scholarly journals CpG content-dependent associations between transcription factors and histone modifications

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249985
Author(s):  
Jonas Fischer ◽  
Fatemeh Behjati Ardakani ◽  
Kathrin Kattler ◽  
Jörn Walter ◽  
Marcel H. Schulz
Keyword(s):  
Transcription Factors ◽  
Histone Modifications ◽  
Linear Regression Models ◽  
Regulatory Machinery ◽  
Active Transcription ◽  
Gene Regulatory ◽  
On Chip ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

Understanding the factors that underlie the epigenetic regulation of genes is crucial to understand the gene regulatory machinery as a whole. Several experimental and computational studies examined the relationship between different factors involved. Here we investigate the relationship between transcription factors (TFs) and histone modifications (HMs), based on ChIP-seq data in cell lines. As it was shown that gene regulation by TFs differs depending on the CpG class of a promoter, we study the impact of the CpG content in promoters on the associations between TFs and HMs. We suggest an approach based on sparse linear regression models to infer associations between TFs and HMs with respect to CpG content. A study of the partial correlation of HMs for the two classes of high and low CpG content reveals possible CpG dependence and potential candidates for confounding factors in our models. We show that the models are accurate, inferred associations reflect known biological relationships, and we give new insight into associations with respect to CpG content. Moreover, analysis of a ChIP-seq dataset in HepG2 cells of the HM H3K122ac, an HM about little is known, reveals novel TF associations and supports a previously established link to active transcription.

scholarly journals Prediction of genome-wide effects of single nucleotide variants on transcription factor binding

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sebastian Carrasco Pro ◽  
Katia Bulekova ◽  
Brian Gregor ◽  
Adam Labadorf ◽  
Juan Ignacio Fuxman Bass
Keyword(s):  
Binding Sites ◽  
Cancer Type ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Regulatory Regions ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Gene Regulatory ◽  
The Impact ◽  
The Relationship

Abstract Single nucleotide variants (SNVs) located in transcriptional regulatory regions can result in gene expression changes that lead to adaptive or detrimental phenotypic outcomes. Here, we predict gain or loss of binding sites for 741 transcription factors (TFs) across the human genome. We calculated ‘gainability’ and ‘disruptability’ scores for each TF that represent the likelihood of binding sites being created or disrupted, respectively. We found that functional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population. In addition, we show that cancer somatic mutations have different effects on TF binding sites from different TF families on a cancer-type basis. Finally, we discuss the relationship between these results and cancer mutational signatures. Altogether, we provide a blueprint to study the impact of SNVs derived from genetic variation or disease association on TF binding to gene regulatory regions.

The impact of tinnitus characteristics and associated variables on tinnitus-related handicap

2015 ◽  
Vol 130 (1) ◽  
pp. 25-31 ◽  
Author(s):  
S Degeest ◽  
P Corthals ◽  
I Dhooge ◽  
H Keppler
Keyword(s):  
Additional Insight ◽  
Tinnitus Handicap Inventory ◽  
Hearing Status ◽  
Questionnaire Score ◽  
Relationship Of ◽  
The Impact ◽  
The Relationship ◽  
Sample Case ◽  
Insight Into ◽  
Associated Variables

AbstractObjective:This study aimed to determine the characteristics of tinnitus and tinnitus-related variables and explore their possible relationship with tinnitus-related handicap.Methods:Eighty-one patients with chronic tinnitus were included. The study protocol measured hearing status, tinnitus pitch, loudness, maskability and loudness discomfort levels. All patients filled in the Tinnitus Sample Case History Questionnaire, the Hyperacusis Questionnaire and the Tinnitus Handicap Inventory. The relationship of each variable with the Tinnitus Handicap Inventory score was evaluated by univariate and multivariate analyses.Results:Five univariables were associated with the Tinnitus Handicap Inventory score: loudness discomfort level, subjective tinnitus loudness, tinnitus awareness, noise intolerance and Hyperacusis Questionnaire score. Multiple regression analysis showed that the Hyperacusis Questionnaire score and tinnitus awareness were independently associated with the Tinnitus Handicap Inventory score.Conclusion:Hyperacusis and tinnitus awareness were independently associated with the Tinnitus Handicap Inventory score. Questionnaires on tinnitus and hyperacusis are especially suited to providing additional insight into tinnitus-related handicap and are therefore useful for evaluating tinnitus patients.

