Impact of non synonymous single nucleotide variants on protein fitness: experimental analysis for a comparative study

Proteins are large biological molecules that control most vital cellular functions. They consist of one or more chains of amino acids in an order determined by the base sequence of nucleotides in the DNA coding for the protein. Thanks to the information from the genetic code and according to the energy landscape, proteins fold into their correct three-dimensional structures and exert their specific function. The correct fold of large portion of the structure is generally related to specific protein functions and when any even small alterations occur, it is possible to observe a decrease, an increase or a drastic change in the protein function. In several cases alterations at the amino acid level can influence the conformational rearrangement, the function or the binding properties of a given protein. On this premise, knowledge on protein structure-function relationships can be crucial in finding the molecular basis for hereditary diseases and in predicting protein function from structure and vice versa. Therefore, the study of structure-function relationships is really important nowadays to better understand several diseases at their molecular level. In particular, this kind of approach seems to be relevant in cancer research considering that several somatic variants resulting from alterations at the amino acid level have been detected in cancer genome for several proteins. The analysis of this kind of alterations is key to understand the genetic bases of disease progression, patient survival and also response to therapy. Since knowledge of protein function in health and disease is essential to identify new and more specific cures for different diseases and to design pharmacologically active and more selective drugs, the information resulting from the analysis of somatic mutations found in cancer tissues can improve the available therapies and create new and more specific ones suggesting that precision and personalized medicine is not anymore a daydream

On the link between global volcanic activity and global mean sea level

Studying a large number of volcanic eruptions is a way to decipher general characteristics related to volcano dynamics but also on external forcing influencing it, such as solid Earth and ocean tides. Many studies have tackled this tidal influence on the onset of volcanic eruptions and more generally, on volcanic activity. However, the interplay between this quasi-permanent forcing and volcanic systems is still poorly understood. With the present study, we propose to consider a global viewpoint to address this interaction. We analyzed the number of monthly volcanic eruptions and the global mean sea level between 1880 and 2009 using the Singular Spectrum Analysis time-series analysis technique to evaluate the existence of common periodicities. We found multi-decadal components of similar periodicities present in both time-series which we link to those already recognized in the polar motion. Its multi-decadal variations result in a mass reorganization in the oceans whose associated stress changes may impact processes generating volcanic eruptions worldwide. Our results show the influence of global processes on volcanic activity and open many questions to further investigate these multi-scale interactions.info:eu-repo/semantics/publishedVersio

Unveiling the folding mechanism of the bromodomains

Bromodomains (BRDs) are small protein domains often present in large multidomain proteins involved in transcriptional regulation in eukaryotic cells. They currently represent valuable targets for the development of inhibitors of aberrant transcriptional processes in a variety of human diseases. Here we report urea-induced equilibrium unfolding experiments monitored by circular dichroism (CD) and fluorescence on two structurally similar BRDs: BRD2(2) and BRD4(1), showing that BRD4(1) is more stable than BRD2(2). Moreover, we report a description of their kinetic folding mechanism, as obtained by careful analysis of stopped-flow and temperature-jump data. The presence of a high energy intermediate for both proteins, suggested by the non-linear dependence of the folding rate on denaturant concentration in the millisec time regime, has been experimentally observed by temperature-jump experiments. Quantitative global analysis of all the rate constants obtained over a wide range of urea concentrations, allowed us to propose a common, three-state, folding mechanism for these two BRDs. Interestingly, the intermediate of BRD4(1) appears to be more stable and structurally native-like than that populated by BRD2(2). Our results underscore the role played by structural topology and sequence in determining and tuning the folding mechanism

Effect of bet missense mutations on bromodomain function, inhibitor binding and stability

Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence and acetylation dependent way regulating the recruitment of transcriptional regulators and chromatin remodelling enzymes to acetylated sites in chromatin. Recent studies revealed that bromodomains are highly druggable protein interaction domains resulting in the development of a large number of bromodomain inhibitors. BET bromodomain inhibitors received a lot of attention in the oncology field resulting in the rapid translation of early BET bromodomain inhibitors into clinical studies. Here we investigated the effects of mutations present as polymorphism or found in cancer on BET bromodomain function and stability and the influence of these mutants on inhibitor binding. We found that most BET missense mutations localize to peripheral residues in the two terminal helices. Crystal structures showed that the three dimensional structure is not compromised by these mutations but mutations located in close proximity to the acetyl-lysine binding site modulate acetyl-lysine and inhibitor binding. Most mutations affect significantly protein stability and tertiary structure in solution, suggesting new interactions and an alternative network of protein-protein interconnection as a consequence of single amino acid substitution. To our knowledge this is the first report studying the effect of mutations on bromodomain function and inhibitor binding

The Human Microbiome and Recurrent Abdominal Pain in Children

This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS). Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain. 3. Perform functional gut metagenomics by evaluation of whole community gene expression profiles and discovery of disease-specific pathway signatures. Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies included 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes were applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 Demo project, from a set of healthy and IBS children (7-12 yo) may enable the identification of core microbiomes in children, in addition to variable components that may distinguish healthy from diseased pediatric states. Twenty-two children with IBS and twenty-two healthy children were enrolled and analyzed in the UH2 phase of this study. The planned enrollment targets for the UH2/3 phases include 50 healthy children, 50 children with FAP and 50 children with IBS (minimum of 3 time points per child). We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status in addition to IBS subtype (e.g., diarrhea-vs constipation-predominant). In the next phase, whole genome shotgun sequencing and metatranscriptomics will be performed with a subset of children in each group. This study explores the nature of core and variable human microbiome in pre-adolescent healthy children and children with IBS. 
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Increased levels of palmitoylethanolamide and other bioactive lipid mediators and enhanced local mast cell proliferation in canine atopic dermatitis

Background: Despite the precise pathogenesis of atopic dermatitis (AD) is unknown, an immune dysregulation that causes Th2-predominant inflammation and an intrinsic defect in skin barrier function are currently the two major hypotheses, according to the so-called outside-inside-outside model. Mast cells (MCs) are involved in AD both by releasing Th2 polarizing cytokines and generating pruritus symptoms through release of histamine and tryptase. A link between MCs and skin barrier defects was recently uncovered, with histamine being found to profoundly contribute to the skin barrier defects. Palmitoylethanolamide and related lipid mediators are endogenous bioactive compounds, considered to play a protective homeostatic role in many tissues: evidence collected so far shows that the anti-inflammatory effect of palmitoylethanolamide depends on the down-modulation of MC degranulation. Based on this background, the purpose of the present study was twofold: (a) to determine if the endogenous levels of palmitoylethanolamide and other bioactive lipid mediators are changed in the skin of AD dogs compared to healthy animals; (b) to examine if MC number is increased in the skin of AD dogs and, if so, whether it depends on MC in-situ proliferation. Results: The amount of lipid extract expressed as percent of biopsy tissue weight was significantly reduced in AD skin while the levels of all analyzed bioactive lipid mediators were significantly elevated, with palmitoylethanolamide showing the highest increase. In dogs with AD, the number of MCs was significantly increased in both the subepidermal and the perifollicular compartments and their granule content was significantly decreased in the latter. Also, in situ proliferation of MCs was documented. Conclusions: The levels of palmitoylethanolamide and other bioactive lipid mediators were shown to increase in AD skin compared to healthy samples, leading to the hypothesis that they may be part of the body's innate mechanisms to maintain cellular homeostasis when faced with AD-related inflammation. In particular, the increase may be considered a temptative response to down-regulating the observed elevation in the number, functionality and proliferative state of MCs in the skin of AD dogs. Further studies are warranted to confirm the hypothesis

Iodine status and supplementation in pregnancy: an overview of the evidence provided by meta-analyses

