Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions

Little is known about the role of global phosphorylation events in the control of prokaryote metabolism. By performing a detailed analysis of all protein phosphorylation events previously reported in Escherichia coli, dynamic changes in protein phosphorylation were elucidated under three different culture conditions. Using scheduled reaction monitoring, the phosphorylation ratios of 82 peptides corresponding to 71 proteins were quantified to establish whether serine (S), threonine (T) and tyrosine (Y) phosphorylation events displayed a dynamic profile under changing culture conditions. The ratio of phosphorylation for 23 enzymes from central carbon metabolism was found to be dynamic. The data presented contributes to our understanding of the global role of phosphorylation in bacterial metabolism and highlight that phosphorylation is an important, yet poorly understood, regulatory mechanism of metabolism control in bacteria

Predictors of Hearing Aid Use Time in Children With Mild-to-Severe Hearing Loss

Purpose—This study investigated predictors of hearing aid (HA) use time for children with mild-severe hearing loss. Barriers to consistent HA use and reliability of parent report measures were also examined. Method—Participants included parents of 272 children with hearing loss. Parents estimated the amount of time the child used HAs daily. Regression analysis examined the relationships among independent variables and HA use time. To determine parental accuracy of HA use time, datalogging from the HA was compared to parental estimates. Results—Longer HA use related to older age, poorer hearing, and higher maternal education. Parental consistency ratings revealed similar findings; younger children and children with milder hearing losses wore HAs less consistently than older children and children with more severe hearing loss. Parents’ estimates and datalogging were significantly correlated; however, results suggested parents overestimate the amount of time their children wear their hearing aids. Conclusions—The findings provide evidence that certain variables were significantly related to the amount of time children wore their HAs. Consistency rating scales provided insight into circumstances that were challenging for families. Use of both parental reports and datalogging may allow clinicians and researchers to obtain a general estimate of HA use time

Lipidomics for the Prediction of the Unstable Coronary Plaque

Plaques that build up in the lining of the coronary arteries are made up of lipids, inflammatory cells, smooth muscle cells and connective tissue. Thormbosis of a not necessarily occlusive but unstable plaque most often causes episodes of unstable angina and myocardial infarction (MI). Preventing this sudden and adverse event seems to be the only effective startegy to reduce mortality and morbidity of coronary artery disease (CAD). Countries in the Middle East bear a heavy burden from cardiovascular disease. The population of Qatar is particularly prone to CAD with patients presenting with MI at a young age. The prevalence of CAD is in turn promoted by risk factors such as smoking, hypertension, dyslipidemia, diabetes and sedentary lifestyles. Metabolomics approaches to the identification of disease biomarkers rely principally on the comparitive analysis of metabolite expression in normal and disease patients, animal models or cell cultures to identify aberrantly expressed proteins or concentration changes in metabolites that may represent new biomarkers or elucidate a disease mechanism. Lipidomics is the global identification and quantification of a diverse range of lipids in biological systems and is a subset field in metabolomics. The eukaryotic lipidome might compise of 10,000 to 100,000 individual species of lipids originating from a few hundred lipid classes. These lipids are distributed as part of biological membranes, energy storage substances and sometimes function as signal transducers. Altered lipid metabolism and dyslipidemia in the context of inflammation and oxidative stress are driving forces in the transition from stable to unstable plaques. Therefore, a characteristic lipid signature within unstable human plaques and also in the circulating blood plasma could be a predictor of an oncoming cardiac event. This ongoing study was conducted on samples volunteered by acute coronary syndrome (ACS) patients at the Heart Hospital, Doha, Qatar. ACS is a term that describes any condition brought on by the sudden reduced blood flow to the heart due to thrombosis in the coronary arteries and encompasses unstable angina (UA) and both ST-segment elevation (STEMI) and non ST-segment elevation myocardial infarction (NSTEMI). A complete occlusive thrombi leads to extensive myocardial cell death and typically produces an elevated ST-segment in the electrocardiogram. In UA, ischemia occurs unpredictably and suddenly and is caused by the temporary formation of blood clots within the coronary arteries. Unstable angina often occurs before a MI. Distinguished from ACS are patients with stable angina (SA) who develop symptoms due to exertional ischemia. The aim of this study was to profile the global individual lipid levels of subjects in Qatar with unstable CAD, comparing global lipid levels between patients with unstable angina and ST-elevated myocardial infarction. We chose to discover the lipid biomarkers using a workflow utilizing tandem mass spectrometry with on-line ultra-high pressure liquid chromatography (UPLC-MS/MS). Mass spectrometry is a powerful technique that can be used to identify unknown compounds, to quantify known materials and to elucidate the structure and chemical properties of molecules. Recent advances in the accuracy and speed to the technology allow data acquisition for the global analysis of proteins, lipids and metabolites from complex samples such as blood plasma or serum. As we were trying to discover a new lipid biomarker, a technique that would maximise the number of compounds detected, identified and quantified them was favourable. Once the samples were analysed by tandem mass spectrometry, the ion intensity data from each sample was aligned with each other by retention time and lipid mass, normalised and deconvoluted. The signals were then attributed to a particular lipid species by utilising a lipid database and comparing the mass of the detected lipid and piecing together information gained from the fragment data of that lipid from the orbitrap. Statistical analyses of the signals for each individual lipid were then conducted by comparing within group percent coefficient of variation (?CV), fold change and analysis of variance (ANOVA) tests between sample groups and q-value and power calculations. Principal component analysis (PCA) was conducted in order to differentiate the samples under supervised conditions into STEMI and UA groups. A total of 1,663 and 874 lipid compounds were identified in positive and negative modes of mass spectrometry respectively. Of these, 7 compounds showed a significant change (ANOVA p-value < or equal to 0.001) between the STEMI and UA groups. The identities of these compounds are yet to be elucidated. Of the compounds with a significant change between sample groups of ANOVA p-value < or equal to 0.005, five compounds were able to be identified by mass and spectral matching with a lipid database. The PCA scores plot, which distributes samples in multi-dimensional space according to the variance seen in each principal component, showed very low evidence of discrimination between the sample groups with sample scores clustered in a single mixed pattern. This analysis suggests that the lipid abundance changes between the sample groups were difficult to find. This was most likely due to a combination of two reasons: (1) large within-group biological variance that needs to be overcome to detect the between-group variances and (2) the low differences in lipid concentrations between the sample groups. With a greater number of samples, this results is expected to change as the power of the study would increase. Successful results obtained from this study will aid healthcare professional in intervening with appropriate treatment in persons showing no symptoms but are under threat of developing angina or acute MI. The discovery of a lipid biomarker could assist healthcare professionals in prevention of an acute cardiac event thereby saving lives.qscienc

