Predicting the targeting of tail-anchored proteins to subcellular compartments in mammalian cells

This is the author accepted manuscript. The final version is available from Company of Biologists via the DOI in this record.Tail-anchored (TA) proteins contain a single transmembrane domain (TMD) at the Cterminus, anchoring them to organelle membranes where they mediate a variety of critical cellular processes. Mutations in individual TA proteins cause a number of severe inherited disorders. However, the molecular mechanisms and signals facilitating proper TA protein targeting are not fully understood, in particular in mammals. Here, we identify additional TA proteins at peroxisomes or shared by multiple organelles in mammals and reveal that a combination of TMD hydrophobicity and tail charge determines targeting to distinct organelles. Specifically, an increase in tail charge can override a hydrophobic TMD signal and re-direct a protein from the ER to peroxisomes or mitochondria and vice versa. We demonstrate that subtle alterations in those physicochemical parameters can shift TA protein targeting between organelles, explaining why peroxisomes and mitochondria share many TA proteins. Our analyses enabled us to allocate characteristic physicochemical parameters to different organelle groups. This classification allows for the first time, successful prediction of the location of uncharacterized TA proteins.We thank colleagues who provided materials (see Tables S1-S4) and acknowledge support from A. C. Magalhães, M. Almeida, D. Tuerker, S. Kuehl and C. Davies. This work was supported by the Biotechnology and Biological Sciences Research Council (BB/K006231/1 to M.S.), a Wellcome Trust Institutional Strategic Support Award (WT097835MF, WT105618MA to M.S.), the Portuguese Foundation for Science and Technology and FEDER/COMPETE (PTDC/BIA-BCM/118605/2010 to M.S.; SFRH/BD/37647/2007 to N.B.; SFRH/BPD/77619/2011 and UID/BIM/04501/2013 to D.R.). M.W., E.A.G., and M.S. are supported by Marie Curie Initial Training Network (ITN) action PerFuMe (316723)

Effect of mixture proportions on the drying shrinkage and permeation properties of high strength concrete containing class F fly ash

Sustainability of concrete can be improved by using large volume of fly ash as a replacement of cement and by ensuring improved durability of concrete. Durability of concrete containing large volume of class F fly ash is dependent on the design of mixture proportions. This paper presents an experimental study on the effect of mixture proportions on the drying shrinkage and permeation properties of high strength concrete containing large volume local class F fly ash. Concrete mixtures were designed with and without adjustments in the water to binder ratio (w/b) and the total binder content to take into account the incorporation of fly ash up to 40% of total binder. Concretes, in which the mixture proportions were adjusted for fly ash inclusion achieved equivalent strength of the control concrete and showed enhanced properties of drying shrinkage, sorptivity, water permeability and chloride penetration as compared to the control concrete. The improvement of durability properties was less significant when no adjustments were made to the w/b ratio and total binder content. The results show the necessity of the adjustments in mixture proportions of concrete to achieve improved durability properties when using class F fly ash as a cement replacement

Socioeconomic Inequalities in the Prevalence of Nine Established Cardiovascular Risk Factors in a Southern European Population

The evaluation of the gender-specific prevalence of cardiovascular risk factors across socioeconomic position (SEP) categories may unravel mechanisms involved in the development of coronary heart disease. Using a sample of 1704 community dwellers of a Portuguese urban center aged 40 years or older, assessed in 1999–2003, we quantified the age-standardized prevalence of nine established cardiovascular risk factors (diabetes mellitus, hypertension, hypercholesterolemia, smoking, sedentariness, abdominal obesity, poor diet, excessive alcohol intake and depression) across SEP and gender categories. Data on individual education and occupation were collected by questionnaire and used to characterize SEP. The prevalence of seven out of nine well-established risk factors was higher in men. Among women, the prevalence of most of the studied risk factors was higher in lower SEP groups. The main exception was smoking, which increased with education and occupation levels. Among men, socioeconomic gradients were less clear, but lower SEP was associated with a higher prevalence of diabetes, excessive alcohol intake and depression in a graded mode. The historical cultural beliefs and practices captured throughout the lifecourse frame the wide socioeconomic gradients discernible in our study conducted in an unequal European developed population. While men were more exposed to most risk factors, the clearer associations between SEP and risk factors among women support that their adoption of particular healthy behaviors is more dependent on material and symbolic conditions. To fully address the issue of health inequalities, interventions within the health systems should be complemented with population-based policies specifically designed to reduce socioeconomic gradients

Clinical and organizational factors associated with mortality during the peak of first COVID-19 wave: the global UNITE-COVID study

Purpose: To accommodate the unprecedented number of critically ill patients with pneumonia caused by coronavirus disease 2019 (COVID-19) expansion of the capacity of intensive care unit (ICU) to clinical areas not previously used for critical care was necessary. We describe the global burden of COVID-19 admissions and the clinical and organizational characteristics associated with outcomes in critically ill COVID-19 patients. Methods: Multicenter, international, point prevalence study, including adult patients with SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) and a diagnosis of COVID-19 admitted to ICU between February 15th and May 15th, 2020. Results: 4994 patients from 280 ICUs in 46 countries were included. Included ICUs increased their total capacity from 4931 to 7630 beds, deploying personnel from other areas. Overall, 1986 (39.8%) patients were admitted to surge capacity beds. Invasive ventilation at admission was present in 2325 (46.5%) patients and was required during ICU stay in 85.8% of patients. 60-day mortality was 33.9% (IQR across units: 20%–50%) and ICU mortality 32.7%. Older age, invasive mechanical ventilation, and acute kidney injury (AKI) were associated with increased mortality. These associations were also confirmed specifically in mechanically ventilated patients. Admission to surge capacity beds was not associated with mortality, even after controlling for other factors. Conclusions: ICUs responded to the increase in COVID-19 patients by increasing bed availability and staff, admitting up to 40% of patients in surge capacity beds. Although mortality in this population was high, admission to a surge capacity bed was not associated with increased mortality. Older age, invasive mechanical ventilation, and AKI were identified as the strongest predictors of mortality

