Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multi-scale dynamics of glycine receptors in the neuronal membrane

Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions governing the motion. Here, we present a method combining high-density single-molecule imaging and statistical inference to separately map the diffusion and energy landscapes of membrane proteins across the cell surface at ~100 nm resolution (with acquisition of a few minutes). When applying these analytical tools to glycine neurotransmitter receptors (GlyRs) at inhibitory synapses, we find that gephyrin scaffolds act as shallow energy traps (~3 kBT) for GlyRs, with a depth modulated by the biochemical properties of the receptor-gephyrin interaction loop. In turn, the inferred maps can be used to simulate the dynamics of proteins in the membrane, from the level of individual receptors to that of the population, and thereby, to model the stochastic fluctuations of physiological parameters (such as the number of receptors at synapses). Overall, our approach provides a powerful and comprehensive framework with which to analyze biochemical interactions in living cells and to decipher the multi-scale dynamics of biomolecules in complex cellular environments.Comment: 23 pages, 4 figure

Thermoneutrality improves skeletal impairment in adult Prader-Willi syndrome mice

International audienc

Beth Levine in memoriam

Beth Levine was born on 7 April 1960 in Newark, New Jersey. She went to college at Brown University where she received an A.B. Magna Cum Laude, and she attended medical school at Cornell University Medical College, receiving her MD in 1986. She completed her internship and residency in Internal Medicine at Mount Sinai Hospital in New York, and her fellowship in Infectious Diseases at The Johns Hopkins Hospital. Most recently, Beth was a Professor of Internal Medicine and Microbiology, Director of the Center for Autophagy Research, and holder of the Charles Sprague Distinguished Chair in Biomedical Science at the University of Texas Southwestern Medical Center in Dallas. Beth died on 15 June 2020 from cancer. Beth is survived by her husband, Milton Packer, and their two children, Rachel (26 years old) and Ben (25 years old). Dr. Levine was as an international leader in the field of autophagy research. Her laboratory identified the mammalian autophagy gene BECN1/beclin 1; identified conserved mechanisms underlying the regulation of autophagy (e.g. BCL2-BECN1 complex formation, insulin-like signaling, EGFR, ERBB2/HER2 and AKT1-mediated BECN1 phosphosphorylation); and provided the first evidence that autophagy genes are important in antiviral host defense, tumor suppression, lifespan extension, apoptotic corpse clearance, metazoan development, Na,K-ATPase-regulated cell death, and the beneficial metabolic effects of exercise. She developed a potent autophagy-inducing cell permeable peptide, Tat-beclin 1, which has potential therapeutic applications in a range of diseases. She was a founding Associate Editor of the journal Autophagy and an editorial board member of Cell and Cell Host & Microbe. She has received numerous awards/honors in recognition of her scientific achievement, including: The American Cancer Society Junior Faculty Research Award (1994); election into the American Society of Clinical Investigation (2000); the Ellison Medical Foundation Senior Scholars Award in Global Infectious Diseases (2004); elected member, American Association of Physicians (2005); appointment as a Howard Hughes Medical Institute Investigator (2008); Edith and Peter O’Donnell Award in Medicine (2008); elected fellow, American Association for the Advancement of Science (2012); election into the National Academy of Sciences (2013); election into the Academy of Medicine, Engineering and Science of Texas (2013); the ASCI Stanley J. Korsmeyer Award (2014); Phyllis T. Bodel Women in Medicine Award, Yale University School of Medicine (2018); recipient, Barcroft Medal, Queen’s University Belfast (2018).Fil: An, Zhenyi. No especifíca;Fil: Ballabi, Andrea. No especifíca;Fil: Bennett, Lynda. No especifíca;Fil: Boya, Patricia. No especifíca;Fil: Cecconi, Francesco. No especifíca;Fil: Chiang, Wei Chung. No especifíca;Fil: Codogno, Patrice. No especifíca;Fil: Colombo, Maria Isabel. No especifíca;Fil: Cuervo, Ana Maria. No especifíca;Fil: Debnath, Jayanta. No especifíca;Fil: Deretic, Vojo. No especifíca;Fil: Dikic, Ivan. No especifíca;Fil: Dionne, Keith. No especifíca;Fil: Dong, Xiaonan. No especifíca;Fil: Elazar, Zvulun. No especifíca;Fil: Galluzzi, Lorenzo. No especifíca;Fil: Gentile, Frank. No especifíca;Fil: Griffin, Diane E.. No especifíca;Fil: Hansen, Malene. No especifíca;Fil: Hardwick, J. Marie. No especifíca;Fil: He, Congcong. No especifíca;Fil: Huang, Shu Yi. No especifíca;Fil: Hurley, James. No especifíca;Fil: Jackson, William T.. No especifíca;Fil: Jozefiak, Cindy. No especifíca;Fil: Kitsis, Richard N.. No especifíca;Fil: Klionsky, Daniel J.. No especifíca;Fil: Kroemer, Guido. No especifíca;Fil: Meijer, Alfred J.. No especifíca;Fil: Meléndez, Alicia. No especifíca;Fil: Melino, Gerry. No especifíca;Fil: Mizushima, Noboru. No especifíca;Fil: Murphy, Leon O.. No especifíca;Fil: Nixon, Ralph. No especifíca;Fil: Orvedahl, Anthony. No especifíca;Fil: Pattingre, Sophie. No especifíca;Fil: Piacentini, Mauro. No especifíca;Fil: Reggiori, Fulvio. No especifíca;Fil: Ross, Theodora. No especifíca;Fil: Rubinsztein, David C.. No especifíca;Fil: Ryan, Kevin. No especifíca;Fil: Sadoshima, Junichi. No especifíca;Fil: Schreiber, Stuart L.. No especifíca;Fil: Scott, Frederick. No especifíca;Fil: Sebti, Salwa. No especifíca;Fil: Shiloh, Michael. No especifíca;Fil: Shoji, Sanae. No especifíca;Fil: Simonsen, Anne. No especifíca;Fil: Smith, Haley. No especifíca;Fil: Sumpter, Kathryn M.. No especifíca;Fil: Thompson, Craig B.. No especifíca;Fil: Thorburn, Andrew. No especifíca;Fil: Thumm, Michael. No especifíca;Fil: Tooze, Sharon. No especifíca;Fil: Vaccaro, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Bioquímica y Medicina Molecular. Universidad de Buenos Aires. Facultad Medicina. Instituto de Bioquímica y Medicina Molecular; ArgentinaFil: Virgin, Herbert W.. No especifíca;Fil: Wang, Fei. No especifíca;Fil: White, Eileen. No especifíca;Fil: Xavier, Ramnik J.. No especifíca;Fil: Yoshimori, Tamotsu. No especifíca;Fil: Yuan, Junying. No especifíca;Fil: Yue, Zhenyu. No especifíca;Fil: Zhong, Qing. No especifíca

