scholarly journals Role of interaction network topology in controlling microbial population in consortia

2018 ◽  
Author(s):  
Xinying Ren ◽  
Richard M. Murray
Keyword(s):  
Network Topology ◽  
Microbial Population ◽  
Interaction Network

scholarly journals Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunmiao Jiang ◽  
Gongbo Lv ◽  
Jinxin Ge ◽  
Bin He ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Gata Transcription Factor ◽  
Starting Point ◽  
Evolutionary Features ◽  
First Time

AbstractGATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.

scholarly journals Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance

2009 ◽  
Vol 185 (3) ◽  
pp. 475-491 ◽  
Author(s):  
Evgeny Onischenko ◽  
Leslie H. Stanton ◽  
Alexis S. Madrid ◽  
Thomas Kieselbach ◽  
Karsten Weis
Keyword(s):  
Nuclear Pore Complex ◽  
Structural Integrity ◽  
Fluorescent Protein ◽  
Interaction Network ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Binding Partners ◽  
Interaction Partners ◽  
Redundant Functions

The nuclear pore complex (NPC) mediates all nucleocytoplasmic transport, yet its structure and biogenesis remain poorly understood. In this study, we have functionally characterized interaction partners of the yeast transmembrane nucleoporin Ndc1. Ndc1 forms a distinct complex with the transmembrane proteins Pom152 and Pom34 and two alternative complexes with the soluble nucleoporins Nup53 and Nup59, which in turn bind to Nup170 and Nup157. The transmembrane and soluble Ndc1-binding partners have redundant functions at the NPC, and disruption of both groups of interactions causes defects in Ndc1 targeting and in NPC structure accompanied by significant pore dilation. Using photoconvertible fluorescent protein fusions, we further show that the depletion of Pom34 in cells that lack NUP53 and NUP59 blocks new NPC assembly and leads to the reversible accumulation of newly made nucleoporins in cytoplasmic foci. Therefore, Ndc1 together with its interaction partners are collectively essential for the biosynthesis and structural integrity of yeast NPCs.

scholarly journals Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

2009 ◽  
Vol 7 (44) ◽  
pp. 423-437 ◽  
Author(s):  
Tijana Milenković ◽  
Vesna Memišević ◽  
Anand K. Ganesan ◽  
Nataša Pržulj
Keyword(s):  
Protein Interaction ◽  
Network Topology ◽  
Interaction Network ◽  
Biological Processes ◽  
Cancer Gene ◽  
Cancer Genes ◽  
Clustering Methods ◽  
Ppi Network ◽  
Graph Theoretic ◽  
Ppi Networks

Many real-world phenomena have been described in terms of large networks. Networks have been invaluable models for the understanding of biological systems. Since proteins carry out most biological processes, we focus on analysing protein–protein interaction (PPI) networks. Proteins interact to perform a function. Thus, PPI networks reflect the interconnected nature of biological processes and analysing their structural properties could provide insights into biological function and disease. We have already demonstrated, by using a sensitive graph theoretic method for comparing topologies of node neighbourhoods called ‘graphlet degree signatures’, that proteins with similar surroundings in PPI networks tend to perform the same functions. Here, we explore whether the involvement of genes in cancer suggests the similarity of their topological ‘signatures’ as well. By applying a series of clustering methods to proteins' topological signature similarities, we demonstrate that the obtained clusters are significantly enriched with cancer genes. We apply this methodology to identify novel cancer gene candidates, validating 80 per cent of our predictions in the literature. We also validate predictions biologically by identifying cancer-related negative regulators of melanogenesis identified in our siRNA screen. This is encouraging, since we have done this solely from PPI network topology. We provide clear evidence that PPI network structure around cancer genes is different from the structure around non-cancer genes. Understanding the underlying principles of this phenomenon is an open question, with a potential for increasing our understanding of complex diseases.

Carbon mineralization in semi-arid northeastern Australia: the role of termites

1987 ◽  
Vol 3 (3) ◽  
pp. 255-263 ◽  
Author(s):  
John A. Holt
Keyword(s):  
Regression Analysis ◽  
Carbon Flux ◽  
Microbial Population ◽  
Carbon Mineralization ◽  
Termite Mounds ◽  
Interaction Term ◽  
Temperature Interaction ◽  
Soil Carbon Mineralization ◽  
Semi Arid

ABSTRACTThe contribution of a population of mound building, detritivorous termites (Amitermes laurensis (Mjöberg)) to nett carbon mineralization in an Australian tropical semi-arid woodland has been examined. Carbon mineralization rates were estimated by measuring daily CO2 flux from five termite mounds at monthly intervals for 12 months. Carbon flux from the mounds was found to be due to microbial activity as well as termite activity. It is conservatively estimated that the association of A. laurensis and the microbial population present in their mounds is responsible for between 4%–10% of carbon mineralized in this ecosystem, and the contribution of all termites together (mound builders and subterranean) may account for up to 20% of carbon mineralized. Regression analysis showed that rates of carbon mineralization in termite mounds were significantly related to mound moisture and mound temperature. Soil moisture was the most important factor in soil carbon mineralization, with temperature and a moisture X temperature interaction term also exerting significant affects.

