scholarly journals Longitudinal network theory approaches identify crucial factors affecting sporulation efficiency in yeast

2016 ◽  
Author(s):  
Camellia Sarkar ◽  
Saumya Gupta ◽  
Rahul Kumar Verma ◽  
Himanshu Sinha ◽  
Sarika Jalan
Keyword(s):  
Gene Expression ◽  
Network Theory ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Clustering Coefficient ◽  
Regulatory Control ◽  
Global Network ◽  
Node Degree ◽  
Developmental Processes ◽  
Network Properties

ABSTRACTIntegrating network theory approaches over longitudinal genome-wide gene expression data is a robust approach to understand the molecular underpinnings of a dynamic biological process. Here, we performed a network-based investigation of longitudinal gene expression changes during sporulation of a yeast strain, SK1. Using global network attributes, viz. clustering coefficient, degree distribution of a node, degree-degree mixing of the connected nodes and disassortativity, we observed dynamic changes in these parameters indicating a highly connected network with inter-module crosstalk. Analysis of local attributes, such as clustering coefficient, hierarchy, betweenness centrality and Granovetter’s weak ties showed that there was an inherent hierarchy under regulatory control that was determined by specific nodes. Biological annotation of these nodes indicated the role of specifically linked pairs of genes in meiosis. These genes act as crucial regulators of sporulation in the highly sporulating SK1 strain. An independent analysis of these network properties in a less efficient sporulating strain helped to understand the heterogeneity of network profiles. We show that comparison of network properties has the potential to identify candidate nodes contributing to the phenotypic diversity of developmental processes in natural populations. Therefore, studying these network parameters as described in this work for dynamic developmental processes, such as sporulation in yeast and eventually in disease progression in humans, can help in identifying candidate factors which are potential regulators of differences between normal and perturbed processes and can be causal targets for intervention.

scholarly journals Influence of number of individuals and observations per individual on a model of community structure

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252471
Author(s):  
Julia Sunga ◽  
Quinn M. R. Webber ◽  
Hugh G. Broders
Keyword(s):  
Community Structure ◽  
Network Structure ◽  
Natural Populations ◽  
Clustering Coefficient ◽  
Global Network ◽  
Missing Information ◽  
Network Measures ◽  
Graph Density ◽  
Density Clustering ◽  
Number Of Individuals

Social network analysis is increasingly applied to understand animal groups. However, it is rarely feasible to observe every interaction among all individuals in natural populations. Studies have assessed how missing information affects estimates of individual network positions, but less attention has been paid to metrics that characterize overall network structure such as modularity, clustering coefficient, and density. In cases such as groups displaying fission-fusion dynamics, where subgroups break apart and rejoin in changing conformations, missing information may affect estimates of global network structure differently than in groups with distinctly separated communities due to the influence single individuals can have on the connectivity of the network. Using a bat maternity group showing fission-fusion dynamics, we quantify the effect of missing data on global network measures including community detection. In our system, estimating the number of communities was less reliable than detecting community structure. Further, reliably assorting individual bats into communities required fewer individuals and fewer observations per individual than to estimate the number of communities. Specifically, our metrics of global network structure (i.e., graph density, clustering coefficient, Rcom) approached the ‘real’ values with increasing numbers of observations per individual and, as the number of individuals included increased, the variance in these estimates decreased. Similar to previous studies, we recommend that more observations per individual should be prioritized over including more individuals when resources are limited. We recommend caution when making conclusions about animal social networks when a substantial number of individuals or observations are missing, and when possible, suggest subsampling large datasets to observe how estimates are influenced by sampling intensity. Our study serves as an example of the reliability, or lack thereof, of global network measures with missing information, but further work is needed to determine how estimates will vary with different data collection methods, network structures, and sampling periods.

Research on the Evolution of the Complex Network Theory Based on the International Coal Trade

2014 ◽  
Vol 672-674 ◽  
pp. 2173-2177
Author(s):  
Yang Yang He ◽  
Ling Wang
Keyword(s):  
Network Analysis ◽  
Complex Network ◽  
Network Theory ◽  
Clustering Coefficient ◽  
Node Degree ◽  
Degree Centrality ◽  
Trade Data ◽  
Complex Network Theory ◽  
The Difference ◽  
Coal Trade

According to the international coal trade data of the years from 1996 to 2011 published by UN COMTRADE (UNSD), it can be inferred that the data is mainly about international trade of raw coal and related coal products. By adopting the theory of complex network analysis, this paper calculates the complex network of international coal trade in the aspect of its density, node degree, centrality, point strength, clustering coefficient. Based on these properties, this paper further analyzes the evolution rule for international coal trade network of raw coal, coal briquettes and ovate coal over the last 16 years, as well as the difference between the pre-and after financial crisis.

