scholarly journals Characterization of DNA methylation as a function of biological complexity via dinucleotide inter-distances

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150227 ◽  
Author(s):  
Giulia Paci ◽  
Giampaolo Cristadoro ◽  
Barbara Monti ◽  
Marco Lenci ◽  
Mirko Degli Esposti ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Statistical Study ◽  
The Other ◽  
Biological Complexity ◽  
Functional Roles ◽  
Exponential Tails ◽  
Cg Dinucleotide ◽  
Cg Dinucleotides

We perform a statistical study of the distances between successive occurrences of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the CG dinucleotide distribution in mammalian DNA, pointing towards a connection with the role of such dinucleotide in DNA methylation. While the CG distributions of mammals exhibit exponential tails with comparable parameters, the picture for the other organisms studied (e.g. fish, insects, bacteria and viruses) is more heterogeneous, possibly because in these organisms DNA methylation has different functional roles. Our analysis suggests that the distribution of the distances between CG dinucleotides provides useful insights into characterizing and classifying organisms in terms of methylation functionalities.

Structural role of copper in the minerals of the pearceite-polybasite group: the case of the new minerals cupropearceite and cupropolybasite

2007 ◽  
Vol 71 (06) ◽  
pp. 641-650 ◽  
Author(s):  
L. Bindi ◽  
M. Evain ◽  
P. G. Spry ◽  
K. T. Tait ◽  
S. Menchetti
Keyword(s):  
Chemical Characterization ◽  
Sample Space ◽  
The Other ◽  
Crystal Chemical ◽  
Structural Position ◽  
Space Group ◽  
Cu Content ◽  
Own Name

Abstract The pearceite-polybasite group of minerals, general formula [M6T2S7][Ag9CuS4] with M = Ag, Cu; and T = As, Sb, show a crystal structure which can be described as the succession, along the c axis, of two pseudo-layer modules: a [M6T2S7]2– A module layer and a [Ag9CuS4]2+ B module layer. Copper is present in one structural position of the B module layer and replaces Ag in the only fully occupied M position of the A module layer. When the Cu content is >4.00 a.p.f.u., the structural position of the A module layer becomes Cu-dominant and, consequently, the mineral deserves its own name. In this paper we report the crystal-chemical characterization of two Cu-rich members exhibiting the 111 unitcell type (corresponding to the Tac polytype). One sample (space group (P )m1, a 7.3218(8), c 11.8877(13) Å, V 551.90(10) Å3, Z = 1) having As >Sb and with the structural position of the A module layer dominated by Cu, has been named cupropearceite and the other sample (space group (P3̄)m1, a 7.3277(3), c 11.7752(6) Å, V 547.56(8) Å3, Z = 1) having Sb >As has been named cupropolybasite. Both the new minerals and mineral names have been approved by the IMA-CNMNC.

scholarly journals Ontology, Ontologies and the “I” of FAIR

2020 ◽  
Vol 2 (1-2) ◽  
pp. 181-191 ◽  
Author(s):  
Giancarlo Guizzardi
Keyword(s):  
Value Of Information ◽  
Direct Consequence ◽  
Semantic Interoperability ◽  
The Other ◽  
Added Value ◽  
Computational Tools ◽  
Other Hand ◽  
Guiding Principles

According to the FAIR guiding principles, one of the central attributes for maximizing the added value of information artifacts is interoperability. In this paper, I discuss the importance, and propose a characterization of the notion of Semantic Interoperability. Moreover, I show that a direct consequence of this view is that Semantic Interoperability cannot be achieved without the support of, on one hand, (i) ontologies, as meaning contracts capturing the conceptualizations represented in information artifacts and, on the other hand, of (ii) Ontology, as a discipline proposing formal meth- ods and theories for clarifying these conceptualizations and articulating their representations. In particular, I discuss the fundamental role of formal ontological theories (in the latter sense) to properly ground the construction of representation languages, as well as methodological and computational tools for supporting the engineering of ontologies (in the former sense) in the context of FAIR.

