Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy

Imprisonment and internment: Comparing penal facilities North and South

Recent references to the ‘warehouse prison’ in the United States and the prisión-depósito in Latin America seem to indicate that penal confinement in the western hemisphere has converged on a similar model. However, this article suggests otherwise. It contrasts penal facilities in North America and Latin America in terms of six interrelated aspects: regimentation; surveillance; isolation; supervision; accountability; and formalization. Quantitatively, control in North American penal facilities is assiduous (unceasing, persistent and intrusive), while in Latin America it is perfunctory (sporadic, indifferent and cursory). Qualitatively, North American penal facilities produce imprisonment (which enacts penal intervention through confinement), while in Latin America they produce internment (which enacts penal intervention through release). Closely entwined with this qualitative difference are distinct practices of judicial involvement in sentencing and penal supervision. Those practices, and the cultural and political factors that underpin them, represent an interesting starting point for the explanation of the contrasting nature of imprisonment and internment

Effective Rheology of Bubbles Moving in a Capillary Tube

We calculate the average volumetric flux versus pressure drop of bubbles moving in a single capillary tube with varying diameter, finding a square-root relation from mapping the flow equations onto that of a driven overdamped pendulum. The calculation is based on a derivation of the equation of motion of a bubble train from considering the capillary forces and the entropy production associated with the viscous flow. We also calculate the configurational probability of the positions of the bubbles.Comment: 4 pages, 1 figur

A new perspective of the climatological features of upper-level cut-off lows in the Southern Hemisphere

This study presents a detailed view of the seasonal variability of upper-level cut-off lows (COLs) in the Southern Hemisphere. The COLs are identified and tracked using data from a 36-year period of the European Centre for Medium Range Weather Forecast reanalysis (ERA-Interim). The objective identification of the COLs uses a new approach, which is based on 300 hPa relative vorticity minima, and three restrictive criteria of the presence of a cold-core, stratospheric potential vorticity intrusion, and cut-off cyclonic circulation. The highest COL activity is in agreement with previous studies, located near three main continental areas (Australia, South America, and Africa), with maximum frequencies usually observed in the austral autumn. The COL mean intensity values show a marked seasonal and spatial variation, with maximum (minimum) values during the austral winter (summer), a unique feature that has not been observed previously in studies based on the geopotential. The link between intensity and lysis is examined, and finds that weaker systems are more susceptible to lysis in the vicinity of the Andes Cordillera, associated with the topographic Rossby wave. Lysis and genesis regions are close to each other, confirming that COLs are quasi-stationary systems. Also, COLs tend to move eastward and are faster over the higher latitudes. The mean growth/decay rates coincide with the major genesis and lysis density regions, such as the significant decay values across the Andes all year. As a consequence of using vorticity for the tracking method a longer lifetime of COLs is detected than in other studies, but this does not affect the total frequency of occurrence. Comparisons with other studies suggest that the differences in seasonality are due to uncertainties in the reanalyses and the methods used to identify COLs