Network-based approach to explore basin network comparing observed and satellite dataset

2021 ◽  
Author(s):  
Mayuri Gadhawe ◽  
Ravi Kumar Guntu ◽  
Ankit Agarwal
Keyword(s):  
Correlation Coefficient ◽  
Random Network ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Small World ◽  
Clustering Coefficient ◽  
Node Degree ◽  
Network Measures ◽  
Network Properties ◽  
Precipitation Network

<p>Complex network is a relatively young, multidisciplinary field with an objective to unravel the spatiotemporal interaction in natural processes. Though network theory has become a very important paradigm in many fields, the applications in the hydrology field are still at an emerging stage.  In this study, we employed the Pearson correlation coefficient and Spearman correlation coefficient as a similarity measure with varying threshold ranges to construct the precipitation network of the Ganga River Basin (GRB). Ground-based observed dataset (IMD) and satellite precipitation product (TRMM) are used. Different network properties such as node degree, degree distribution, clustering coefficient, and architecture were computed on each resultant precipitation network of GRB. We also ranked influential grid points in the precipitation network by using weighted degree betweenness to identify the importance of each grid station in the network Our results reveal that the choice of correlation method does not significantly affect the network measures and reconfirm that the thresholds significantly influence network construction and network properties in the case of both datasets. The spatial distribution of the clustering coefficient value is high to low from center to boundary and inverse in the case of degree.  In addition, there is a positive correlation between the average neighbor degree and node degree. Again, we analyzed the architecture of precipitation networks and found that the network has a small world with random network behavior.   Our results also indicated that both products have similar network measures and showed similar kinds of spatial patterns.</p>

Post-Transcriptional Regulation of Cardiac Sarcomere Protein Titin Through 3’ Untranslated Regions

2013 ◽  
Vol 9 ◽  
Author(s):  
Tara A Shrout
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Striated Muscle ◽  
Binding Capacity ◽  
Structural Features ◽  
Neonatal Rat ◽  
Regulatory Control ◽  
Untranslated Regions ◽  
Luciferase Reporter ◽  
Regulatory Effects

Titin is the largest known protein in the human body, and forms the backbone of all striated muscle sarcomeres. The elastic nature of titin is an important component of muscle compliance and functionality. A significant amount of energy is expended to synthesize titin, thus we postulate that titin gene expression is under strict regulatory control in order to conserve cellular resources. In general, gene expression is mediated in part by post-transcriptional control elements located within the 5’ and 3’ untranslated regions (UTRs) of mature mRNA. The 3’UTR in particular contains structural features that affect binding capacity to other RNA components, such as MicroRNA, which control mRNA localization, translation, and degradation. The degree and significance of the regulatory effects mediated by two determined variants of titin’s 3’ UTR were evaluated in Neonatal Rat Ventricular Myocyte and Human Embryonic Kidney cell lines. Recombinant plasmids to transfect these cells lines were engineered by insertion of the variant titin 3’UTR 431- and 1047-base pairs sequences into luciferase reporter vectors. Expression due to an unaltered reporter vector served as the control. Quantitative changes in luciferase activity due to the recombinants proportionally represented the effect titin’s respective 3’UTR conferred on downstream post-transcriptional expression relative to the control. The effect due to titin’s shorter 3’UTR sequence was inconclusive; however, results illustrated that titin’s longer 3’UTR sequence caused a 35 percent decrease in protein expression. Secondary structural analysis of the two sequences revealed differential folding patterns that affect the stability and degree of MicroRNA-binding within titin’s variant 3’UTR sequences.

scholarly journals Reproduction in Trypanosomatids: Past and Present

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 471
Author(s):  
Camino Gutiérrez-Corbo ◽  
Bárbara Domínguez-Asenjo ◽  
María Martínez-Valladares ◽  
Yolanda Pérez-Pertejo ◽  
Carlos García-Estrada ◽  
...  
Keyword(s):  
Low Income ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Genetic Exchange ◽  
Health Concern ◽  
Current Debate ◽  
Naturally Occurring ◽  
Experimental Works ◽  
Genomic Recombination ◽  
The Impact

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

Implications of DNA replication for eukaryotic gene expression

1991 ◽  
Vol 99 (2) ◽  
pp. 201-206 ◽  
Author(s):  
A.P. Wolffe
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Replication Fork ◽  
Recent Progress ◽  
Gene Activity ◽  
Nucleosome Assembly ◽  
Developmental Processes ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

DNA replication has a key role in many developmental processes. Recent progress in understanding events at the replication fork suggests mechanisms for both establishing and maintaining programs of eukaryotic gene activity. In this review, I discuss the consequences of replication fork passage for preexisting chromatin structures and describe how the mechanism of nucleosome assembly at the replication fork may facilitate the formation of either transcriptionally active or repressed chromatin.