Genome Wide DNA Methylation Profiling In Patients with Multiple Myeloma.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3622-3622
Author(s):  
Yang Liu ◽  
Shenghua Duan ◽  
Xavier Leleu ◽  
Yong Zhang ◽  
Abdel Kareem A. Azab ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bone Marrow ◽  
Cell Lines ◽  
Promoter Region ◽  
Genomic Dna ◽  
Research Funding ◽  
Plasma Cells ◽  
Genome Wide

Abstract Abstract 3622 Introduction: Epigenetic factors such as DNA methylation have been shown to play a crucial role in the pathogenesis and progression of multiple myeloma (MM), yet studies of DNA methylation in MM are still limited. Therefore, in order to better understand the role of DNA methylation and identify specific genes that may be affected by differential methylation in MM patients, we conducted genome-wide DNA methylation profiling in cd138+ plasma cells purified from bone marrow of the patients with MM and normal donors. Methods: Genomic DNA of CD138+ Plasma cell selected from both MM patients and normal primary bone marrow was extracted using QIAGEN genome isolation kit. Following extraction, methylated DNA was isolated by Chip and hybridized to Affymetrix Human 2.0 tiling arrays. Chip assay and array hybridization was performed by Genepathway Inc. CEL files were processed and normalized using the MAT program, and methylation peaks were called from the resulting MAT scores using a custom segmentation method. Peak annotation and characterization of different genomic regions was done with custom tools and using genome annotation files from the UCSC genome database. All peaks were visualized by IGB online software. Medip-PCR was done in human MM cell lines to validate the methylation status. Methylated gene expression was determined by both Semi-quantitative PCR and real-time PCR. 5′aza was used for demethylation in human MM cell lines. Methylated gene expression with or without 5′aza treatment was determined by both Semi-quantitative PCR and real-time PCR. Results: Genomic DNA from CD138+ plasma cells from bone marrow of MM patients showed a significant increase in methylation levels compared to normal controls. We demonstrated that the hypermethylated sites were distributed across the genome in the following proportions: 3.2% in the promoter region; 45.6% in the intragenic region; 5.4 % in the 3′ end region; and 46.8 % in the intergenic region. Furthermore, around 9 % promoter CpG islands (CGIs); 11% intragenic CGIs; 15 % CGIs in 3′end region; and 14.3 % intergenic CGIs of patients genomic DNA were methylated. Moreover 2.1% promoter CGIs; 2.3 % intragenic CGIs; 2.5% CGIs in 3′end region; and 4.7% intergenic CGIs were methylated for the normal control. Medip-PCR showed that the identified methylation pattern in MM patients showed similar results in MM cell lines. Expectedly, we also observed that suppressor of cytokine signaling 1 (SOCS1) was hypermethylated at the promoter region (MAT score=19.986) as has been reported in human cell lines. Importantly, another member of SOCS family SOCS3 showed much stronger signal in the promoter region with CpG island (MAT score=31.707) in MM patients compared to normal control. Notably, the expression of two members of TNFR superfamily TNFRSF18 and TNFRSF4 which play an important role in development and programmed cell death of lymphocyte significantly have increased 283 and 141-fold after treatment with 5′aza in MM cell lines. Conclusion: These findings enhance our understanding of the role of DNA methylation in MM, as one of the epigenetic changes that may contribute to the pathogenesis of this disease. The identification and functional characterization of novel key molecules affected by DNA methylation will provide deeper insight into the molecular basis of MM disease. Disclosures: Leleu: Celgene: Consultancy, Research Funding; Janssen Cilag: Consultancy, Research Funding; Leo Pharma: Consultancy; Amgen: Consultancy; Chugai: Research Funding; Roche: Consultancy, Research Funding; Novartis: Consultancy, Research Funding. Anderson:Millennium Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau.

Introduction

2019 ◽  
pp. 1-32
Author(s):  
Ángel J. Gallego
Keyword(s):  
The Other ◽  
Syntactic Variation ◽  
Other Hand ◽  
Unexplored Area ◽  
American Spanish ◽  
Morphological Differences ◽  
The One ◽  
Spanish Dialects

This introduction offers a summary of the antecedents, goals, and prospects of the present volume. On the one hand, it emphasizes the important role of this collection of papers. It’s the first attempt to provide a global characterization of the syntactic variation of Spanish dialects. This is a very rich, but largely unexplored, area of inquiry, a situation that is probably due to a combination of various factors: lack of theoretical tools, interest in more easily observable (lexical, phonetic, or morphological) differences, etc. On the other hand, it introduces chapters that show varying and complementary formal approaches to the study of the syntactic phenomena of both American Spanish and European Spanish dialects.

scholarly journals Construction and Characterization of a Derivative of Neisseria gonorrhoeae Strain MS11 Devoid of AllopaGenes

