rheumatoid Arthritis (RA) commonly affects the hands and wrists with inflammation, deformity, pain, weakness and restricted mobility leading to reduced function. The effectiveness of exercise for RA hands is uncertain, although evidence from small scale studies is promising. The Strengthening And Stretching for Rheumatoid Arthritis of the Hand (SARAH) trial is a pragmatic, multi-centre randomised controlled trial evaluating the clinical and cost effectiveness of adding an optimised exercise programme for hands and upper limbs to best practice usual care for patients with RA.Methods/design: 480 participants with problematic RA hands will be recruited through 17 NHS trusts. Treatments will be provided by physiotherapists and occupational therapists. Participants will be individually randomised to receive either best practice usual care (joint protection advice, general exercise advice, functional splinting and assistive devices) or best practice usual care supplemented with an individualised exercise programme of strengthening and stretching exercises. The study assessors will be blinded to treatment allocation and will follow participants up at four and 12 months. The primary outcome measure is the Hand function subscale of the Michigan Hand Outcome Questionnaire, and secondary outcomes include hand and wrist impairment measures, quality of life, and resource use. Economic and qualitative studies will also be carried out in parallel.Discussion: This paper describes the design and development of a trial protocol of a complex intervention study based in therapy out-patient departments. The findings will provide evidence to support or refute the use of an optimised exercise programme for RA of the hand in addition to best practice usual care.Trial registration: Current Controlled Trials ISRCTN89936343Keywords: Randomised controlled trial, Rheumatoid arthritis, Exercise, Hand, Rehabilitatio

GRB 050117: Simultaneous Gamma-ray and X-ray Observations with the Swift Satellite

The Swift Gamma-Ray Burst Explorer performed its first autonomous, X-ray follow-up to a newly detected GRB on 2005 January 17, within 193 seconds of the burst trigger by the Swift Burst Alert Telescope. While the burst was still in progress, the X-ray Telescope obtained a position and an image for an un-catalogued X-ray source; simultaneous with the gamma-ray observation. The XRT observed flux during the prompt emission was 1.1 x 10^{-8} ergs cm^{-2} s^{-1} in the 0.5-10 keV energy band. The emission in the X-ray band decreased by three orders of magnitude within 700 seconds, following the prompt emission. This is found to be consistent with the gamma-ray decay when extrapolated into the XRT energy band. During the following 6.3 hours, the XRT observed the afterglow in an automated sequence for an additional 947 seconds, until the burst became fully obscured by the Earth limb. A faint, extremely slowly decaying afterglow, alpha=-0.21$, was detected. Finally, a break in the lightcurve occurred and the flux decayed with alpha<-1.2$. The X-ray position triggered many follow-up observations: no optical afterglow could be confirmed, although a candidate was identified 3 arcsecs from the XRT position.Comment: 27 pages, 6 figures. Accepted for publication in Ap

Postpartum-specific anxiety as a predictor of infant-feeding outcomes and perceptions of infant-feeding behaviours: new evidence for childbearing specific measures of mood

Studies of pregnancy-specific anxiety suggest that it is a distinct construct which predicts perinatal outcomes more effectively than other general measures of anxiety. In response, a novel measure of postpartum-specific anxiety (PSAS) has been developed and validated, but it is not yet clear whether it possesses the same predictive power as its pregnancy-specific counterparts. The aim of this short-term prospective study was to (a) test the predictive validity of the PSAS in the context of one specific perinatal outcome, infant-feeding, and (b) examine whether the PSAS may be more efficacious at predicting infant-feeding outcomes and behaviours than the more commonly used general measures. Eight hundred mothers of infants aged between 0 and 6 months completed the PSAS alongside general measures of anxiety and depression at baseline. A subsample (n = 261) returned to complete a follow-up questionnaire examining infant-feeding outcomes and behaviours two weeks later. Hierarchical regression models revealed that the PSAS was associated with lower odds of breastfeeding exclusively, and breastfeeding in any quantity in the first 6 months postpartum. PSAS scores were also significantly associated with infant-feeding behaviours including a lower perceived enjoyment of food, and greater perceived food responsiveness and satiety responsiveness in the infant. As hypothesised, the PSAS was a stronger predictor of infant-feeding outcomes and behaviours than general anxiety and depression. The findings provide evidence for the predictive validity of the PSAS and call for the use of childbearing specific measures of mood when attempting to predict perinatal outcomes. Replication of these findings across other indices of maternal and infant health is now necessary