Search results for "Interaction network"

An evolutionary restricted neighborhood search clustering approach for PPI networks

2014

Protein-protein interaction networks have been broadly studied in the last few years, in order to understand the behavior of proteins inside the cell. Proteins interacting with each other often share common biological functions or they participate in the same biological process. Thus, discovering protein complexes made of a group of proteins strictly related can be useful to predict protein functions. Clustering techniques have been widely employed to detect significant biological complexes. In this paper, we integrate one of the most popular network clustering techniques, namely the Restricted Neighborhood Search Clustering (RNSC), with evolutionary computation. The two cost functions intr…

A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus

2017

MicroRNAs (miRNAs) are small noncoding RNAs that modulate the cellular transcriptome at the post-transcriptional level. miRNA plays important roles in different disease manifestation, including type 2 diabetes mellitus (T2DM). Many studies have characterized the changes of miRNAs in T2DM, a complex systematic disease; however, few studies have integrated these findings and explored the functional effects of the dysregulated miRNAs identified. To investigate the involvement of miRNAs in T2DM, we obtained and analyzed all relevant studies published prior to 18 October 2016 from various literature databases. From 59 independent studies that met the inclusion criteria, we identified 158 dysregu…

Identifying Early Warning Signals for the Sudden Transition from Mild to Severe Tobacco Etch Disease by Dynamical Network Biomarkers

2019

This article belongs to the Special Issue The Complexity of the Potyviral Interaction Network.

Modular organization in the reductive evolution of protein-protein interaction networks

2006

Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.

Study of the role of the CDC48 chaperone protein in plant immunity

2018

The chaperone protein CDC48 (Cell division cycle 48) is a major regulator of the quality control of proteins and is involved in various cellular processes in animals and yeast. In contrast, the role of CDC48 in plants is poorly known. In the present work, we investigated the function of CDC48 in plant immunity thanks to the cryptogein/tobacco biological model, cryptogein being produced by the oomycete phytophthora cryptogea.Three strategies were carried out. First, the dynamic of accumulation CDC48 together with intracellular events inherent to the immune response were analyzed in both wild-type and CDC48 overexpressing tobacco cells (CDC48-TAP line). Second, a list if CDC48 partners was es…

Biotic homogenisation in bird communities leads to large‐scale changes in species associations

2021

The impact of global change on biodiversity is commonly assessed in terms of changes in species distributions, community richness and community composition. Whether and how much associations between species are also changing is much less documented. In this study, we quantify changes in large-scale patterns of species associations in bird communities in relation to changes in species composition. We use network approaches to build three community-aggregated indices reflecting complementary aspects of species association networks. We characterise the spatio–temporal dynamics of these indices using a large-scale and high-resolution dataset of bird co-abundances of 109 species monitored for 17…

Statistical Validation of a Comprehensive Gene/miRNA Expression Profile Dataset for miRNA:mRNA Interaction Analysis

2014

Identifying Host Molecular Features Strongly Linked With Responses to Huanglongbing Disease in Citrus Leaves

2018

© 2018 Balan, Ibáñez, Dandekar, Caruso and Martinelli. A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76%. Only 16 HLB-regulated genes were commonly identified between the three leaf datasets. Among them were key genes encoding proteins involved in cell wall modification such as CESA8, pecti…

Molecular signatures of silencing suppression degeneracy from a complex RNA virus

2021

As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA sil…

Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids

2018

Symbiotic relationships benefit organisms in utilization of new niches. In parasitoid wasps, symbiotic viruses and venom that are injected together with wasp eggs into the host caterpillar suppress immune responses of the host and enhance parasitoid survival. We found that the virus also has negative effects on offspring survival when placing these interactions in a community context. The virus and venom drive a chain of interactions that includes the herbivore and its food plant and attracts the hyperparasitoid enemies of the parasitoid. Our results shed new light on the importance of symbionts associated with their host in driving ecological interactions and highlight the intricacy of how…