scholarly journals On the Study of Reverse Degree-Based Topological Properties for the Third Type of p  th Chain Hex-Derived Network

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Ali N. A. Koam ◽  
Ali Ahmad ◽  
Ashfaq Ahmed Qummer
Keyword(s):  
Computer Science ◽  
Regulatory Networks ◽  
Metabolic Networks ◽  
Environmental Chemistry ◽  
Global Network ◽  
Network Characteristics ◽  
The Third ◽  
Degree Of A Vertex ◽  
Wide Range ◽  
Gene Regulatory

Vertices and edges are made from a network, with the degree of a vertex referring to the number of connected edges. The chance of every vertex possessing a given degree is represented by a network’s degree appropriation, which reveals important global network characteristics. Many fields, including sociology, public health, business, medicine, engineering, computer science, and basic sciences, use network theory. Logistical networks, gene regulatory networks, metabolic networks, social networks, and driven networks are some of the most significant networks. In physical, theoretical, and environmental chemistry, a topological index is a numerical value assigned to a molecular structure/network that is used for correlation analysis. Hexagonal networks of dimension t are used to build hex-derived networks, which have a wide range of applications in computer science, medicine, and engineering. For the third type of hex-derived networks, topological indices of reverse degree based are discussed in this study.

scholarly journals Computation of reverse degree-based topological indices of hex-derived networks

2021 ◽  
Vol 6 (10) ◽  
pp. 11330-11345
Author(s):  
Ali N. A. Koam ◽  
◽  
Ali Ahmad ◽  
Yasir Ahmad ◽  
Keyword(s):  
Computer Science ◽  
Network Theory ◽  
Regulatory Networks ◽  
Metabolic Networks ◽  
Environmental Chemistry ◽  
Medical Science ◽  
Science And Engineering ◽  
Degree Of A Vertex ◽  
Network Properties ◽  
Worldwide Network

<abstract><p>Network theory gives an approach to show huge and complex frameworks through a complete arrangement of logical devices. A network is made is made of vertices and edges, where the degree of a vertex refers to the number of joined edges. The degree appropriation of a network represents the likelihood of every vertex having a particular degree and shows significant worldwide network properties. Network theory has applications in many disciplines like basic sciences, computer science, engineering, medical, business, public health and sociology. There are some important networks like logistical networks, gene regulatory networks, metabolic networks, social networks, derived networks. Topological index is a numerical number assigned to the molecular structure/netwrok which is used for correlation analysis in physical, theoretical and environmental chemistry. The hex-derived networks are created by hexagonal networks of dimension $ t $, these networks have an assortment of valuable applications in computer science, medical science and engineering. In this paper we discuss the reverse degree-based topological for third type of hex-derived networks.</p></abstract>

scholarly journals Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

2021 ◽  
Vol 9 ◽  
Author(s):  
Amruta Tendolkar ◽  
Aaron F. Pomerantz ◽  
Christa Heryanto ◽  
Paul D. Shirk ◽  
Nipam H. Patel ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Targeted Mutagenesis ◽  
Junonia Coenia ◽  
Wing Venation ◽  
Loss Of Function ◽  
Color Patterns ◽  
Wide Range ◽  
Range Of Functions ◽  
Gene Regulatory ◽  
Pyralid Moth

The forewings and hindwings of butterflies and moths (Lepidoptera) are differentiated from each other, with segment-specific morphologies and color patterns that mediate a wide range of functions in flight, signaling, and protection. The Hox gene Ultrabithorax (Ubx) is a master selector gene that differentiates metathoracic from mesothoracic identities across winged insects, and previous work has shown this role extends to at least some of the color patterns from the butterfly hindwing. Here we used CRISPR targeted mutagenesis to generate Ubx loss-of-function somatic mutations in two nymphalid butterflies (Junonia coenia, Vanessa cardui) and a pyralid moth (Plodia interpunctella). The resulting mosaic clones yielded hindwing-to-forewing transformations, showing Ubx is necessary for specifying many aspects of hindwing-specific identities, including scale morphologies, color patterns, and wing venation and structure. These homeotic phenotypes showed cell-autonomous, sharp transitions between mutant and non-mutant scales, except for clones that encroached into the border ocelli (eyespots) and resulted in composite and non-autonomous effects on eyespot ring determination. In the pyralid moth, homeotic clones converted the folding and depigmented hindwing into rigid and pigmented composites, affected the wing-coupling frenulum, and induced ectopic scent-scales in male androconia. These data confirm Ubx is a master selector of lepidopteran hindwing identity and suggest it acts on many gene regulatory networks involved in wing development and patterning.

