Ligand-regulated oligomerization of β2-adrenoceptors in a model lipid bilayer

The β2-adrenoceptor (β2AR) was one of the first Family A G protein-coupled receptors (GPCRs) shown to form oligomers in cellular membranes, yet we still know little about the number and arrangement of protomers in oligomers, the influence of ligands on the organization or stability of oligomers, or the requirement for other proteins to promote oligomerization. We used fluorescence resonance energy transfer (FRET) to characterize the oligomerization of purified β2AR site-specifically labelled at three different positions with fluorophores and reconstituted into a model lipid bilayer. Our results suggest that the β2AR is predominantly tetrameric following reconstitution into phospholipid vesicles. Agonists and antagonists have little effect on the relative orientation of protomers in oligomeric complexes. In contrast, binding of inverse agonists leads to significant increases in FRET efficiencies for most labelling pairs, suggesting that this class of ligand promotes tighter packing of protomers and/or the formation of more complex oligomers by reducing conformational fluctuations in individual protomers. The results provide new structural insights into β2AR oligomerization and suggest a possible mechanism for the functional effects of inverse agonists

Non-linear models for black carbon exposure modelling using air pollution datasets

Black carbon (BC) is a product of incomplete combustion, present in urban aerosols and sourcing mainly from road traffic. Epidemiological evidence reports positive associations between BC and cardiovascular and respiratory disease. Despite this, BC is currently not regulated by the EU Air Quality Directive, and as a result BC data are not available in urban areas from reference air quality monitoring networks in many countries. To fill this gap, a machine learning approach is proposed to develop a BC proxy using air pollution datasets as an input. The proposed BC proxy is based on two machine learning models, support vector regression (SVR) and random forest (RF), using observations of particle mass and number concentrations (N), gaseous pollutants and meteorological variables as the input. Experimental data were collected from a reference station in Barcelona (Spain) over a 2-year period (2018–2019). Two months of additional data were available from a second urban site in Barcelona, for model validation. BC concentrations estimated by SVR showed a high degree of correlation with the measured BC concentrations (R2 = 0.828) with a relatively low error (RMSE = 0.48 µg/m3). Model performance was dependent on seasonality and time of the day, due to the influence of new particle formation events. When validated at the second station, performance indicators decreased (R2 = 0.633; RMSE = 1.19 µg/m3) due to the lack of N data and PM2.5 and the smaller size of the dataset (2 months). New particle formation events critically impacted model performance, suggesting that its application would be optimal in environments where traffic is the main source of ultrafine particles. Due to its flexibility, it is concluded that the model can act as a BC proxy, even based on EU-regulatory air quality parameters only, to complement experimental measurements for exposure assessment in urban areas.The authors would like to acknowledge the support from the Generalitat de Catalunya (Dept. Medi Ambient) by providing the air quality data. This work was partly supported by H2020 project RI-URBANS (H2020-LC-GD-2020-6, reference 101036245), the Spanish Ministry of Science and Innovation (projects CEX2018-000794-S and PID2019- 107910RB-I00), Academy of Finland via flagship on Atmosphere and Climate Competence Center (ACCC, project number 337549) and by AGAUR (project 2017 SGR41 and 2017 SGR 990). It was carried out in the framework of a joint collaboration between IDAEA-CSIC and University of Barcelona (Physics Faculty).Peer ReviewedPostprint (published version

An entropy test for single-locus genetic association analysis

<p>Abstract</p> <p>Background</p> <p>The etiology of complex diseases is due to the combination of genetic and environmental factors, usually many of them, and each with a small effect. The identification of these small-effect contributing factors is still a demanding task. Clearly, there is a need for more powerful tests of genetic association, and especially for the identification of rare effects</p> <p>Results</p> <p>We introduce a new genetic association test based on symbolic dynamics and symbolic entropy. Using a freely available software, we have applied this entropy test, and a conventional test, to simulated and real datasets, to illustrate the method and estimate type I error and power. We have also compared this new entropy test to the Fisher exact test for assessment of association with low-frequency SNPs. The entropy test is generally more powerful than the conventional test, and can be significantly more powerful when the genotypic test is applied to low allele-frequency markers. We have also shown that both the Fisher and Entropy methods are optimal to test for association with low-frequency SNPs (MAF around 1-5%), and both are conservative for very rare SNPs (MAF<1%)</p> <p>Conclusions</p> <p>We have developed a new, simple, consistent and powerful test to detect genetic association of biallelic/SNP markers in case-control data, by using symbolic dynamics and symbolic entropy as a measure of gene dependence. We also provide a standard asymptotic distribution of this test statistic. Given that the test is based on entropy measures, it avoids smoothed nonparametric estimation. The entropy test is generally as good or even more powerful than the conventional and Fisher tests. Furthermore, the entropy test is more computationally efficient than the Fisher's Exact test, especially for large number of markers. Therefore, this entropy-based test has the advantage of being optimal for most SNPs, regardless of their allele frequency (Minor Allele Frequency (MAF) between 1-50%). This property is quite beneficial, since many researchers tend to discard low allele-frequency SNPs from their analysis. Now they can apply the same statistical test of association to all SNPs in a single analysis., which can be especially helpful to detect rare effects.</p

Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling

Background Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs. Methodology/Principal Findings Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. Conclusions/Significance A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin.This study was financially supported by GrapeGen Project funded by Genoma España within a collaborative agreement with Genome Canada. The authors also thank The Ministerio de Ciencia e Innovacion for project BIO2008-03892 and a bilateral collaborative grant with Argentina (AR2009-0021). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe

The IDENTIFY study: the investigation and detection of urological neoplasia in patients referred with suspected urinary tract cancer - a multicentre observational study

Objective To evaluate the contemporary prevalence of urinary tract cancer (bladder cancer, upper tract urothelial cancer [UTUC] and renal cancer) in patients referred to secondary care with haematuria, adjusted for established patient risk markers and geographical variation. Patients and Methods This was an international multicentre prospective observational study. We included patients aged ≥16 years, referred to secondary care with suspected urinary tract cancer. Patients with a known or previous urological malignancy were excluded. We estimated the prevalence of bladder cancer, UTUC, renal cancer and prostate cancer; stratified by age, type of haematuria, sex, and smoking. We used a multivariable mixed-effects logistic regression to adjust cancer prevalence for age, type of haematuria, sex, smoking, hospitals, and countries. Results Of the 11 059 patients assessed for eligibility, 10 896 were included from 110 hospitals across 26 countries. The overall adjusted cancer prevalence (n = 2257) was 28.2% (95% confidence interval [CI] 22.3–34.1), bladder cancer (n = 1951) 24.7% (95% CI 19.1–30.2), UTUC (n = 128) 1.14% (95% CI 0.77–1.52), renal cancer (n = 107) 1.05% (95% CI 0.80–1.29), and prostate cancer (n = 124) 1.75% (95% CI 1.32–2.18). The odds ratios for patient risk markers in the model for all cancers were: age 1.04 (95% CI 1.03–1.05; P < 0.001), visible haematuria 3.47 (95% CI 2.90–4.15; P < 0.001), male sex 1.30 (95% CI 1.14–1.50; P < 0.001), and smoking 2.70 (95% CI 2.30–3.18; P < 0.001). Conclusions A better understanding of cancer prevalence across an international population is required to inform clinical guidelines. We are the first to report urinary tract cancer prevalence across an international population in patients referred to secondary care, adjusted for patient risk markers and geographical variation. Bladder cancer was the most prevalent disease. Visible haematuria was the strongest predictor for urinary tract cancer

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M&gt;70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0&lt;e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Regulation of Beta2-adrenergic Receptor Structure and Function

Background: G Protein-Coupled Receptors (GPCRs) represent the largest class of membrane proteins in our genome. They are responsible for communicating extracellular information to the cell in a remarkably wide variety of metabolic processes. It is now clear that lipid-protein interactions are important modulators of membrane protein function and several studies have proposed a functional role for lipids, especially cholesterol, on the function of GPCRs. For instance it has been shown that the b2-adrenergic receptor (b2AR) preferentially localizes in cholesterol-rich caveolae (1), is stabilized by cholesterol and its crystal structure clearly shows two cholesterol molecules tightly bound on the outside of the transmembrane bundle (2). Our work aims at characterizing the role of the membrane lipid composition on the structural and functional regulation of the b2AR. By reconstituting the b2AR in proteoliposomes of given compositions, we intend to identify the effect of the different lipid species of the mammalian membrane on the receptor function (binding affinity and agonist-induced activation). Using biophysical approaches, such as fluorescence spectroscopy and Attenuated Total Reflection Fourier transformation Infrared Spectroscopy (ATR-FTIR) we characterize the conformational modulation of the b2-adrenergic receptor by specific lipid species.Results: We compared reconstitutions of b2AR in DOPC/CHS and in heart and liver lipids extracts.Preliminary data suggest that binding of b2AR to its antagonist Alprenolol is modified by the lipid composition of the proteoliposomes. Bimane Fluorescence experiments used to monitor the ionic lock changes also show that the activation and inhibition of the receptor are modulated by the lipidic environment.Perspectives: More lipid composition, not only tissues extracts but also native membrane, and given lipid mixtures. functional assays will be done, i.e. G protein coupling and oligomerization of the receptor. Finally we will record ATR-FTIR spectral profiles of stimulated and non stimulated b2AR in all lipid composition used for functional assays. This will reveal possible tertiary conformational changes and orientational changes associated with modification of the lipidic environmentinfo:eu-repo/semantics/nonPublishe

Obstetric Anesthesia in a Patient with Takayasu Arteritis

Introduction: Takayasu arteritis is an inflammatory disease that affects the aorta and its branches, and shows a predilection for the Asian population.Objective: To describe anesthetic management in an obstetric patient with Takayasu arteritis.Case presentation: Female patient, 20 years old, 39 weeks of pregnancy, a history of Takayasu arteritis. At six months of gestation, the first symptoms of the disease appeared. Diagnosis is confirmed through CT angiography of the supra-aortic trunk and neck vessels, in addition to carotid Doppler. Occlusive vascular disorders, as well as concentric stenosis of both carotids and the main branches of the aortic arch are observed. Finally, the diagnosis of type I Takayasu arteritis was confirmed. At the end of her pregnancy, an elective cesarean section was decided to avoid labor.Conclusions: Obstetric anesthesia for patients with this disease is highly complicated due to its complex management, observation and interpretation of multiparametric and imaging monitoring. During anesthetic conduction, strict hemodynamic control is essential, avoiding low blood flow syndrome and maternal or fetal ischemic damage.</p