scholarly journals TOWARDS UNDERSTANDING THE MECHANISMS OF EPIGENETIC REGULATION: PART 1. AN EVOLUTIONAL INSIGHT INTO PCG-MEDIATED GENE REPRESSION

2008 ◽  
Vol 6 (1) ◽  
pp. 12-19
Author(s):  
Elena M Fedorova ◽  
Alexander V Rodionov
Keyword(s):  
Epigenetic Regulation ◽  
Current Knowledge ◽  
Gene Repression ◽  
Epigenetic Repression ◽  
Insight Into

The evolutionary conserved PcG proteins maintain stable transcriptional epigenetic repression, established earlier by transiently acting regulator proteins. The exact mechanism of PcG-mediated repression is not identified yet, and here we outline existing models of the repression mechanism. We also shortly summarize the current knowledge about PcG proteins and their role in various processes and present an insight into the evolution of PRC1 and PRC2 complexes.

scholarly journals Visualization of PRC2-Dinucleosome Interactions Leading to Epigenetic Repression

2018 ◽  
Author(s):  
Simon Poepsel ◽  
Vignesh Kasinath ◽  
Eva Nogales
Keyword(s):  
Epigenetic Regulation ◽  
Protein Complexes ◽  
Histone H3 ◽  
Gene Repression ◽  
Dna Interactions ◽  
Heterochromatin Formation ◽  
Polycomb Repressive Complex 2 ◽  
Nucleosomal Dna ◽  
Epigenetic Regulator ◽  
Epigenetic Repression

AbstractEpigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a gene silencer that methylates lysine 27 of histone H3, is stimulated upon recognition of its own catalytic product, and has been shown to be more active on dinucleosomes than H3 tails or single nucleosomes. These properties likely facilitate local H3K27me2/3 spreading causing heterochromatin formation and gene repression. Here, cryo-EM reconstructions of human PRC2 bound to dinucleosomes show how a single PRC2, interacting with nucleosomal DNA, precisely positions the H3 tails to recognize a H3K27me3 mark in one nucleosome and is stimulated to modify a neighboring nucleosome. The geometry of the PRC2-DNA interactions allow PRC2 to tolerate different dinucleosome geometries due to varying lengths of the linker DNA. Our structures are the first to illustrate how an epigenetic regulator engages with a complex chromatin substrate.

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

Epigenetic Regulator Signatures in Regenerative Capacity

2019 ◽  
Vol 14 (7) ◽  
pp. 598-606
Author(s):  
Sarah Albogami
Keyword(s):  
Epigenetic Regulation ◽  
Animal Species ◽  
Current Knowledge ◽  
Regeneration Process ◽  
Body Parts ◽  
Lysine Methylation ◽  
Regenerative Capacity ◽  
Biological Phenomena ◽  
Epigenetic Regulator

Background:: Regeneration is the process by which body parts lost as a result of injury are replaced, as observed in certain animal species. The root of regenerative differences between organisms is still not very well understood; if regeneration merely recycles developmental pathways in the adult form, why can some animals regrow organs whereas others cannot? In the regulation of the regeneration process as well as other biological phenomena, epigenetics plays an essential role. Objective:: This review aims to demonstrate the role of epigenetic regulators in determining regenerative capacity. Results:: In this review, we discuss the basis of regenerative differences between organisms. In addition, we present the current knowledge on the role of epigenetic regulation in regeneration, including DNA methylation, histone modification, lysine methylation, lysine methyltransferases, and the SET1 family. Conclusion:: An improved understanding of the regeneration process and the epigenetic regulation thereof through the study of regeneration in highly regenerative species will help in the field of regenerative medicine in future.

scholarly journals Effects of Glucosinolate-Derived Isothiocyanates on Fungi: A Comprehensive Review on Direct Effects, Mechanisms, Structure-Activity Relationship Data and Possible Agricultural Applications

2021 ◽  
Vol 7 (7) ◽  
pp. 539
Author(s):  
Tamás Plaszkó ◽  
Zsolt Szűcs ◽  
Gábor Vasas ◽  
Sándor Gonda
Keyword(s):  
Mycorrhizal Fungi ◽  
Current Knowledge ◽  
Synergistic Activity ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Structure Activity ◽  
Agricultural Applications ◽  
Antifungal Action ◽  
Insight Into ◽  
Soil Microbial Composition

Plants heavily rely on chemical defense systems against a variety of stressors. The glucosinolates in the Brassicaceae and some allies are the core molecules of one of the most researched such pathways. These natural products are enzymatically converted into isothiocyanates (ITCs) and occasionally other defensive volatile organic constituents (VOCs) upon fungal challenge or tissue disruption to protect the host against the stressor. The current review provides a comprehensive insight on the effects of the isothiocyanates on fungi, including, but not limited to mycorrhizal fungi and pathogens of Brassicaceae. In the review, our current knowledge on the following topics are summarized: direct antifungal activity and the proposed mechanisms of antifungal action, QSAR (quantitative structure-activity relationships), synergistic activity of ITCs with other agents, effects of ITCs on soil microbial composition and allelopathic activity. A detailed insight into the possible applications is also provided: the literature of biofumigation studies, inhibition of post-harvest pathogenesis and protection of various products including grains and fruits is also reviewed herein.

scholarly journals Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zi Wang ◽  
Pan Wang ◽  
Yanan Li ◽  
Hongling Peng ◽  
Yu Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Hematological Malignancies ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Hematologic Disorders ◽  
Cell Lineages ◽  
Stage Of Development ◽  
Transcription Complexes ◽  
Insight Into

AbstractHematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.