COVID-19 vaccine acceptance and hesitancy in low- and middle-income countries

Widespread acceptance of COVID-19 vaccines is crucial for achieving sufficient immunization coverage to end the global pandemic, yet few studies have investigated COVID-19 vaccination attitudes in lower-income countries, where large-scale vaccination is just beginning. We analyze COVID-19 vaccine acceptance across 15 survey samples covering 10 low- and middle-income countries (LMICs) in Asia, Africa and South America, Russia (an upper-middle-income country) and the United States, including a total of 44,260 individuals. We find considerably higher willingness to take a COVID-19 vaccine in our LMIC samples (mean 80.3%; median 78%; range 30.1 percentage points) compared with the United States (mean 64.6%) and Russia (mean 30.4%). Vaccine acceptance in LMICs is primarily explained by an interest in personal protection against COVID-19, while concern about side effects is the most common reason for hesitancy. Health workers are the most trusted sources of guidance about COVID-19 vaccines. Evidence from this sample of LMICs suggests that prioritizing vaccine distribution to the Global South should yield high returns in advancing global immunization coverage. Vaccination campaigns should focus on translating the high levels of stated acceptance into actual uptake. Messages highlighting vaccine efficacy and safety, delivered by healthcare workers, could be effective for addressing any remaining hesitancy in the analyzed LMICs.Publisher PDFPeer reviewe

SAWECKI-2019-Reproduction-and-Oxidative-Stress-in-a-Mouthbrooding-Cichlid-Fish

This zip file contains two excel documents. One document used for analysis of female oxidative stress and the other for analysis of the male status shifts in stable and unstable environments. There are also 4 R scripts that were used for running linear mixed models and generalized linear mixed models

Quantification of L-alanyl-L-glutamine in mammalian cell culture broth: Evaluation of different detectors

L-Alanyl-L-glutamine (also known as Ala-Gin or GlutaMAX) is widely used as a stable L-glutamine source in cell culture for the production of biopharmaceuticals. System approaches for the optimization of production processes require the analysis of all major substrates and products. We have compared four alternative detection systems for L-alanyl-L-glutamine in culture broth. Matrix effects prevented the use of ultraviolet or evaporative light scattering detection. Fluorescence detection used in routine amino acid protocols is compatible with culture broth and has a broad linear dynamic range. Mass spectrometry has superior sensitivity and can be integrated into quantitative metabolomic workflows. (C) 2011 Elsevier Inc. All rights reserved