scholarly journals Robustness and lethality in multilayer biological molecular networks

2019 ◽  
Author(s):  
Xueming Liu ◽  
Enrico Maiorino ◽  
Arda Halu ◽  
Joseph Loscalzo ◽  
Jianxi Gao ◽  
...  
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Metabolic Diseases ◽  
Biological Systems ◽  
Interaction Network ◽  
Network Models ◽  
Global Network ◽  
Molecular Networks ◽  
Cancer Genes ◽  
Gene Regulatory

AbstractRobustness is a prominent feature of most biological systems. In a cell, the structure of the interactions between genes, proteins, and metabolites has a crucial role in maintaining the cell’s functionality and viability in presence of external perturbations and noise. Despite advances in characterizing the robustness of biological systems, most of the current efforts have been focused on studying homogeneous molecular networks in isolation, such as protein-protein or gene regulatory networks, neglecting the interactions among different molecular substrates. Here we propose a comprehensive framework for understanding how the interactions between genes, proteins and metabolites contribute to the determinants of robustness in a heterogeneous biological network. We integrate heterogeneous sources of data to construct a multilayer interaction network composed of a gene regulatory layer, and protein-protein interaction layer and a metabolic layer. We design a simulated perturbation process to characterize the contribution of each gene to the overall system’s robustness, defined as its influence over the global network. We find that highly influential genes are enriched in essential and cancer genes, confirming the central role of these genes in critical cellular processes. Further, we determine that the metabolic layer is more vulnerable to perturbations involving genes associated to metabolic diseases. By comparing the robustness of the network to multiple randomized network models, we find that the real network is comparably or more robust than expected in the random realizations. Finally, we analytically derive the expected robustness of multilayer biological networks starting from the degree distributions within or between layers. These results provide new insights into the non-trivial dynamics occurring in the cell after a genetic perturbation is applied, confirming the importance of including the coupling between different layers of interaction in models of complex biological systems.

scholarly journals Input dose differentiation by NF-κB

2019 ◽  
Author(s):  
Minjun Son ◽  
Andrew Wang ◽  
Hsiung-Lin Tu ◽  
Marie O Metzig ◽  
Parthiv Patel ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Short Term Memory ◽  
Single Cells ◽  
Absolute Difference ◽  
Transcriptional Responses ◽  
Wide Range ◽  
Negative Feedbacks ◽  
Gene Regulatory ◽  
Complex Signaling ◽  
Simple Network

AbstractCells receive a wide range of dynamic signaling inputs during immune regulation, but how gene regulatory networks measure and interpret such dynamic inputs is not understood. Here, we used microfluidic live-cell analysis and mathematical modeling to study how NF-κB pathway in single-cells responds to time-varying immune inputs such as increasing, decreasing or fluctuating cytokine signals. Surprisingly, we found that NF-κB acts as a differentiator, responding strictly to the absolute difference in cytokine concentration, and not to the concentration itself. Our analyses revealed that negative feedbacks by the regulatory proteins A20 and IκBα enable dose differentiation by providing short-term memory of prior cytokine level and continuously resetting kinase cycling and receptor levels. Investigation of NF-κB target gene expression showed that cells create unique transcriptional responses under different dynamic cytokine profiles. Our results demonstrate how cells use simple network motifs and transcription factor dynamics to efficiently extract information from complex signaling environments.

