Molecular, Enzymatic, and Cellular Characterization of Soluble Adenylyl Cyclase From Aquatic Animals.

The enzyme soluble adenylyl cyclase (sAC) is the most recently identified source of the messenger molecule cyclic adenosine monophosphate. sAC is evolutionarily conserved from cyanobacteria to human, is directly stimulated by [Formula: see text] ions, and can act as a sensor of environmental and metabolic CO2, pH, and [Formula: see text] levels. sAC genes tend to have multiple alternative promoters, undergo extensive alternative splicing, be translated into low mRNA levels, and the numerous sAC protein isoforms may be present in various subcellular localizations. In aquatic organisms, sAC has been shown to mediate various functions including intracellular pH regulation in coral, blood acid/base regulation in shark, heart beat rate in hagfish, and NaCl absorption in fish intestine. Furthermore, sAC is present in multiple other species and tissues, and sAC protein and enzymatic activity have been reported in the cytoplasm, the nucleus, and other subcellular compartments, suggesting even more diverse physiological roles. Although the methods and experimental tools used to study sAC are conventional, the complexity of sAC genes and proteins requires special considerations that are discussed in this chapter

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity

Background: Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID), our understanding of the disease mechanisms is still limited. In particular, more than 90% of the risk variants lie in non-coding regions, and almost 10% of these map to long non-coding RNA transcripts (lncRNAs). lncRNAs are known to show more cell-type specificity than protein-coding genes. Methods: We aimed to characterize lncRNAs and protein-coding genes located in loci associated with nine AIDs which have been well-defined by Immunochip analysis and by transcriptome analysis across seven populations of peripheral blood leukocytes (granulocytes, monocytes, natural killer (NK) cells, B cells, memory T cells, naive CD4(+) and naive CD8(+) T cells) and four populations of cord blood-derived T-helper cells (precursor, primary, and polarized (Th1, Th2) T-helper cells). Results: We show that lncRNAs mapping to loci shared between AID are significantly enriched in immune cell types compared to lncRNAs from the whole genome (a <0.005). We were not able to prioritize single cell types relevant for specific diseases, but we observed five different cell types enriched (a <0.005) in five AID (NK cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, and psoriasis; memory T and CD8(+) T cells in juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis; Th0 and Th2 cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis). Furthermore, we show that co-expression analyses of lncRNAs and protein-coding genes can predict the signaling pathways in which these AID-associated lncRNAs are involved. Conclusions: The observed enrichment of lncRNA transcripts in AID loci implies lncRNAs play an important role in AID etiology and suggests that lncRNA genes should be studied in more detail to interpret GWAS findings correctly. The co-expression results strongly support a model in which the lncRNA and protein-coding genes function together in the same pathways

Hereditary thrombotic thrombocytopenic purpura and COVID-19: Impacts of vaccination and infection in this rare disease.

Introduction Severe COVID-19 is associated with an important increase of von Willebrand factor and mild lowering of ADAMTS13 activity that may, in the presence of a strong inflammatory reaction, increase the risk of acute thrombotic thrombocytopenic purpura (TTP). Although acute episodes of immune-mediated TTP associated with COVID-19 or SARS-CoV-2 vaccination have been reported, data about clinical evolution of hereditary TTP (hTTP) during the pandemic are scarce. Method We conducted a survey among adult patients of the International Hereditary TTP Registry about SARS-CoV-2 vaccination, COVID-19, and occurrence of acute hTTP episodes. Results Of 122 adult hTTP patients invited to participate, 86 (70.5%) responded. Sixty-five had been vaccinated (75.6%), of which 14 had received in addition a booster, resulting in 139 individual vaccine shots. Although vaccinations in patients on plasma prophylaxis were done within 1 week of the last plasma infusion, all 23 patients treated with plasma on demand were vaccinated without prior plasma infusions. One patient on uninterrupted weekly plasma infusions presented within 3 days from his second vaccination with neurological symptoms and computed tomography scan 9 days later showed subacute ischemic/hemorrhagic frontal lobe infarction. A second male patient developed acute myocarditis after his second dose of mRNA-1273 vaccine. Twelve (14%) patients had COVID-19, associated with an acute hTTP episode in three of them: one patient had a transient ischemic attack, one a stroke, and a pregnant woman was hospitalized to intensify plasma treatment. Discussion The risk of an acute episode triggered by COVID-19 seems higher than following vaccination in hTTP patients, who can be safely vaccinated against SARS-CoV-2