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Abstract:  Several scientific studies have shown contradictory results regarding the effect of probiotic supplementation on the inhibition of pro-inflammatory cytokines and the improvement of the clinical nutritional profile in people with cardiometabolic diseases. This research aimed to analyze the relationship between the intake of probiotic foods and supplements with probiotics and inflammation markers in cardiometabolic diseases in adults, through a systematic review, during the period between 2015 and 2020. The systematic review was carried out according to the Cochrane recommendations and the GRADE guidelines; different databases such as Pubmed, Oxford and BVS were used. Three reviewers participated in this process. Papers that did not meet the quality of evidence criteria were excluded: risk of bias, imprecise results, inconsistent results, problems of applicability of the evidence, and the existence of publication bias. To control bias, the checklist proposed by Downs and Black was used. Of the 859 articles identified, 17 met the inclusion requirements. Controlled trials and randomized clinical trials were considered among the eligibility criteria. Of all the studies that analyzed the effect of probiotics (bifidobacterium, lactobacillus, lactococcus, acetobacter) on the biomarkers of inflammation in cardiometabolic diseases, a decrease in interleukin concentrations (IL-1, IL-6, IL- 8 and IL-12) in eight of them and the same happened with TNFα; in the case of INFγ, it was decreased in one of the three studies that analyzed it; while, the consumption of probiotics caused a decrease in the concentration of hsCRP, an effect that was observed in three of six studies. According to the checklist proposed by Downs and Black, 88% of the included studies correspond to high quality and 12% to intermediate quality. The intake of probiotics presented diverse results, being necessary more studies to identify the effect of the strains, doses and duration, in order to implement more consistent nutritional clinical treatments with the aim of improving the levels of inflammation biomarkers and risk factors in people with cardiometabolic diseases.Resumen:  Diversos estudios científicos han demostrado resultados contradictorios en cuanto al efecto que tiene la suplementación con probióticos sobre la inhibición de citoquinas proinflamatorias y la mejora del perfil clínico nutricional en personas con enfermedades cardiometabólicas.  Esta investigación tuvo como objetivo analizar la relación entre la ingesta de alimentos probióticos y suplementos con probióticos y marcadores de inflamación en enfermedades cardiometabólicas en personas adultas, a través de una revisión sistemática, durante el período comprendido entre 2015 y 2020. La revisión sistemática se realizó de acuerdo a las recomendaciones Cochrane y las guías GRADE; se utilizaron diferentes bases de datos como Pubmed, Oxford y BVS. Participaron de este proceso tres revisores. Se excluyeron los trabajos que no cumplian con los criterios de calidad de la evidencia: riesgo de sesgo, resultados imprecisos, resultados inconsistentes, problemas de aplicabilidad de la evidencia y la existencia de sesgo de publicación. Para el control del sesgo se utilizó la lista de verificación propuesta por Downs y Black. De los 859 artículos identificados, 17 cumplieron los requisitos de inclusión. Entre los criterios de elegibilidad se consideraron los ensayos controlados y ensayos clínicos aleatorizados. Del total de los estudios que analizaron el efecto de los probióticos (bifidobacterium, lactobacillus, lactococcus, acetobacter) sobre los biomarcadores de inflamación en enfermedades cardiometabólicas, se evidenció una disminución de las concentraciones de interleucinas (IL-1, IL-6, IL-8 e IL-12) en ocho de ellos, lo mismo sucedió con el FNTα; en el caso del IFNγ se vio disminuido en uno de tres estudios que lo analizaron; mientras que, el consumo de probióticos provocó el descenso de la concentración de PCRus, efecto que se observó en tres de seis estudios. Según la lista de verificación propuesta por Downs y Black, el 88% de los estudios incluidos corresponde a calidad alta y el 12% a calidad intermedia.  La ingesta de probióticos presentó resultados diversos, siendo necesarios más estudios para identificar el efecto de las cepas, dosis y duración, a fin de poder implementar tratamientos clínicos nutricionales más consistentes con el objetivo de mejorar los niveles de biomarcadores de inflamación y los factores de riesgo en personas con enfermedades cardiometabólicas.

Protein misfolding and dysregulated protein homeostasis in autoinflammatory diseases and beyond.

Cells have a number of mechanisms to maintain protein homeostasis, including proteasome-mediated degradation of ubiquitinated proteins and autophagy, a regulated process of ‘self-eating’ where the contents of entire organelles can be recycled for other uses. The unfolded protein response prevents protein overload in the secretory pathway. In the past decade, it has become clear that these fundamental cellular processes also help contain inflammation though degrading pro-inflammatory protein complexes such as the NLRP3 inflammasome. Signaling pathways such as the UPR can also be co-opted by toll-like receptor and mitochondrial reactive oxygen species signaling to induce inflammatory responses. Mutations that alter key inflammatory proteins, such as NLRP3 or TNFR1, can overcome normal protein homeostasis mechanisms, resulting in autoinflammatory diseases. Conversely, Mendelian defects in the proteasome cause protein accumulation, which can trigger interferon-dependent autoinflammatory disease. In non-Mendelian inflammatory diseases, polymorphisms in genes affecting the UPR or autophagy pathways can contribute to disease, and in diseases not formerly considered inflammatory such as neurodegenerative conditions and type 2 diabetes, there is increasing evidence that cell intrinsic or environmental alterations in protein homeostasis may contribute to pathogenesis

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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Phenotyping Superagers Using Resting-State fMRI

BACKGROUND AND PURPOSE: Superagers are defined as older adults with episodic memory performance similar or superior to that in middle-aged adults. This study aimed to investigate the key differences in discriminative networks and their main nodes between superagers and cognitively average elderly controls. In addition, we sought to explore differences in sensitivity in detecting these functional activities across the networks at 3T and 7T MR imaging fields. MATERIALS AND METHODS: Fifty-five subjects 80 years of age or older were screened using a detailed neuropsychological protocol, and 31 participants, comprising 14 superagers and 17 cognitively average elderly controls, were included for analysis. Participants underwent resting-state-fMRI at 3T and 7T MR imaging. A prediction classification algorithm using a penalized regression model on the measurements of the network was used to calculate the probabilities of a healthy older adult being a superager. Additionally, ORs quantified the influence of each node across preselected networks. RESULTS: The key networks that differentiated superagers and elderly controls were the default mode, salience, and language networks. The most discriminative nodes (ORs > 1) in superagers encompassed areas in the precuneus posterior cingulate cortex, prefrontal cortex, temporoparietal junction, temporal pole, extrastriate superior cortex, and insula. The prediction classification model for being a superager showed better performance using the 7T compared with 3T resting-state-fMRI data set. CONCLUSIONS: Our findings suggest that the functional connectivity in the default mode, salience, and language networks can provide potential imaging biomarkers for predicting superagers. The 7T field holds promise for the most appropriate study setting to accurately detect the functional connectivity patterns in superagers