scholarly journals Neuron subtype-specific effector gene expression in the Motor Ganglion of Ciona

2019 ◽  
Author(s):  
Susanne Gibboney ◽  
Kwantae Kim ◽  
Christopher J. Johnson ◽  
Jameson Orvis ◽  
Paula Martínez-Feduchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Gene Expression Analysis ◽  
Transcriptome Profiling ◽  
Matrix Proteins ◽  
Wide Range ◽  
Specific Effector ◽  
The Central Nervous System ◽  
Differential Gene ◽  
Gene Regulatory

AbstractThe central nervous system of the Ciona larva contains only 177 neurons. The precise regulation of neuron subtype-specific morphogenesis and differentiation observed in during the formation of this minimal connectome offers a unique opportunity to dissect gene regulatory networks underlying chordate neurodevelopment. Here we compare the transcriptomes of two very distinct neuron types in the hindbrain/spinal cord homolog of Ciona, the Motor Ganglion (MG): the Descending decussating neuron (ddN, proposed homolog of Mauthner Cells in vertebrates) and the MG Interneuron 2 (MGIN2). Both types are invariantly represented by a single bilaterally symmetric left/right pair of cells in every larva. Supernumerary ddNs and MGIN2s were generated in synchronized embryos and isolated by fluorescence-activated cell sorting for transcriptome profiling. Differential gene expression analysis revealed ddN- and MGIN2-specific enrichment of a wide range of genes, including many encoding potential “effectors” of subtype-specific morphological and functional traits. More specifically, we identified the upregulation of centrosome-associated, microtubule-stabilizing/bundling proteins and extracellular matrix proteins and axon guidance cues as part of a single intrinsic regulatory program that might underlie the unique polarization of the ddNs, the only descending MG neurons that cross the midline.

scholarly journals Ubx orchestrates tissue identity through regional and bidirectional changes to chromatin accessibility

2021 ◽  
Author(s):  
Ryan Loker ◽  
Jordyn E. Sanner ◽  
Richard S. Mann
Keyword(s):  
Transcription Factor ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Chromatin Accessibility ◽  
Thoracic Segment ◽  
Hox Proteins ◽  
The Third ◽  
Gene Regulatory ◽  
Hox Protein ◽  
Hox Cofactors

AbstractHox proteins are homeodomain transcription factors that diversify serially homologous segments along the animal body axis, as revealed by the classic bithorax phenotype of Drosophila melanogaster where mutations in Ultrabithorax (Ubx) transform the third thoracic segment into the likeness of the second thoracic segment. To specify segment identity we show that Ubx both increases and decreases chromatin accessibility, coinciding with its role as both an activator and repressor of transcription. Surprisingly, whether Ubx functions as an activator or repressor differs depending on the proximal-distal position in the segment and the availability of Hox cofactors. Ubx-mediated changes to chromatin accessibility positively and negatively impact the binding of Scalloped (Sd), a transcription factor that is required for appendage development in both segments. These findings reveal how a single Hox protein can modify complex gene regulatory networks to transform the identity of an entire tissue.

Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network

2015 ◽  
Vol 11 (3) ◽  
pp. 760-769 ◽  
Author(s):  
Meng Zhou ◽  
Xiaojun Wang ◽  
Jiawei Li ◽  
Dapeng Hao ◽  
Zhenzhen Wang ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Biological Processes ◽  
Disease Network ◽  
Wide Range ◽  
Gene Regulatory ◽  
Non Coding Rnas

Accumulated evidence has shown that long non-coding RNAs (lncRNA) act as a widespread layer in gene regulatory networks and are involved in a wide range of biological processes.

scholarly journals ENDOGENOUS RETROVIRUSES AS GENETIC MODULES THAT SHAPE THE GENOME REGULATORY NETWORKS DURING EVOLUTION

2018 ◽  
Keyword(s):  
Regulatory Networks ◽  
Gene Activation ◽  
Cell Types ◽  
Regulatory Elements ◽  
Endogenous Retroviruses ◽  
Protein Coding ◽  
Transcriptional Enhancers ◽  
Wide Range ◽  
Gene Regulatory Elements ◽  
Gene Regulatory

