scholarly journals Clinical and molecular heterogeneity of pineal parenchymal tumors: a consensus study

2020 ◽  
Author(s):  
Anthony P. Y. Liu ◽  
Bryan K. Li ◽  
Elke Pfaff ◽  
Brian Gudenas ◽  
Alexandre Vasiljevic ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Molecular Heterogeneity ◽  
Genomic Features ◽  
Pineal Parenchymal Tumors ◽  
Biologically Relevant ◽  
Genomic Studies ◽  
Microrna Processing ◽  
Bioinformatic Approaches ◽  
Shed Light

Background: Recent genomic studies have shed light on the biology and inter-tumoral heterogeneity underlying pineal parenchymal tumors, in particular pineoblastomas (PBs) and pineal parenchymal tumors of intermediate differentiation (PPTIDs). Previous reports, however, had modest sample sizes and lacked power to fully integrate molecular findings, clinical factors and patient outcome. The different subgroup structures proposed also called for a need to reconcile and reach consensus on a robust and relevant classification system. Methods: We performed a meta-analysis on 221 patients with molecularly characterized PBs and PPTIDs. DNA methylation profiles were analyzed through complementary bioinformatic approaches and molecular subgrouping was harmonized. Demographic, clinical and genomic features of patients and samples from these consensus subgroups were annotated. Findings: Four clinically and biologically relevant consensus PB subgroups were defined: PB-miRNA1 (n=96), PB-miRNA2 (n=23), PB-MYC/FOXR2 (n=34) and PB-RB1 (n=25); with PPTID (n=43) remaining as a molecularly distinct entity. Genomic and transcriptomic profiling allowed the characterization of oncogenic drivers for individual subgroups, specifically, alterations in the microRNA processing pathway in PB-miRNA1/2, MYC amplification and FOXR2 overexpression in PB-MYC/FOXR2, RB1 alteration in PB-RB1, and KBTBD4 insertion in PPTID. Age at diagnosis, sex predilection and metastatic status varied significantly among tumor subgroups. While patients from PB-miRNA2 and PPTID had superior outcome, survival for patients with PB-miRNA1 was intermediate and those from PB-MYC/FOXR2 and PB-RB1 dismal. Interpretation: We systematically interrogated the clinical and molecular heterogeneity within pineal parenchymal tumors and proposed a consensus nomenclature for disease subgroups, laying the groundwork for future clinical and preclinical studies as well as routine use in tumor classification.

scholarly journals Ni Oxidation State and Ligand Saturation Impact on the Capability of Octaazamacrocyclic Complexes to Bind and Reduce CO2

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4139
Author(s):  
Barbora Vénosová ◽  
Ingrid Jelemenská ◽  
Jozef Kožíšek ◽  
Peter Rapta ◽  
Michal Zalibera ◽  
...  
Keyword(s):  
Quantum Theory ◽  
Oxidation State ◽  
Central Atom ◽  
Population Analysis ◽  
Mulliken Population Analysis ◽  
Mulliken Population ◽  
Theoretical Methods ◽  
Ni Oxidation ◽  
Shed Light

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO2. In the first complex 1[NiIIL]0, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while in the second 1[NiIILH]2+ one, the macrocycle is saturated with hydrogens. One and two-electron reductions are described using Mulliken population analysis, quantum theory of atoms in molecules, localized orbitals, and domain averaged fermi holes, including the characterization of the Ni-CCO2 bond and the oxidation state of the central Ni atom. It was found that in the [NiLH] complex, the central atom is reduced to Ni0 and/or NiI and is thus able to bind CO2 via a single σ bond. In addition, the two-electron reduced 3[NiL]2− species also shows an affinity forwards CO2.

scholarly journals Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

2021 ◽  
Vol 22 (9) ◽  
pp. 4707
Author(s):  
Mariana Lopes ◽  
Sandra Louzada ◽  
Margarida Gama-Carvalho ◽  
Raquel Chaves
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Nucleotide Composition ◽  
Genomic Component ◽  
Genomic Studies ◽  
Human Genomic ◽  
Definition Of ◽  
High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

scholarly journals scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chantriolnt-Andreas Kapourani ◽  
Ricard Argelaguet ◽  
Guido Sanguinetti ◽  
Catalina A. Vallejos
Keyword(s):  
Single Cell ◽  
Bayesian Modeling ◽  
Bayesian Model ◽  
Regulation Of Gene Expression ◽  
Differential Methylation ◽  
Hierarchical Bayesian Model ◽  
Genomic Features ◽  
Distinct Cell ◽  
Biological Heterogeneity

AbstractHigh-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression. scMET is available at https://github.com/andreaskapou/scMET.

scholarly journals Genome-wide binding potential and regulatory activity of the glucocorticoid receptor’s monomeric and dimeric forms

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Thomas A. Johnson ◽  
Ville Paakinaho ◽  
Sohyoung Kim ◽  
Gordon L. Hager ◽  
Diego M. Presman
Keyword(s):  
Receptor Binding ◽  
Site Response ◽  
Physiological Role ◽  
Binding Potential ◽  
Open Chromatin ◽  
Imaging Data ◽  
Response Elements ◽  
Genome Wide ◽  
Genomic Studies

AbstractA widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies based on recovery of enriched half-site response elements suggest monomeric engagement on DNA. Here, we perform genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding even to open chromatin. We also find that GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids.