Genomic and phenotypic diversity for adaption to future climate in natural populations of perennial ryegrass

2021 ◽  
Author(s):  
José Luis Blanco-Pastor ◽  
Thomas Keep ◽  
Philippe Barre ◽  
Abraham Escobar-Gutiérrez ◽  
Evelin Willner ◽  
...  
Keyword(s):  
Perennial Ryegrass ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Future Climate

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

2017 ◽  
Vol 303 (8) ◽  
pp. 1061-1079 ◽  
Author(s):  
Julie Ferreira de Carvalho ◽  
Julien Boutte ◽  
Pierre Bourdaud ◽  
Houda Chelaifa ◽  
Kader Ainouche ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Populations ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Spartina Species

scholarly journals Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents

2021 ◽  
Author(s):  
Weizheng Liang ◽  
Guipeng Li ◽  
Huanhuan Cui ◽  
Yukai Wang ◽  
Wencheng Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Phenotypic Diversity ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Protein Sequence Analysis ◽  
Systematic Analysis

AbstractDifferences in gene expression, which can arise from divergence in cis-regulatory elements or alterations in transcription factors binding specificity, are one of the most important causes of phenotypic diversity during evolution. By protein sequence analysis, we observed high sequence conservation in the DNA binding domain (DBD) of the transcription factor Cdx2 across many vertebrates, whereas three amino acid changes were exclusively found in mouse Cdx2 (mCdx2), suggesting potential positive selection in the mouse lineage. Multi-omics analyses were then carried out to investigate the effects of these changes. Surprisingly, there were no significant functional differences between mCdx2 and its rat homologue (rCdx2), and none of the three amino acid changes had any impact on its function. Finally, we used rat-mouse allodiploid embryonic stem cells (RMES) to study the cis effects of Cdx2-mediated gene regulation between the two rodents. Interestingly, whereas Cdx2 binding is largely divergent between mouse and rat, the transcriptional effect induced by Cdx2 is conserved to a much larger extent.Author summaryOur study 1) represented a first systematic analysis of species-specific adaptation in DNA binding pattern of transcription factor. Although the mouse-specific amino acid changes did not manifest functional impact in our system, several explanations may account for it (See Discussion part for the detail); 2) represented a first study of cis-regulation between two reproductively isolated species by using a novel allodiploid system; 3) demonstrated a higher conservation of transcriptional output than that of DNA binding, suggesting the evolvability/plasticity of the latter; 4) finally provided a rich data resource for Cdx2 mediated regulation, including gene expression, chromatin accessibility and DNA binding etc.

scholarly journals Gene body methylation mediates epigenetic inheritance of plant traits

2021 ◽  
Author(s):  
Zaigham Shahzad ◽  
Jonathan D. Moore ◽  
Daniel Zilberman
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Cytosine Methylation ◽  
Plant Traits ◽  
Phenotypic Diversity ◽  
Strong Association ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Gene Body ◽  
Gene Body Methylation

AbstractCytosine methylation is an epigenetically heritable DNA modification common in plant and animal genes, but the functional and evolutionary significance of gene body methylation (gbM) has remained enigmatic. Here we show that gbM enhances gene expression in Arabidopsis thaliana. We also demonstrate that natural gbM variation influences drought and heat tolerance and flowering time by modulating gene expression, including that of Flowering Locus C (FLC). Notably, epigenetic variation accounts for as much trait heritability in natural populations as DNA sequence polymorphism. Furthermore, we identify gbM variation in numerous genes associated with environmental variables, including a strong association between flowering time, spring atmospheric NO2 – a by-product of fossil fuel burning – and FLC epialleles. Our study demonstrates that gbM is an important modulator of gene expression, and its natural variation fundamentally shapes phenotypic diversity in plant populations. Thus, gbM provides an epigenetic basis for adaptive evolution independent of genetic polymorphism.

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