Iodine supplementation during pregnancy in areas with mild-moderate defciency is still a matter of debate. The present study aimed at systematically reviewing currently available evidences provided by meta-analyses with the aim to further clarify controversial aspects regarding the need of iodine supplementation in pregnancy as well as to provide guidance on clinical decision-making, even in areas with mild-moderate defciency. Medline, Embase and Cochrane search from 1969 to 2022 were performed. For the purpose of this review, only studies containing meta-analytic data were selected. A total of 7 meta-analyses were retrieved. Four meta-analyses evaluated the relationship between iodine status during pregnancy and neonatal and maternal outcomes suggesting the existence of a U-shaped correlation between iodine status and several maternal and neonatal consequences, especially if iodine status is evaluated at the beginning of pregnancy. Three meta-analyses evaluating the results of intervention trials failed to provide straightforward conclusions on the benefts of iodine supplementation in pregnant women in areas with mild-moderate iodine defciency. Although evidence coming from meta-analyses suggests a role of iodine status during pregnancy in determining maternal and child outcomes, results of meta-analyses of intervention trials are still controversial. Several factors including, degree of iodine defciency, and pooling studies conducted in areas with diferent iodine intake, may account for the lack of benefts reported by metaanalyses of intervention trials. More high-quality, randomized, controlled trials including information on timing, dose and regimen of iodine supplementation are needed to further elucidate this issue

Characterization of human frataxin missense variants in cancer tissues

Human frataxin is an iron binding protein involved in the mitochondrial Fe-S clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumour initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions, however some of the variants show a decreased stability and a decreased functional activity in comparison to that of the wild type protein. This article is protected by copyright. All rights reserved

Deltaic and Coastal Sediments as Recorders of Mediterranean Regional Climate and Human Impact Over the Past Three Millennia

This work was financially supported by the MISTRALS/PaleoMex program and by the Project of Strategic Interest NextData PNR 2011–2013 (www. nextdataproject.it). Lionel Savignan is thanked for his participation in the biomarker analysis. Radiocarbon datings for core KESC9-14 have been funded by Institut Carnot Ifremer-EDROME (grant A0811101). We also thank the Holocene North-Atlantic Gyres and Mediterranean Overturning dynamic through Climate Changes (HAMOC) project for financial support. The biomarker data presented here are available in the supporting information.Peer reviewedPublisher PD

Radiomic and Artificial Intelligence Analysis with Textural Metrics, Morphological and Dynamic Perfusion Features Extracted by Dynamic Contrast-Enhanced Magnetic Resonance Imaging in the Classification of Breast Lesions

The aim of the study was to estimate the diagnostic accuracy of textural, morpho- logical and dynamic features, extracted by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) images, by carrying out univariate and multivariate statistical analyses including artificial intelligence approaches. Methods: In total, 85 patients with known breast lesion were enrolled in this retrospective study according to regulations issued by the local Institutional Review Board. All patients underwent DCE-MRI examination. The reference standard was pathology from a surgical specimen for malignant lesions and pathology from a surgical specimen or fine needle aspiration cytology, core or Tru-Cut needle biopsy for benign lesions. In total, 91 samples of 85 patients were ana- lyzed. Furthermore, 48 textural metrics, 15 morphological and 81 dynamic parameters were extracted by manually segmenting regions of interest. Statistical analyses including univariate and multivari- ate approaches were performed: non-parametric Wilcoxon–Mann–Whitney test; receiver operating characteristic (ROC), linear classifier (LDA), decision tree (DT), k-nearest neighbors (KNN), and support vector machine (SVM) were utilized. A balancing approach and feature selection methods were used. Results: The univariate analysis showed low accuracy and area under the curve (AUC) for all considered features. Instead, in the multivariate textural analysis, the best performance (accuracy (ACC) = 0.78; AUC = 0.78) was reached with all 48 metrics and an LDA trained with balanced data. The best performance (ACC = 0.75; AUC = 0.80) using morphological features was reached with an SVM trained with 10-fold cross-variation (CV) and balanced data (with adaptive synthetic (ADASYN) function) and a subset of five robust morphological features (circularity, rectangularity, sphericity, gleaning and surface). The best performance (ACC = 0.82; AUC = 0.83) using dynamic features was reached with a trained SVM and balanced data (with ADASYN function). Conclusion: Multivariate analyses using pattern recognition approaches, including all morphological, textural and dynamic features, optimized by adaptive synthetic sampling and feature selection operations obtained the best results and showed the best performance in the discrimination of benign and malignant lesions