2012 ◽  
Vol 194 (23) ◽  
pp. 6468-6478 ◽  
Author(s):  
Adriana LeVan ◽  
Lindsey I. Zimmerman ◽  
Amanda C. Mahle ◽  
Karen V. Swanson ◽  
Philip DeShong ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
The Other ◽  
Flow Cytometry Analysis ◽  
Wild Type ◽  
Homogeneous Population ◽  
Host Cell Interactions ◽  
Strain Ms11 ◽  
Adherence Ability

ABSTRACTTo better understand the role of Opa in gonococcal infections, we created and characterized a derivative of MS11 (MS11Δopa) that had the coding sequence for all 11 Opa proteins deleted. The MS11Δopa bacterium lost the ability to bind to purified lipooligosaccharide (LOS). While nonpiliated MS11Δopa and nonpiliated Opa-expressing MS11 cells grew at the same rate, nonpiliated MS11Δopa cells rarely formed clumps of more than four bacteria when grown in broth with vigorous shaking. Using flow cytometry analysis, we demonstrated that MS11Δopa produced a homogeneous population of bacteria that failed to bind monoclonal antibody (MAb) 4B12, a MAb specific for Opa. Opa-expressing MS11 cells consisted of two predominant populations, where ∼85% bound MAb 4B12 to a significant level and the other population bound little if any MAb. Approximately 90% of bacteria isolated from a phenotypically Opa-negative colony (a colony that does not refract light) failed to bind MAb 4B12; the remaining 10% bound MAb to various degrees. Piliated MS11Δopa cells formed dispersed microcolonies on ME180 cells which were visually distinct from those of piliated Opa-expressing MS11 cells. When Opa expression was reintroduced into MS11Δopa, the adherence ability of the strain recovered to wild-type levels. These data indicate that Opa contributes to both bacterium-bacterium and bacterium-host cell interactions.

scholarly journals Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

2021 ◽  
Author(s):  
Zhikai Liang ◽  
Sarah N Anderson ◽  
Jaclyn M Noshay ◽  
Peter A Crisp ◽  
Tara A Enders ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Leaf Tissue ◽  
Inbred Lines ◽  
Stress Conditions ◽  
The Other ◽  
Epigenetic Variation ◽  
Genome Wide ◽  
Repetitive Nature ◽  
The Family

Abstract Transposable elements (TEs) pervade most eukaryotic genomes. The repetitive nature of TEs complicates the analysis of their expression. Evaluation of the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress reveals no evidence for genome-wide activation of TEs, however some specific TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the different genotypes. In order to understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family that contain regions lacking DNA methylation. Comparisons of the expression of TEs in different genotypes revealed both genetic and epigenetic variation. Many of the specific TEs that are activated in stress in one inbred are not present in the other inbred, explaining the lack of activation. Among the elements that are shared in both genomes but only expressed in one genotype, we found that many exhibit differences in DNA methylation such that the genotype without expression is fully methylated. This study provides insights into the regulation of expression of TEs in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression variation. The highly repetitive nature of many transposable elements (TEs) complicates the analysis of their expression. Although most TEs are not expressed, some exhibit expression in certain tissues or conditions. We monitored the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress. While genome-wide activation of TEs did not occur, some TE families generated transcripts only in stress conditions with variation by genotype. To better understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. In most cases stress-responsive activation of a TE family was attributed to a small number of elements in the family. The elements that contained small regions lacking DNA methylation regions showed enriched expression while fully methylated elements were rarely expressed in control or stress conditions. The cause of varied expression in the different genotypes was due to both genetic and epigenetic variation. Many specific TEs activated by stress in one inbred were not present in the other inbred. Among the elements shared in both genomes, full methylation inhibited expression in one of the genotypes. This study provides insights into the regulation of TE expression in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression.

scholarly journals Zlata Tkach’s Concerto for Piano and Orchestra as a Culmination of the Composer Symphonic Thinking

2021 ◽  
Vol 4 (2) ◽  
pp. 287-295
Author(s):  
Alyona Vardanyan
Keyword(s):  
Research Methodology ◽  
Deep Understanding ◽  
The Other ◽  
Late Period ◽  
Piano Concerto ◽  
Thematic Structure ◽  
Creative Personality ◽  
First Time