Exome Sequencing and the Management of Neurometabolic Disorders

BACKGROUND: Whole-exome sequencing has transformed gene discovery and diagnosis in rare diseases. Translation into disease-modifying treatments is challenging, particularly for intellectual developmental disorder. However, the exception is inborn errors of metabolism, since many of these disorders are responsive to therapy that targets pathophysiological features at the molecular or cellular level. METHODS: To uncover the genetic basis of potentially treatable inborn errors of metabolism, we combined deep clinical phenotyping (the comprehensive characterization of the discrete components of a patient's clinical and biochemical phenotype) with whole-exome sequencing analysis through a semiautomated bioinformatics pipeline in consecutively enrolled patients with intellectual developmental disorder and unexplained metabolic phenotypes. RESULTS: We performed whole-exome sequencing on samples obtained from 47 probands. Of these patients, 6 were excluded, including 1 who withdrew from the study. The remaining 41 probands had been born to predominantly nonconsanguineous parents of European descent. In 37 probands, we identified variants in 2 genes newly implicated in disease, 9 candidate genes, 22 known genes with newly identified phenotypes, and 9 genes with expected phenotypes; in most of the genes, the variants were classified as either pathogenic or probably pathogenic. Complex phenotypes of patients in five families were explained by coexisting monogenic conditions. We obtained a diagnosis in 28 of 41 probands (68%) who were evaluated. A test of a targeted intervention was performed in 18 patients (44%). CONCLUSIONS: Deep phenotyping and whole-exome sequencing in 41 probands with intellectual developmental disorder and unexplained metabolic abnormalities led to a diagnosis in 68%, the identification of 11 candidate genes newly implicated in neurometabolic disease, and a change in treatment beyond genetic counseling in 44%. (Funded by BC Children's Hospital Foundation and others.)

Biofonctionnalisation de points quantiques pour le suivi de récepteurs synaptiques

La membrane cellulaire est un environnement très dynamique où diffusent plusieurs familles de protéines. Pour assurer la communication entre neurones, certains récepteurs membranaires diffusant librement doivent être stabilisés aux jonctions de communication neuronales: les synapses. Des changements dans le comportement diffusif de ces récepteurs induisent des variations de leurs populations à la synapse. La capacité d'observer ces protéines diffuser individuellement est donc importante pour mieux comprendre certains mécanismes cellulaires associés au fonctionnement du système nerveux. Alors que les fluorophores organiques (Alexa, Atto, ...) et génétiquement encodées (GFP, RFP, ...) photoblanchissent rapidement, les nanocristaux semi-conducteurs fluorescents (points quantiques: QDs) sont photo-stables, ce qui permet de suivre les protéines marquées sur de plus longues périodes. Même si la structure cristalline du QD dépasse rarement les 10nm de diamètre, la taille de la sonde fonctionnalisée, une fois équipée d'un enrobage hydrophile et de protéines d'hameçonnage, est d'environ 30 nm, limitant leur accessibilité dans la fente synaptique (environ 20 nm). De plus, la multivalence des versions commerciales des QDs fonctionnalisés pose problème, en leur permettant de lier plusieurs récepteurs à la fois. Dans ce mémoire, nous présentons donc différentes approches pour la biofonctionnalisation de petit QDs monovalents, ainsi que les principales stratégies pour marquer des récepteurs synaptiques uniques à partir de QDs. De plus, nous présentons une étude de la diffusion de récepteurs synaptiques diffusant à l'intérieur et à l'extérieur de synapses et comparons les résultats en fonction des 2 types de sondes utilisés : QDs enrobés d'anticorps et QDs enrobés de streptavidine. Ces travaux devraient contribuer à l'optimisation d'une approche pour suivre les dynamiques des récepteurs synaptiques dans des modèles de plasticité synaptique