Consumerism

2014 ◽  
pp. 1-17
Author(s):  
Ioanna Papasolomou
Keyword(s):  
Historical Development ◽  
Sustainable Consumption ◽  
Compulsive Buying ◽  
Future Research ◽  
Sustainable Marketing ◽  
Definition Of ◽  
Corporate Social ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

This chapter reveals that the term ‘consumerism' encompasses a number of meanings which create confusion regarding the term. The discussion that follows, attempts to distinguish the different perspectives regarding the term by presenting its historical development and discussing the three definitions that have marked it. It explores the relationship between consumerism, marketing and corporate social responsibility (CSR). The growth of consumerism has led to the over-use of marketing which provided a flourishing ground for compulsive buying and consumption. There is evidence in the literature to suggest that in an era of increasing social problems and environmental challenges, there is a need for CSR and sustainable marketing. In fact, the second definition of consumerism is inextricably linked with CSR and societal marketing. The chapter is conceptual in nature and provides an in-depth review and discussion of some fundamental dimensions associated to consumerism based on the existent literature. The overarching aim is to provide an insight into the evolution and growth of consumerism based on the existent literature related to the topic. The discussion also focuses on exploring the relationship between marketing and consumerism shedding light onto compulsive buying, consumer attitudes and concerns on the micro consumerism issues, sustainable consumption and sustainable marketing. The chapter proceeds to raise some concerns related to the impact of the global economic crisis on consumerism by using as an example Cyprus based on the author's observations and thoughts. The chapter concludes with a list of suggestions to practitioners and directions for future research.

scholarly journals A Quantitative Analysis of the Impact on Chromatin Accessibility by Histone Modifications and Binding of Transcription Factors in DNase I Hypersensitive Sites

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Peng Cui ◽  
Jing Li ◽  
Bo Sun ◽  
Menghuan Zhang ◽  
Baofeng Lian ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Quantitative Analysis ◽  
Histone Modifications ◽  
Chromatin Accessibility ◽  
Dnase I ◽  
Open Chromatin ◽  
Dnase I Hypersensitive Sites ◽  
Biological Phenomena ◽  
Hypersensitive Sites ◽  
The Impact

It is known that chromatin features such as histone modifications and the binding of transcription factors exert a significant impact on the “openness” of chromatin. In this study, we present a quantitative analysis of the genome-wide relationship between chromatin features and chromatin accessibility in DNase I hypersensitive sites. We found that these features show distinct preference to localize in open chromatin. In order to elucidate the exact impact, we derived quantitative models to directly predict the “openness” of chromatin using histone modification features and transcription factor binding features, respectively. We show that these two types of features are highly predictive for chromatin accessibility in a statistical viewpoint. Moreover, our results indicate that these features are highly redundant and only a small number of features are needed to achieve a very high predictive power. Our study provides new insights into the true biological phenomena and the combinatorial effects of chromatin features to differential DNase I hypersensitivity.

scholarly journals PHYSICAL ACTIVITY AND TRACE ELEMENT METABOLISM

2020 ◽  
Vol 21 (2) ◽  
pp. 3-12
Author(s):  
A.A. Skalny ◽  
Keyword(s):  
Physical Activity ◽  
Trace Elements ◽  
Trace Element ◽  
The Body ◽  
Cobalt Chromium ◽  
Essential Trace Elements ◽  
Trace Element Metabolism ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

Currently, there is no doubt about the prevailing influence of the level of physical activity of an individual on the functional state of the body. However, the available literature data on the impact of physical stress on the body's supply of trace elements and their distribution in tissues are largely contradictory. This review of available literature data provides an insight into the relationship between physical activity and microelement homeostasis. The influence of human physical activity on the exchange of toxic (lead, cadmium, Nickel, etc.) and essential trace elements, such as iron, selenium, copper, cobalt, chromium, and zinc is reviewed. Based on the analyzed works, it is concluded that in order to correct the metabolic and microelement status of a person during physical activity, the most reasonable and necessary is the modulation of homeostasis of zinc and selenium.