scholarly journals On Synchronizing Coupled Retinogeniculocortical Pathways: A Toy Model

2018 ◽  
Vol 2018 ◽  
pp. 1-6
Author(s):  
B. L. Mayer ◽  
L. H. A. Monteiro
Keyword(s):  
Neural Network ◽  
Visual Cortex ◽  
Corpus Callosum ◽  
Neuronal Activity ◽  
Network Topology ◽  
Cerebral Hemisphere ◽  
State Transition ◽  
Regular Lattice ◽  
Visual Cortices

A Newman-Watts graph is formed by including random links in a regular lattice. Here, the emergence of synchronization in coupled Newman-Watts graphs is studied. The whole neural network is considered as a toy model of mammalian visual pathways. It is composed by four coupled graphs, in which a coupled pair represents the lateral geniculate nucleus and the visual cortex of a cerebral hemisphere. The hemispheres communicate with each other through a coupling between the graphs representing the visual cortices. This coupling makes the role of the corpus callosum. The state transition of neurons, supposed to be the nodes of the graphs, occurs in discrete time and it follows a set of deterministic rules. From periodic stimuli coming from the retina, the neuronal activity of the whole network is numerically computed. The goal is to find out how the values of the parameters related to the network topology affect the synchronization among the four graphs.

scholarly journals The diminishing role of hubs in dynamical processes on complex networks

2013 ◽  
Vol 10 (88) ◽  
pp. 20130568 ◽  
Author(s):  
Rick Quax ◽  
Andrea Apolloni ◽  
Peter M. A. Sloot
Keyword(s):  
Interaction Network ◽  
Macroscopic System ◽  
Protein Protein Interaction ◽  
Equilibrium Dynamics ◽  
Qualitative Evidence ◽  
Individual Unit ◽  
System Of Units ◽  
Protein Protein Interaction Network

It is notoriously difficult to predict the behaviour of a complex self-organizing system, where the interactions among dynamical units form a heterogeneous topology. Even if the dynamics of each microscopic unit is known, a real understanding of their contributions to the macroscopic system behaviour is still lacking. Here, we develop information-theoretical methods to distinguish the contribution of each individual unit to the collective out-of-equilibrium dynamics. We show that for a system of units connected by a network of interaction potentials with an arbitrary degree distribution, highly connected units have less impact on the system dynamics when compared with intermediately connected units. In an equilibrium setting, the hubs are often found to dictate the long-term behaviour. However, we find both analytically and experimentally that the instantaneous states of these units have a short-lasting effect on the state trajectory of the entire system. We present qualitative evidence of this phenomenon from empirical findings about a social network of product recommendations, a protein–protein interaction network and a neural network, suggesting that it might indeed be a widespread property in nature.

scholarly journals Social networks predict selective observation and information spread in ravens

2016 ◽  
Vol 3 (7) ◽  
pp. 160256 ◽  
Author(s):  
Ipek G. Kulahci ◽  
Daniel I. Rubenstein ◽  
Thomas Bugnyar ◽  
William Hoppitt ◽  
Nace Mikus ◽  
...  
Keyword(s):  
Social Rank ◽  
Interaction Network ◽  
Social Connections ◽  
Strongly Correlated ◽  
Aggressive Interactions ◽  
Diffusion Analysis ◽  
Observation Network ◽  
Transmission Of Information ◽  
Group Member

Animals are predicted to selectively observe and learn from the conspecifics with whom they share social connections. Yet, hardly anything is known about the role of different connections in observation and learning. To address the relationships between social connections, observation and learning, we investigated transmission of information in two raven ( Corvus corax ) groups. First, we quantified social connections in each group by constructing networks on affiliative interactions, aggressive interactions and proximity. We then seeded novel information by training one group member on a novel task and allowing others to observe. In each group, an observation network based on who observed whose task-solving behaviour was strongly correlated with networks based on affiliative interactions and proximity. Ravens with high social centrality (strength, eigenvector, information centrality) in the affiliative interaction network were also central in the observation network, possibly as a result of solving the task sooner. Network-based diffusion analysis revealed that the order that ravens first solved the task was best predicted by connections in the affiliative interaction network in a group of subadult ravens, and by social rank and kinship (which influenced affiliative interactions) in a group of juvenile ravens. Our results demonstrate that not all social connections are equally effective at predicting the patterns of selective observation and information transmission.

scholarly journals Role of network topology in the synchronization of power systems

2012 ◽  
Vol 85 (7) ◽  
Author(s):  
S. Lozano ◽  
L. Buzna ◽  
A. Díaz-Guilera
Keyword(s):  
Power Systems ◽  
Network Topology
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