Endogenous retroviruses (ERV) are the descendants of exogenous retroviruses that integrated into the germ cells genome, fixed and became inheritable. ERVs have evolved transcriptional enhancers and promoters that allow their replication in a wide range of tissue. Because ERVs comprise the regulatory elements it could be assume that ERVs capable to shape and reshape genomic regulatory networks by inserting their promoters and enhancers in new genomic loci upon retrotransposition. Thus retroransposition events can build new regulatory regions and lead to a new pattern of gene activation in the cell. In this review we summarize evidence which revealed that ERVs provide a plethora of novel gene regulatory elements, including tissue specific promoters and enhancers for protein-coding genes or long noncoding RNAs in a wide range of cell types. The accumulated findings support the hypothesis that the ERVs have rewired the gene regulatory networks and act as a major source of genomic regulatory innovation during evolution.

scholarly journals In Silico Design of Self-Optimizing Integrated Metabolic and Gene Regulatory Networks

2014 ◽  
Author(s):  
Timo Maarleveld ◽  
Bennet K NG ◽  
Herbert Sauro ◽  
Kyung Kim
Keyword(s):  
Gene Regulatory Networks ◽  
Environmental Conditions ◽  
In Silico ◽  
Regulatory Networks ◽  
Metabolic Networks ◽  
Self Regulation ◽  
Protein Signaling ◽  
Target Network ◽  
Gene Regulatory ◽  
Protein Signaling Networks

Biological organisms acclimatize to varying environmental conditions via active self-regulation of internal gene regulatory networks, metabolic networks, and protein signaling networks. While much work has been done to elucidate the topologies of individual networks in isolation, understanding of inter-network regulatory mechanisms remains limited. This shortcoming is of particular relevance to synthetic biology. Synthetic biological circuits tend to lose their engineered functionality over generational time, primarily due to the deleterious stress that they exert on their host organisms. To reduce this stress (and thus minimize loss of functionality) synthetic circuits must be sensitive to the health of the host organism. Development of integrated regulatory systems is therefore essential to robust synthetic biological systems. The aim of this study was to develop integrated gene-regulatory and metabolic networks which self-optimize in response to varying environmental conditions. We performed \emph{in silico} evolution to develop such networks using a two-step approach: (1) We optimized metabolic networks given a constrained amount of available enzyme. Here, we found that a proportional relationship between flux control coefficients and enzyme mass holds in all linear sub-networks of branched networks, except those sub-networks which contain allosteric regulators. Network optimization was performed by iteratively redistributing enzyme until flux through the network was maximized. Optimization was performed for a range of boundary metabolite conditions to develop a profile of optimal enzyme distributions as a function of environmental conditions. (2) We generated and evolved randomized gene regulatory networks to modulate the enzymes of a target metabolic pathway. The objective of the gene regulatory networks was to produce the optimal distribution of metabolic network enzymes given specific boundary metabolite conditions of the target network. Competitive evolutionary algorithms were applied to optimize the specific structures and kinetic parameters of the gene regulatory networks. With this method, we demonstrate the possibility of algorithmic development of integrated adaptive gene and metabolic regulatory networks which dynamically self-optimize in response to changing environmental conditions.

scholarly journals Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

2021 ◽  
Vol 12 ◽  
Author(s):  
Skyler D. Hebdon ◽  
Alida T. Gerritsen ◽  
Yi-Pei Chen ◽  
Joan G. Marcano ◽  
Katherine J. Chou
Keyword(s):  
Dna Binding ◽  
Genetic Engineering ◽  
Gene Regulatory Networks ◽  
Binding Sites ◽  
Clostridium Thermocellum ◽  
Regulatory Networks ◽  
Cellulosic Biomass ◽  
Global Network ◽  
Genome Wide ◽  
Gene Regulatory

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to &gt; 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

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