The purpose of the article is to characterize Zlata Tkach’s Piano Concerto as the culminating composition in the genre of the composer’s symphonic music. The research methodology is based on the method of complex musicological analysis, due to which, the role of this work in the system of memorial genres of the author is determined, typical style features of her work late period are revealed, the thematic structure of the Concerto is characterized from the position of the manifestation of the principle of dialogicity and monothematism. The scientific novelty of the research is that for the first time, intonation processes in a Piano Concerto by Z. Tkach are systematically analyzed and the correlation of its traditional and innovative features is characterized. Being by genre attribution an opus with a pronounced desire to use modern means of expression, the concert is distinguished by the manifestation of the principle of microthematism and textural thematism. In the dramaturgical solution, the author conducts a constructive search in dynamic, timbre and rhythmic comparisons. At the same time, the intonational unity between the sections of the form, being the development of the romantic principle of poetry, is expressed in the form of monothematism. Conclusions. The creative method of Z. Tkach manifests itself in the synthesis of tradition and experiment. This is confirmed by the intonation-thematic structure of the Piano Concerto, in which the convergence of contrasting material contributes to the formation of an integral musical and dramatic concept. The motifs that form the basis of the monothematism complex establish intonation arches between the sections of a one-part composition, fastening them and subordinating them to a common plan. Important importance belongs to the opposition of the roles of the participants in the performance. Their dialogical activity is manifested in a peculiar way by the composer, primarily in the dialogue between the soloist and the orchestra: the interweaving of two contrasting figurative spheres is realized primarily in terms of content. The principle of monothematism is manifested especially vividly in the characterization of tragic reflections, painful reflections on the eternal conflict of the creative personality with the surrounding world, leading to a deep understanding of what exists. The other embodies the dynamism of life, dominating in the culmination of ‘action’, the accumulation of energy. Both the piano and the orchestra are equally involved in the development of both figurative principles. The resulting translational, purposeful movement towards the finale determines, along with the principle of monothematism, the integrity of the entire composition.

Human homologues of Delta-1 and Delta-4 function as mitogenic regulators of primitive human hematopoietic cells

Blood ◽  
2001 ◽  
Vol 97 (7) ◽  
pp. 1960-1967 ◽  
Author(s):  
Francis N. Karanu ◽  
Barbara Murdoch ◽  
Tomoyuki Miyabayashi ◽  
Mitsuhara Ohno ◽  
Masahide Koremoto ◽  
...  
Keyword(s):  
Cell Fate ◽  
Hematopoietic Cells ◽  
Functional Roles ◽  
Cell Fate Decisions ◽  
Wide Range ◽  
Deficient Mice

Delta-mediated Notch signaling controls cell fate decisions during invertebrate and murine development. However, in the human, functional roles for Delta have yet to be described. This study reports the characterization of Delta-1 and Delta-4 in the human. Human Delta-4 was found to be expressed in a wide range of adult and fetal tissues, including sites of hematopoiesis. Subsets of immature hematopoietic cells, along with stromal and endothelial cells that support hematopoiesis, were shown to express Notch and both Delta-1 and Delta-4. Soluble forms of human Delta-1 (hDelta-1) and hDelta-4 proteins were able to augment the proliferation of primitive human hematopoietic progenitors in vitro. Intravenous transplantation of treated cultures into immune-deficient mice revealed that hDelta-1 is capable of expanding pluripotent human hematopoietic repopulating cells detected in vivo. This study provides the first evidence for a role of Delta ligands as a mitogenic regulator of primitive hematopoietic cells in the human.

Translational Collocational Strategies of Arab Learners of English

Babel ◽  
2003 ◽  
Vol 49 (1) ◽  
pp. 59-81 ◽  
Author(s):  
Muhammad Raji Zughoul ◽  
Hussein Abdul-Fattah
Keyword(s):  
Undergraduate Students ◽  
English Translation ◽  
English Language ◽  
Multiple Choice ◽  
The Other ◽  
Instructional Focus ◽  
Communicative Strategies ◽  
Free Translation

Arab learners of English encounter a serious problem with collocational sequences. The present study purports to determine the extent to which university English language majors can use English collocations properly. A two-form translation test of 16 Arabic collocations was administered to both graduate and undergraduate students of English. The first form included the English translation in a multiple-choice format whereas the other was given as a free translation task. The findings confirmed the writers’ hypothesis that Arab learners of English at all levels face difficulty with English collocations. Moreover, the study aimed at the characterization of the communicative strategies imple-mented by the subjects in their attempts to convey the English meaning. Twelve such strategies have been identified, exemplified and described. The findings have substanti-ated the role of the NL in FL production as well as the need for explicit instructional focus on collocation in school and university.

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