Difference Between Persistent Aneurysm, Regressed Aneurysm, and Coronary Dilation in Kawasaki Disease: An Optical Coherence Tomography Study

BACKGROUND Coronary artery (CA) aneurysms are a serious complication of Kawasaki disease (KD). Conventional imaging techniques often described segments with regressed aneurysms as normal, whereas studies have shown significant endothelial dysfunction. METHODS KD patients with aneurysms scheduled for routine coronary angiography underwent optical coherence tomography (OCT) imaging between 2013 and 2016. Microstructural coronary changes were compared between normal CA segments and those with dilation, regressed aneurysms, and persistent aneurysms. RESULTS OCT was performed on 33 patients aged 12.0 ± 5.4 years, 8.5 ± 5.4 years after KD diagnosis. Of the 79 segments analyzed, 25 had persistent aneurysms, 22 regressed aneurysms, 11 CA dilation, and 21 no CA involvement. Intimal thickness was 489 ± 173 μm, 304 ± 158 μm, 102 ± 68 μm, and 63 ± 29 μm, respectively (P < 0.001). There was a linear correlation between the maximum aneurysm size and the intimal thickness, as well as coronary dimension at the time of OCT. Fibrosis (54 segments, 68%) and cellular infiltration (22 segments, 28%) were found more often in segments with CA involvement, but also those without (P = 0.01; P = 0.02). Destruction of the media (34 segments, 43%), calcifications (6 segments, 8%), neovascularization (18 segments, 23%), and white thrombi (8 segments, 10%) were found almost exclusively in segments with a history of aneurysms. CONCLUSIONS Intimal hyperplasia, fibrosis, and cellular infiltration were found in all categories of CA involvement, whereas calcification, destruction of the media, neovascularization, and white thrombi were found essentially only in segments with saccular or fusiform aneurysms. Prospective studies with outcome correlations are needed to see if this is associated with an increased risk of late adverse events

Effects of Lifestyle Interventions That Include a Physical Activity Component in Class II and III Obese Individuals: A Systematic Review and Meta-Analysis

<div><p>Background</p><p>In class II and III obese individuals, lifestyle intervention is the first step to achieve weight loss and treat obesity-related comorbidities before considering bariatric surgery. A systematic review, meta-analysis, and meta-regression were performed to assess the impact of lifestyle interventions incorporating a physical activity (PA) component on health outcomes of class II and III obese individuals.</p><p>Methods</p><p>An electronic search was conducted in 4 databases (Medline, Scopus, CINAHL and Sportdiscus). Two independent investigators selected original studies assessing the impact of lifestyle interventions with PA components on anthropometric parameters, cardiometabolic risk factors (fat mass, blood pressure, lipid and glucose metabolism), behaviour modification (PA and nutritional changes), and quality of life in adults with body mass index (BMI) ≥ 35 kg/m². Estimates were pooled using a random-effect model (DerSimonian and Laird method). Heterogeneity between studies was assessed by the Cochran’s chi-square test and quantified through an estimation of the <i>I</i>^².</p><p>Results</p><p>Of the 3,170 identified articles, 56 met our eligibility criteria, with a large majority of uncontrolled studies (80%). The meta-analysis based on uncontrolled studies showed significant heterogeneity among all included studies. The pooled mean difference in weight loss was 8.9 kg (95% CI, 10.2–7.7; p < 0.01) and 2.8 kg/m^² in BMI loss (95% CI, 3.4–2.2; p < 0.01). Long-term interventions produced superior weight loss (11.3 kg) compared to short-term (7.2 kg) and intermediate-term (8.0 kg) interventions. A significant global effect of lifestyle intervention on fat mass, waist circumference, blood pressure, total cholesterol, LDL-C, triglycerides and fasting insulin was found (p<0.01), without significant effect on HDL-C and fasting blood glucose.</p><p>Conclusions</p><p>Lifestyle interventions incorporating a PA component can improve weight and various cardiometabolic risk factors in class II and III obese individuals. However, further high quality trials are needed to confirm this evidence, especially beyond weight loss.</p></div