scholarly journals Relationship between urban tourism traffic and tourism land use: A case study of Xiamen Island

2021 ◽  
Vol 14 (1) ◽  
pp. 761-776
Author(s):  
Yueer Gao ◽  
Yanqing Liao ◽  
Donggen Wang ◽  
Yongguang Zou
Keyword(s):  
Land Use ◽  
Urban Tourism ◽  
Linear Regression Models ◽  
The Sustainable Development ◽  
Functional Differences ◽  
Period 2 ◽  
Considerable Impact ◽  
The Impact ◽  
The Relationship

The development of tourism leads to changes in land-use demands and patterns, which are complex and dynamic, in tourist cities. Functional differences in land use produce different travel needs and have different impacts on traffic, especially on tourism. This paper explores the relationship between tourism land use and tourism traffic. Taking Xiamen Island as an example, using multivariable linear regression models, tourism land use is divided into accommodation land use, shopping land use and restaurant land use as the independent variables of the model; and the origin-destination (OD) density of traffic analysis zones (TAZs) during National Day in 2018 (October 1 to 5) is chosen as the dependent variable. To compare the different impacts between tourism land use and tourism traffic during the tourism and non-tourism periods, the non-tourism period (March 11 to 15) is further studied. The results show the following: (1) Xiamen, as a tourism city, has not only regular traffic but also tourism traffic, and traffic during the tourism period is totally different than that in the non-tourism period. (2) Tourism land use has a considerable impact on both tourism traffic and non-tourism traffic, but the impact is greater during the tourism period than the non-tourism period. (3) In the morning peak hour of both the tourism period and the non-tourism period, accommodation land use shows prominent effects on traffic. In the evening peak hour, shopping land use significantly impacts traffic. The study provides a basis for urban tourism land use adjustment to achieve the sustainable development of tourism traffic.

scholarly journals Gene regulatory network analysis of Trichoderma reesei grown on glucose-lactose mixtures suggests links between development and cellulase production

2020 ◽  
Author(s):  
Aurélie Pirayre ◽  
Laurent Duval ◽  
Corinne Blugeon ◽  
Cyril Firmo ◽  
Sandrine Perrin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Trichoderma Reesei ◽  
Regulatory Network ◽  
Cellulase Production ◽  
Biofuel Production ◽  
Batch Mode ◽  
Lactose Concentration ◽  
Gene Regulatory ◽  
The Impact

Abstract Background: The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei . Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network.Results: Experimental results confirmed the impact of sugar mixture on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using the BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth.Conclusions: This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1 , clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains.

scholarly journals Quantifying the Stability of Coupled Genetic and Epigenetic Switches With Variational Methods

2021 ◽  
Vol 11 ◽  
Author(s):  
Amogh Sood ◽  
Bin Zhang
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Cell Fate ◽  
Histone Modifications ◽  
Regulatory Networks ◽  
Variational Principles ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Fate Decisions ◽  
The Impact

The Waddington landscape provides an intuitive metaphor to view development as a ball rolling down the hill, with distinct phenotypes as basins and differentiation pathways as valleys. Since, at a molecular level, cell differentiation arises from interactions among the genes, a mathematical definition for the Waddington landscape can, in principle, be obtained by studying the gene regulatory networks. For eukaryotes, gene regulation is inextricably and intimately linked to histone modifications. However, the impact of such modifications on both landscape topography and stability of attractor states is not fully understood. In this work, we introduced a minimal kinetic model for gene regulation that combines the impact of both histone modifications and transcription factors. We further developed an approximation scheme based on variational principles to solve the corresponding master equation in a second quantized framework. By analyzing the steady-state solutions at various parameter regimes, we found that histone modification kinetics can significantly alter the behavior of a genetic network, resulting in qualitative changes in gene expression profiles. The emerging epigenetic landscape captures the delicate interplay between transcription factors and histone modifications in driving cell-fate decisions.