Bioremoval of marker pen inks by exploiting lipase hydrolysis

[EN] New and eco-sustainable methods based on the catalytic activity of lipases for the removal of acrylic marker pen inks were investigated. Different biocleaning methodologies were tested using lipases from different sources (viz. bacteria and fungi) dispersed in aqueous systems and microemulsions. Blue, green, red and black marker pens were selected for their chemical composition. Unglazed ceramic substrates were painted using marker pens, and some of these samples were subjected to natural and artificial ageing in order to compare the effectiveness of cleaning methods on fresh and aged ink layers. It was evidenced that acrylic polymer-based inks may be removed with an oil in water microemulsion, but cleaning effectiveness was generally enhanced when a lipase was added. Moreover, it was found that all the tests were more effective on the unaged samples, therefore, the cleaning intervention should be performed as soon as possible. Cleaning effectiveness was evaluated by measuring colour differences, acquiring visible reflectance spectra and determining the percentage of white in images of the treated samples by Image J open source software, for the first time used to this purpose. The results illustrate that only a multi-technique approach can correctly evaluate the effectiveness of different cleaning methods. (C) 2017 Elsevier B.V. All rights reserved.The present study was carried out with the support of the following projects: PRIN project no. 2010329WPF "Sustainability in cultural heritage: from diagnosis to the development of innovative systems for consolidation, cleaning and protection", financed by the Italian Ministry of Education, University and Research (MIUR); P.O. PUGLIA ERDF 2007-2013, project code 3Z3VZ46 "II restauro delle grandi opere in Puglia: l'innovazione attraverso le nanotecnologie e metodologie diagnostiche avanzate (RESTAUREO)", financed by Puglia Region (Italy); Potenziamento Strutturale PONa3_00369 of the University "A. Moro" of Bari "Laboratorio per lo Sviluppo Integrato delle Scienze e delle Tecnologie dei Materiali Avanzati e per dispositivi innovativi (SISTEMA)", financed by the MIUR (Italy); Fondo di Sviluppo e Coesione 2007-2013 APQ Ricerca Regione Puglia "Programma regionale a sostegno della specializzazione Intelligente e della sostenibilita sociale ed ambientale - Futureln - Research".Germinario, G.; Van Der Werf, ID.; Palazzo, G.; Regidor Ros, JL.; Montes Estellés, RM.; Sabbatini, L. (2017). Bioremoval of marker pen inks by exploiting lipase hydrolysis. Progress in Organic Coatings. 110:162-171. https://doi.org/10.1016/j.porgcoat.2017.02.019S16217111

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

The development of therapeutic strategies to combat immune-associated diseases requires the molecular mechanisms of human Th17 cell differentiation to be fully identified and understood. To investigate transcriptional control of Th17 cell differentiation, we used primary human CD4+ T cells in small interfering RNA (siRNA)-mediated gene silencing and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) to identify both the early direct and indirect targets of STAT3. The integrated dataset presented in this study confirms that STAT3 is critical for transcriptional regulation of early human Th17 cell differentiation. Additionally, we found that a number of SNPs from loci associated with immune-mediated disorders were located at sites where STAT3 binds to induce Th17 cell specification. Importantly, introduction of such SNPs alters STAT3 binding in DNA affinity precipitation assays. Overall, our study provides important insights for modulating Th17-mediated pathogenic immune responses in humans.</p

Poor Reproducibility of Allergic Rhinitis SNP Associations

10.1371/journal.pone.0053975PLoS ONE81

Stratification of candidate genes for Parkinson’s disease using weighted protein interaction network analysis

Genome wide association studies (GWAS) have helped identify large numbers of genetic loci that significantly associate with increased risk of developing diseases. However, translating genetic knowledge into understanding of the molecular mechanisms underpinning disease (i.e. disease-specific impacted biological processes) has to date proved to be a major challenge. This is primarily due to difficulties in confidently defining candidate genes at GWAS-risk loci. The goal of this study was to better characterize candidate genes within GWAS loci using a protein interactome based approach and with Parkinson's disease (PD) data as a test case.We applied a recently developed Weighted Protein-Protein Interaction Network Analysis (WPPINA) pipeline as a means to define impacted biological processes, risk pathways and therein key functional players. We used previously established Mendelian forms of PD to identify seed proteins, and to construct a protein network for genetic Parkinson's and carried out functional enrichment analyses. We isolated PD-specific processes indicating 'mitochondria stressors mediated cell death', 'immune response and signaling', and 'waste disposal' mediated through 'autophagy'. Merging the resulting protein network with data from Parkinson's GWAS we confirmed 10 candidate genes previously selected by pure proximity and were able to nominate 17 novel candidate genes for sporadic PD.With this study, we were able to better characterize the underlying genetic and functional architecture of idiopathic PD, thus validating WPPINA as a robust pipeline for the in silico genetic and functional dissection of complex disorders