Paracrine Mechanisms of Mesenchymal Stromal Cells in Angiogenesis

The role of the mesenchymal stromal cell- (MSC-) derived secretome is becoming increasingly intriguing from a clinical perspective due to its ability to stimulate endogenous tissue repair processes as well as its effective regulation of the immune system, mimicking the therapeutic effects produced by the MSCs. The secretome is a composite product secreted by MSC in vitro (in conditioned medium) and in vivo (in the extracellular milieu), consisting of a protein soluble fraction (mostly growth factors and cytokines) and a vesicular component, extracellular vesicles (EVs), which transfer proteins, lipids, and genetic material. MSC-derived secretome differs based on the tissue from which the MSCs are isolated and under specific conditions (e.g., preconditioning or priming) suggesting that clinical applications should be tailored by choosing the tissue of origin and a priming regimen to specifically correct a given pathology. MSC-derived secretome mediates beneficial angiogenic effects in a variety of tissue injury-related diseases. This supports the current effort to develop cell-free therapeutic products that bring both clinical benefits (reduced immunogenicity, persistence in vivo, and no genotoxicity associated with long-term cell cultures) and manufacturing advantages (reduced costs, availability of large quantities of off-the-shelf products, and lower regulatory burden). In the present review, we aim to give a comprehensive picture of the numerous components of the secretome produced by MSCs derived from the most common tissue sources for clinical use (e.g., AT, BM, and CB). We focus on the factors involved in the complex regulation of angiogenic processes

Chronic Ethanol Consumption Alters Presynaptic Regulation of Dorsal Striatal Dopamine Release in C57BL/6J Mice

Alcohol use disorder (AUD) is characterized by escalating alcohol consumption, preoccupation with alcohol, and continued alcohol consumption despite adverse consequences. Dopamine has been implicated in neural and behavioral processes involved in reward and reinforcement and is a critical neurotransmitter in AUD. Clinical and preclinical research has shown that long-term ethanol exposure can alter dopamine release, though most of this work has focused on nucleus accumbens (NAc). Like the NAc, the dorsal striatum (DS) is implicated in neural and behavioral processes in AUD. However, little work has examined chronic ethanol effects on DS dopamine dynamics. Therefore, we examined the effect of ethanol consumption and withdrawal on dopamine release and its presynaptic regulation with fast-scan cyclic voltammetry in C57BL/6J mice. We found that one month of ethanol consumption did not alter maximal dopamine release or dopamine tissue content. However, we did find that D2 dopamine autoreceptors were sensitized. We also found a decrease in cholinergic control of dopamine release via &beta;2-containing nAChRs on dopamine axons. Interestingly, both effects were reversed following withdrawal, raising the possibility that some of the neuroadaptations in AUD might be reversible in abstinence. Altogether, this work elucidates some of the chronic alcohol-induced neurobiological dysfunctions in the dopamine system

Sphingolipids in Childhood Asthma and Obesity (SOAP Study): A Protocol of a Cross-Sectional Study

Asthma and obesity are two of the most common chronic conditions in children and adolescents. There is increasing evidence that sphingolipid metabolism is altered in childhood asthma and is linked to airway hyperreactivity. Dysregulated sphingolipid metabolism is also reported in obesity. However, the functional link between sphingolipid metabolism, asthma, and obesity is not completely understood. This paper describes the protocol of an ongoing study on sphingolipids that aims to examine the pathophysiology of sphingolipids in childhood asthma and obesity. In addition, this study aims to explore the novel biomarkers through a comprehensive multi-omics approach including genomics, genome-wide DNA methylation, RNA-Seq, microRNA (miRNA) profiling, lipidomics, metabolomics, and cytokine profiling. This is a cross-sectional study aiming to recruit 440 children from different groups: children with asthma and normal weight (n = 100), asthma with overweight or obesity (n = 100), overweight or obesity (n = 100), normal weight (n = 70), and siblings of asthmatic children with normal weight, overweight, or obesity (n = 70). These participants will be recruited from the pediatric pulmonology, pediatric endocrinology, and general pediatric outpatient clinics at Sidra Medicine, Doha, Qatar. Information will be obtained from self-reported questionnaires on asthma, quality of life, food frequency (FFQ), and a 3-day food diary that are completed by the children and their parents. Clinical measurements will include anthropometry, blood pressure, biochemistry, bioelectrical impedance, and pulmonary function tests. Blood samples will be obtained for sphingolipid analysis, serine palmitoyltransferase (SPT) assay, whole-genome sequencing (WGS), genome-wide DNA methylation study, RNA-Seq, miRNA profiling, metabolomics, lipidomics, and cytokine analysis. Group comparisons of continuous outcome variables will be carried out by a one-way analysis of variance or the Kruskal–Wallis test using an appropriate pairwise multiple comparison test. The chi-squared test or a Fisher’s exact test will be used to test the associations between categorical variables. Finally, multivariate analysis will be carried out to integrate the clinical data with multi-omics data. This study will help us to understand the role of dysregulated sphingolipid metabolism in obesity and asthma. In addition, the multi-omics data from the study will help to identify novel genetic and epigenetic signatures, inflammatory markers, and mechanistic pathways that link asthma and obesity in children. Furthermore, the integration of clinical and multi-omics data will help us to uncover the potential interactions between these diseases and to offer a new paradigm for the treatment of pediatric obesity-associated asthma