scholarly journals High-Performance Computing of BEAST/BEAGLE in Bayesian Phylogenetics using SDumont Hybrid Resources

2020 ◽  
Author(s):  
Kary Ocaña ◽  
Micaella Coelho ◽  
Guilherme Freire ◽  
Carla Osthoff
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Current Knowledge ◽  
Data Sets ◽  
Length Estimation ◽  
Computationally Intensive ◽  
Mcmc Chain ◽  
Performance Computing ◽  
Insight Into

Bayesian phylogenetic algorithms are computationally intensive. BEAST 1.10 inferences made use of the BEAGLE 3 high-performance library for efficient likelihood computations. The strategy allows phylogenetic inference and dating in current knowledge for SARS-CoV-2 transmission. Follow-up simulations on hybrid resources of Santos Dumont supercomputer using four phylogenomic data sets, we characterize the scaling performance behavior of BEAST 1.10. Our results provide insight into the species tree and MCMC chain length estimation, identifying preferable requirements to improve the use of high-performance computing resources. Ongoing steps involve analyzes of SARS-CoV-2 using BEAST 1.8 in multi-GPUs.

scholarly journals Vaccinium gaultherioides: Another insight into water relations of alpine dwarf shrubs

2015 ◽  
Vol 2 ◽  
pp. e004 ◽  
Author(s):  
Andrea Ganthaler ◽  
S. Mayr
Keyword(s):  
Growth Form ◽  
Current Knowledge ◽  
European Alps ◽  
Hydraulic Parameters ◽  
Turgor Loss Point ◽  
Dwarf Shrubs ◽  
Hydraulic Safety ◽  
Conductivity Cell ◽  
Osmotic Properties ◽  
Insight Into

Dwarf shrubs exhibit different requirements for a safe and efficient water supply compared to trees due their basitonic branching and low growth height. Though, only few studies dealt with the hydraulics of this growth form. Here we report key hydraulic parameters (vulnerability to drought-induced embolism, xylem hydraulic conductivity, cell osmotic potential, potential at turgor loss point) and related wood anatomical traits for Vaccinium gaultherioides, a wide-spread species in the European Alps. The results affirm the current knowledge, by indicating a relatively risky hydraulic strategy with low hydraulic safety compared to alpine trees and osmotic properties connected to the species’ soil humidity requirements.

Advanced Turbulent Combustion Physics and Applications

2021 ◽  
Keyword(s):  
Graduate Students ◽  
Turbulent Combustion ◽  
Current Knowledge ◽  
Supersonic Flows ◽  
Solid Fuels ◽  
Recent Advances ◽  
The World ◽  
Insight Into

Explore a thorough and up to date overview of the current knowledge, developments and outstanding challenges in turbulent combustion and application. The balance among various renewable and combustion technologies are surveyed, and numerical and experimental tools are discussed along with recent advances. Covers combustion of gaseous, liquid and solid fuels and subsonic and supersonic flows. This detailed insight into the turbulence-combustion coupling with turbulence and other physical aspects, shared by a number of the world leading experts in the field, makes this an excellent reference for graduate students, researchers and practitioners in the field.

scholarly journals The Impact of Environmental Chemicals on the Gut Microbiome

2020 ◽  
Vol 176 (2) ◽  
pp. 253-284 ◽  
Author(s):  
Karen Chiu ◽  
Genoa Warner ◽  
Romana A Nowak ◽  
Jodi A Flaws ◽  
Wenyan Mei
Keyword(s):  
Gut Microbiome ◽  
Current Knowledge ◽  
Environmental Chemicals ◽  
Microbial Composition ◽  
Multiple Factors ◽  
Microbiome Research ◽  
Health Related ◽  
Exogenous Factors ◽  
The Impact ◽  
Insight Into

Abstract Since the surge of microbiome research in the last decade, many studies have provided insight into the causes and consequences of changes in the gut microbiota. Among the multiple factors involved in regulating the microbiome, exogenous factors such as diet and environmental chemicals have been shown to alter the gut microbiome significantly. Although diet substantially contributes to changes in the gut microbiome, environmental chemicals are major contaminants in our food and are often overlooked. Herein, we summarize the current knowledge on major classes of environmental chemicals (bisphenols, phthalates, persistent organic pollutants, heavy metals, and pesticides) and their impact on the gut microbiome, which includes alterations in microbial composition, gene expression, function, and health effects in the host. We then discuss health-related implications of gut microbial changes, which include changes in metabolism, immunity, and neurological function.

scholarly journals Early Airway Pathological Changes in Children: New Insights into the Natural History of Wheezing

2019 ◽  
Vol 8 (8) ◽  
pp. 1180 ◽  
Author(s):  
Matteo Bonato ◽  
Mariaenrica Tiné ◽  
Erica Bazzan ◽  
Davide Biondini ◽  
Marina Saetta ◽  
...  
Keyword(s):  
Natural History ◽  
Genetic Background ◽  
Current Knowledge ◽  
Persistent Asthma ◽  
Epidemiological Studies ◽  
Airflow Limitation ◽  
Clinical Expression ◽  
Heterogeneous Condition ◽  
History Of ◽  
Insight Into

Asthma is a heterogeneous condition characterized by reversible airflow limitation, with different phenotypes and clinical expressions. Although it is known that asthma is influenced by age, gender, genetic background, and environmental exposure, the natural history of the disease is still incompletely understood. Our current knowledge of the factors determining the evolution from wheezing in early childhood to persistent asthma later in life originates mainly from epidemiological studies. The underlying pathophysiological mechanisms are still poorly understood. The aim of this review is to converge epidemiological and pathological evidence early in the natural history of asthma to gain insight into the mechanisms of disease and their clinical expression.

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