Co-infection and ICU-acquired infection in COIVD-19 ICU patients: a secondary analysis of the UNITE-COVID data set

Background: The COVID-19 pandemic presented major challenges for critical care facilities worldwide. Infections which develop alongside or subsequent to viral pneumonitis are a challenge under sporadic and pandemic conditions; however, data have suggested that patterns of these differ between COVID-19 and other viral pneumonitides. This secondary analysis aimed to explore patterns of co-infection and intensive care unit-acquired infections (ICU-AI) and the relationship to use of corticosteroids in a large, international cohort of critically ill COVID-19 patients.Methods: This is a multicenter, international, observational study, including adult patients with PCR-confirmed COVID-19 diagnosis admitted to ICUs at the peak of wave one of COVID-19 (February 15th to May 15th, 2020). Data collected included investigator-assessed co-infection at ICU admission, infection acquired in ICU, infection with multi-drug resistant organisms (MDRO) and antibiotic use. Frequencies were compared by Pearson's Chi-squared and continuous variables by Mann-Whitney U test. Propensity score matching for variables associated with ICU-acquired infection was undertaken using R library MatchIT using the "full" matching method.Results: Data were available from 4994 patients. Bacterial co-infection at admission was detected in 716 patients (14%), whilst 85% of patients received antibiotics at that stage. ICU-AI developed in 2715 (54%). The most common ICU-AI was bacterial pneumonia (44% of infections), whilst 9% of patients developed fungal pneumonia; 25% of infections involved MDRO. Patients developing infections in ICU had greater antimicrobial exposure than those without such infections. Incident density (ICU-AI per 1000 ICU days) was in considerable excess of reports from pre-pandemic surveillance. Corticosteroid use was heterogenous between ICUs. In univariate analysis, 58% of patients receiving corticosteroids and 43% of those not receiving steroids developed ICU-AI. Adjusting for potential confounders in the propensity-matched cohort, 71% of patients receiving corticosteroids developed ICU-AI vs 52% of those not receiving corticosteroids. Duration of corticosteroid therapy was also associated with development of ICU-AI and infection with an MDRO.Conclusions: In patients with severe COVID-19 in the first wave, co-infection at admission to ICU was relatively rare but antibiotic use was in substantial excess to that indication. ICU-AI were common and were significantly associated with use of corticosteroids

Transnational corporations, violence and suffering: the environmental, public health and social impacts from comparative case studies in Zimbabwe and Uganda

The present effects of transnational corporations (TNCs) on social, health, and environmental aspects of local societies have a long history. The preconditions for the insertion of the types of economic initiatives now seen in the Global South, and driven by TNCs, were set through histories of colonialism and development schemes. These initiatives disrupted local economies and modified environments, delivering profound effects on livelihoods. These effects were experienced as structural violence, and have produced social suffering through the decades.In this paper, we compare two African cases across time; the conjunction of development initiatives and structural adjustment in the Zambezi Valley, Zimbabwe in the early 1990s and industrial plantation forestry in present-day Uganda. Each case presents a specific constellation of political and economic forces that has produced prejudicial effects on local populations in their time period of application and are, essentially, different versions of structural violence that produce social suffering. While each case depicts a specific type of violent encounter manifest at a particular historical moment, these are comparable in the domains of environmental impacts, disruptions to societies, co-opting of local economies, disordering of systems of meaning and social reproduction, and nefarious effects on well-being. We analyze the conjunction of these effects through a theoretical lens of structural violence and social suffering. Our analysis draws particular attention to the role of TNCs in driving this structural violence and its effects

Meeting the Requirements of the Silver/Silver Chloride Reference Electrode

Potentiometric cells from which the pH values of standard buffer solutions are computed rely on the silver-silver chloride reference electrode which has proved to be convenient, reproducible and reliable. Of the various methods of preparation of silver-silver chloride electrodes only one concerns us here: the thermal-electrolytic type that has been used more extensively than any other form. Once prepared, the electrodes need to be equilibrated before use and between experiments. The equilibration technique must ensure voltage stability and inter-electrode, or bias, potential below 0.1 mV. In potentiometry the stability of a reference electrode is of utmost importance since an offset of 1 mV is equivalent to a deviation of about 0.02 in the pH value. A thorough study has been conducted, involving a critical assessment of the various protocols which have been developed and adopted by different research schools and have been used in the course of inter-laboratory exercises. Factors that affect the electrode performance, such as size, mass, chloridization, storage and conditioning were systematically investigated, through measurements of bias potential, leading to a set of recommended procedures that meet the requirements for high quality results. In this work, the adequacy of the optimized methodology is confirmed by means of primary pH measurements

Improving the quality of potentiometric pH measurements

Like all experimentally determined physical and chemical properties, pH measurements are affected by the limited precision and accuracy of the measurement procedures. Fundamental studies of pH standards, based on measurement of the potential of an electrochemical cell without transference, known as the Harned cell, containing a platinum-hydrogen electrode and a silver-silver chloride reference electrode, indicate that vapour condensation phenomena on potentiometric cell walls not immersed in the thermostatic bath are a major source of error in assessment of pH values. In this work a study was conducted on phthalate buffer, 0.05 mol kg(-1)supercript stop KHPhth, and results are reported for the effect of this phenomenon on the assignment of pH values and on their corresponding uncertainties. Identification and quantification of this effect constitute an original contribution to improvement of the primary method of pH measurement and, therefore, more rigorous pH (PS) values