scholarly journals Toxic leadership: Effects on job satisfaction, commitment, turnover intention and organisational culture within the South African manufacturing industry

2020 ◽  
Vol 18 ◽  
Author(s):  
Amelda Paltu ◽  
Marissa Brouwers
Keyword(s):  
Job Satisfaction ◽  
South African ◽  
Turnover Intention ◽  
Organisational Culture ◽  
The Body ◽  
Toxic Leadership ◽  
Job Outcomes ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

Orientation: The impact of toxic leadership on employees and organisations has only recently become the focus of certain research studies.Research purpose: The general objective of this research was to investigate the relationship between toxic leadership, job satisfaction, turnover intention and commitment. The aim further was to test whether organisation culture mediates the relationship between toxic leadership and certain job outcomes such as job satisfaction, turnover intention and commitment.Motivation for the study: Currently, no knowledge is available on the relationships between toxic leadership and job outcomes within the context of South African manufacturing organisations. Therefore, this study provides South African organisations and researchers with an insight into such a relationship and the mentioned mediation of organisational culture in the process.Research approach/design and method: A cross-sectional research design with a sample size of N = 600 manufacturing employees was used. Product–moment correlations, multiple regression and structural equation modelling were used.Main findings: The test results returned both direct and indirect effects for all the relationships, which indicated only partial mediation in all the tested relationships.Practical/managerial implications: The results provided organisations’ insight into the possible consequences of toxic leadership on employees and the organisations’ culture.Contribution/value-add: The improved understanding of toxic leadership and the relationship with certain job outcomes contributes to the body of knowledge on both the theory of toxic leadership and on employees’ experience of such leadership styles in the work environment.

Supply chain management and organizational performance: the resonant influence

2019 ◽  
Vol 36 (7) ◽  
pp. 1053-1077 ◽  
Author(s):  
Binh An Thi Duong ◽  
Huy Quang Truong ◽  
Maria Sameiro ◽  
Paulo Sampaio ◽  
Ana Cristina Fernandes ◽  
...  
Keyword(s):  
Supply Chain ◽  
Supply Chain Management ◽  
Organizational Performance ◽  
Hypothetical Model ◽  
Data Set ◽  
Chain Management ◽  
Content Type ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

Purpose A single supply chain management (SCM) practice will have a certain impact on organizational performance (OP). However, since it is placed in a system that many other practices are conducted simultaneously, the practice itself will interact with other ones (i.e. affect/be affected). As a consequence, the efficiency of the affected practice is increased and it is expected to maximize the impact of SCM practices on OP. This mechanism is named the “resonant” influence that is a new approach in the SCM literature. The purpose of this paper is to test the above mechanism toward an insight into the relationship between SCM and OP. Design/methodology/approach Two models were compared: the competitive models only exist in direct effects; and the other contains relationships between practices that are able to show the mechanism of the resonant influence, i.e. the hypothetical model. A data set gained from Vietnamese garment enterprises was used to validate the mechanism of the resonant influence. Findings Empirical evidence from Vietnamese garment sector showed that the competitive models could explain 42.8, 26.3 and 34 percent variance of operational performance, customer satisfaction and financial performance, respectively. In the meantime, the hypothetical model containing the resonant influence is capable to explain 69.5, 33.1 and 57.3 percent. For the impact of each SCM practice on OP, all relationships in the hypothetical model are also greater than those in competitive ones. These results supported the mechanism of the resonant influence. Research limitations/implications This research provides an insight into the relationship between SCM practices and OP. By the resonant influence, the effectiveness of each affected SCM practice itself is magnified and OP is also increased remarkably. Practical implications Understanding the resonant influence, companies can apply this mechanism to enhance effectiveness of SCM practices at the lowest cost. To this end, the SCM practices should be implemented simultaneously as an integrated system rather than independent ones and the structural model proposed in this study is able to be used as “a guide map” for applying this mechanism. Originality/value This is one of pioneer empirical studies in the SCM literature that proposed and validated the concept of “resonant influence.”

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