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

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

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

Road tunnel, roadside, and urban background measurements of aliphatic compounds in size-segregated particulate matter

Particulate matter samples were collected in a road tunnel in Lisbon (PM0.5, PM0.5-1, PM1-2.5, and PM2.5-10) and at two urban locations representing roadside and background stations (PM2.5 and PM2.5-10). Samples were analysed for organic and elemental carbon (OC and EC), n-alkanes, n-alkenes, hopanes, some isoprenoid compounds, and steranes. Particulate matter concentrations in the tunnel were 17-31 times higher than at roadside in the vicinity, evidencing an aerosol origin almost exclusively in fresh vehicle emissions. PM0.5 in the tunnel comprised more than 60% and 80% of the total OC and EC mass in PM10, respectively. Concentrations of the different aliphatic groups of compounds in the tunnel were up to 89 times higher than at roadside and 143 times higher than at urban background. Based on the application of hopane-to-OC or hopanes-to-EC ratios obtained in the tunnel, it was found that vehicle emissions are the dominant contributor to carbonaceous particles in the city but do not represent the only source of these triterpenic compounds. Contrary to what has been observed in other studies, the Sigma hopane-to-EC ratios were higher in summer than in winter, suggesting that other factors (e.g. biomass burning, dust resuspension, and different fuels/engine technologies) prevail in relation to the photochemical decay of triterpenoid hydrocarbons from vehicle exhaustinfo:eu-repo/semantics/publishedVersio

Clinical Influence of Different Intracanal Medications on Th1-type and Th2-type Cytokine Responses in Apical Periodontitis

Introduction: This clinical study assessed the influence of different intracanal medications on Th1-type and Th2-type cytokine responses in apical periodontitis and monitored the levels of bacteria from primarily infection during endodontic procedures. Methods: Thirty primarily infected teeth were randomly divided into 3 groups according to the medication selected: chlorhexidine (CHX), 2% CHX gel; Ca(OH)2/SSL, Ca(OH)2 + SSL; and Ca(OH)2/CHX, Ca(OH)2 + 2% CHX gel (all, n = 10). Bacterial sample was collected from root canals, and the interstitial fluid was sampled from lesions. Culture techniques were used to determine bacterial counts (colony-forming units/mL). Th1 (tumor necrosis factor-a, interferon-gamma, and interleukin [IL]-2) and Th2 cytokines (IL-4, IL-5, and IL-13) were measured by enzyme-linked immunosorbent assay. Results: All intracanal medication protocols were effective in reducing the bacterial load from root canals (all P < .05) and lowering the levels of Th1-type cytokines in apical lesions (all P < .05), with no differences between them (P > .05). Both Ca(OH)2 treatment protocols significantly increased the levels of Th2-type cytokines (P < .05), with no differences between them (P > .05). Thus, chlorhexidine medication showed the lowest effectiveness in increasing the levels of Th2-type cytokine. After treatment, regardless of the type of medication, the linear regression analysis indicated the down-regulation of Th2-type cytokines by Th1-type cytokines. Conclusions: All intracanal medication protocols were effective in reducing bacterial load and lowering the levels of Th1-type cytokines. Thus, the use of Ca(OH)2 medications contributed to the increase in the Th2-type cytokine response in apical periodontitis.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Endodontic retreatment: clinical comparison of reciprocating systems versus rotary system in disinfecting root canals

Introduction This clinical study was conducted to compare the effectiveness of single-file reciprocating systems and rotary systems in removing endotoxins and cultivable bacteria in endodontic retreatment.Methods Thirty endodontically treated teeth with post-treatment apical periodontitis were selected. The specimens were divided into three groups according to the system used: WaveOne (n=10), Reciproc instrument (n=10), and ProTaper Universal Retreatment system (n=10). Samples were collected before and after chemomechanical preparation. The irrigation was performed by using 2.5% sodium hypochlorite. A chromogenic limulus amebocyte lysate assay test was used to quantify endotoxins. Culture techniques were used to determine bacterial colony-forming unit counts.Results At baseline, endotoxins and cultivable bacteria were recovered from 100% of the root canal samples in a median value of 5.84 EU/mL and 4.98x10(3) CFU/mL, respectively. After CMP, no differences were found in the median percentage values of endotoxin reduction achieved with reciprocating systems-WaveOne [94.11%] and Reciproc [93.29%] and with rotary systems-ProTaper [94.98%] (P>0.05). Both single-file reciprocating systems [WaveOne (98.27%) and Reciproc (99.54%)] and rotary system [ProTaper (98.73%)] were effective in reducing bacterial load (P>0.05). Moreover, no differences were found among the systems tested.Conclusions The Reciproc and WaveOne reciprocating systems were as effective as the ProTaper system for removal of endotoxins and bacteria in endodontic retreatment.Clinical relevance All systems tested were effective to remove cultivable bacteria and endotoxin in endodontic retreatment. As no differences among systems were observed, it is possible to suggest that clinicians should choose the preferred technique to perform endodontic.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Measurement of pH. Definition, standards, and procedures

The definition of a "primary method of measurement" [1] has permitted a full consideration of the definition of primary standards for pH, determined by a primary method (cell without transference, Harried cell), of the definition of secondary standards by secondary methods, and of the question whether pH, as a conventional quantity, can be incorporated within the internationally accepted system of measurement, the International System of Units (SI, Systeme International d'Unites). This approach has enabled resolution of the previous compromise IUPAC 1985 Recommendations [2]. Furthermore, incorporation of the uncertainties for the primary method, and for all subsequent measurements, permits the uncertainties for all procedures to be linked to the primary standards by an unbroken chain of comparisons. Thus, a rational choice can be made by the analyst of the appropriate procedure to achieve the target uncertainty of sample pH. Accordingly, this document explains IUPAC recommended definitions, procedures, and terminology relating to pH measurements in dilute aqueous solutions in the temperature range 5-50 degreesC. Details are given of the primary and secondary methods for measuring pH and the rationale for the assignment of pH values with appropriate uncertainties to selected primary and secondary substances