scholarly journals Electrophysiological characterization of a diverse group of sugar transporters from Trichoderma reesei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sami Havukainen ◽  
Jonai Pujol-Giménez ◽  
Mari Valkonen ◽  
Ann Westerholm-Parvinen ◽  
Matthias A. Hediger ◽  
...  
Keyword(s):  
Trichoderma Reesei ◽  
Scientific Literature ◽  
Large Body ◽  
Comprehensive Analysis ◽  
Transport Function ◽  
Sugar Transporters ◽  
New Knowledge ◽  
Electrophysiological Characterization ◽  
Shed Light

AbstractTrichoderma reesei is an ascomycete fungus known for its capability to secrete high amounts of extracellular cellulose- and hemicellulose-degrading enzymes. These enzymes are utilized in the production of second-generation biofuels and T. reesei is a well-established host for their production. Although this species has gained considerable interest in the scientific literature, the sugar transportome of T. reesei remains poorly characterized. Better understanding of the proteins involved in the transport of different sugars could be utilized for engineering better enzyme production strains. In this study we aimed to shed light on this matter by characterizing multiple T. reesei transporters capable of transporting various types of sugars. We used phylogenetics to select transporters for expression in Xenopus laevis oocytes to screen for transport activities. Of the 18 tested transporters, 8 were found to be functional in oocytes. 10 transporters in total were investigated in oocytes and in yeast, and for 3 of them no transport function had been described in literature. This comprehensive analysis provides a large body of new knowledge about T. reesei sugar transporters, and further establishes X. laevis oocytes as a valuable tool for studying fungal sugar transporters.

scholarly journals Insights into Mycobacterium leprae Proteomics and Biomarkers—An Overview

Proteomes ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 7
Author(s):  
Sakshi Gautam ◽  
Devesh Sharma ◽  
Anjana Goel ◽  
Shripad A. Patil ◽  
Deepa Bisht
Keyword(s):  
Early Diagnosis ◽  
Causative Agent ◽  
Mycobacterium Leprae ◽  
Pivotal Role ◽  
New Biomarkers ◽  
Shed Light

Although leprosy is curable, the identification of biomarkers for the early diagnosis of leprosy would play a pivotal role in reducing transmission and the overall prevalence of the disease. Leprosy-specific biomarkers for diagnosis, particularly for the paucibacillary disease, are not well defined. Therefore, the identification of new biomarkers for leprosy is one of the prime themes of leprosy research. Studying Mycobacterium leprae, the causative agent of leprosy, at the proteomic level may facilitate the identification, quantification, and characterization of proteins that could be potential diagnostics or targets for drugs and can help in better understanding the pathogenesis. This review aims to shed light on the knowledge gained to understand leprosy or its pathogen employing proteomics and its role in diagnosis.

scholarly journals Global prevalence and molecular characterization of extended-spectrum β-lactamase producing- in dogs and cats – A scoping review and meta-analysis

One Health ◽  
2021 ◽  
pp. 100236
Author(s):  
Marília Salgado-Caxito ◽  
Julio A. Benavides ◽  
Aiko D. Adell ◽  
Antonio Carlos Paes ◽  
Andrea I. Moreno-Switt
Keyword(s):  
Molecular Characterization ◽  
Scoping Review ◽  
Meta Analysis ◽  
Global Prevalence ◽  
Extended Spectrum

scholarly journals Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 725
Author(s):  
Fernando Clavijo-Coppens ◽  
Nicolas Ginet ◽  
Sophie Cesbron ◽  
Martial Briand ◽  
Marie-Agnès Jacques ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Xylella Fastidiosa ◽  
Infected Plant ◽  
Mediterranean Area ◽  
Genomic Features ◽  
Phylogeny Analysis ◽  
Plant Pest ◽  
European Regulations ◽  
Surrogate Host

Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.

scholarly journals Nanotechnology in Roman Opaque Red Glass from the 2nd Century AD. Archaeometric Investigation in Red Sectilia from the Decoration of the Lucius Verus Villa in Rome

Heritage ◽  
2019 ◽  
Vol 2 (3) ◽  
pp. 2597-2611 ◽  
Author(s):  
Mario Bandiera ◽  
Patrice Lehuédé ◽  
Marco Verità ◽  
Luis Alves ◽  
Isabelle Biron ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Chemical Characterization ◽  
Second Step ◽  
Colorimetric Analysis ◽  
Historical Sources ◽  
Pixe Analysis ◽  
X Ray ◽  
Colorimetric Measurements ◽  
Shed Light

This work aims to characterise the chemical composition of Roman opaque red glass sectilia dated to the 2nd century A.D and to shed light on Roman glassmaking production of different shades of red, from red to reddish-brown. Due to the lack of technical historical sources for this period many questions about technological aspects still remain. In this project a multi-disciplinary approach is in progress to investigate the red glass sectilia with several red hues from the Imperial Villa of Lucius Verus (161–169 A.D.) in Rome. First, colorimetric measurements were taken to identify the various red hues. The second step was chemical characterization of the samples and the identification of crystalline colouring phases. Particle Induced X-Ray Emission (PIXE) analysis was used to investigate the chemical composition of these glass samples, while the crystalline phases were identified by Raman Spectroscopy and Scanning Electrons Microscope with Energy Dispersive X-ray Spectrometry (SEM-EDS). Using SEM-EDS nanoparticles were detected as a colouring agent, the chemical composition and the morphology of which has been studied in depth. This information has been compared with the colorimetric analysis to establish any correlation with the different colour hues.

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