scholarly journals Probing the Unknowns in Cytokinin-Mediated Immune Defense in Arabidopsis with Systems Biology Approaches

2014 ◽  
Vol 8 ◽  
pp. BBI.S13462 ◽  
Author(s):  
Muhammad Naseem ◽  
Meik Kunz ◽  
Thomas Dandekar
Keyword(s):  
Systems Biology ◽  
Immune Responses ◽  
Protein Interactions ◽  
Immune Defense ◽  
Immune Functions ◽  
Protein Protein Interactions ◽  
Cytokinin Signaling ◽  
Host Immune Responses ◽  
Arabidopsis Protein ◽  
Underlying Mechanisms

Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein—protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants.

scholarly journals Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

2005 ◽  
Vol 2 (2) ◽  
pp. S24-S35 ◽  
Author(s):  
Ozlem Keskin ◽  
Buyong Ma ◽  
Kristina Rogale ◽  
K Gunasekaran ◽  
Ruth Nussinov
Keyword(s):  
Systems Biology ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Bottom Up

scholarly journals Evolution of New Variants/Mutants of JE Virus, Its Effect on Neurovirulence, Antigenicity, Host Immune Responses and Disease Transmission in Endemic Areas

2014 ◽  
Vol 2014 ◽  
pp. 1-35 ◽  
Author(s):  
Ravi Kant Upadhyay
Keyword(s):  
Immune Responses ◽  
Disease Transmission ◽  
Genetic Recombination ◽  
Point Mutations ◽  
Immune Defense ◽  
E Proteins ◽  
Virus Envelope ◽  
Host Immune Responses ◽  
Wild Strains ◽  
Endemic Areas

This paper highlights various reasons of evolution of new mutants/variants of JE virus and its effects on neurovirulence, antigenicity, host immune responses, and disease transmission in endemic areas. Virus is reorganizing its genome by making sequence alterations, single site mutations, cluster specific reversions, and amino acid substitutions in neutralizing antigenic sites mainly in N′ glycosylation sites and epitopic regions of S and E proteins. Virus is regularly changing gene order, gene density by making substitution point mutations in important structural genes which make virus envelope proteins. Further, JE virus acquiring new genetic variations and adaptabilities through genetic recombination of wild strains with vaccine strains and assimilating new lethal genes that lead to emergence of molecular variants/mutants. These newly emerged JE virus genotypes have attained the ability to escape the immune defense and show wider resistance against vaccines and therapeutic agents. Thus new strains did significant elevation in the level of neurovirulence, antigenicity and pathogenesis. It is causing very high mortalities in various infant groups and imposing lifelong irreversible disorders in survivors and showing a regular trend of emergence and reemergence in endemic areas. The present review article emphasizes methods to suppress virus replication, reversion of neurovirulence, attenuation and an utmost need of more potential vaccines against cross reactive heterologous genotypes of JE virus to control disease transmission and mortalities occurring in endemic areas.

scholarly journals Issues in performance evaluation for host–pathogen protein interaction prediction

2016 ◽  
Vol 14 (03) ◽  
pp. 1650011 ◽  
Author(s):  
Wajid Arshad Abbasi ◽  
Fayyaz Ul Amir Afsar Minhas
Keyword(s):  
Machine Learning ◽  
Protein Interactions ◽  
Cross Validation ◽  
Protein Protein Interactions ◽  
Evaluation Scheme ◽  
Host Pathogen ◽  
Pathogen Protein ◽  
Protein Interaction Prediction ◽  
Underlying Mechanisms ◽  
Fold Cross Validation

The study of interactions between host and pathogen proteins is important for understanding the underlying mechanisms of infectious diseases and for developing novel therapeutic solutions. Wet-lab techniques for detecting protein–protein interactions (PPIs) can benefit from computational predictions. Machine learning is one of the computational approaches that can assist biologists by predicting promising PPIs. A number of machine learning based methods for predicting host–pathogen interactions (HPI) have been proposed in the literature. The techniques used for assessing the accuracy of such predictors are of critical importance in this domain. In this paper, we question the effectiveness of K-fold cross-validation for estimating the generalization ability of HPI prediction for proteins with no known interactions. K-fold cross-validation does not model this scenario, and we demonstrate a sizable difference between its performance and the performance of an alternative evaluation scheme called leave one pathogen protein out (LOPO) cross-validation. LOPO is more effective in modeling the real world use of HPI predictors, specifically for cases in which no information about the interacting partners of a pathogen protein is available during training. We also point out that currently used metrics such as areas under the precision-recall or receiver operating characteristic curves are not intuitive to biologists and propose simpler and more directly interpretable metrics for this purpose.

scholarly journals Parasites, proteomes and systems: has Descartes’ clock run out of time?

Parasitology ◽  
2012 ◽  
Vol 139 (9) ◽  
pp. 1103-1118 ◽  
Author(s):  
J. M. WASTLING ◽  
S. D. ARMSTRONG ◽  
R. KRISHNA ◽  
D. XIA
Keyword(s):  
Systems Biology ◽  
Protein Interactions ◽  
Biological Data ◽  
Protein Protein Interactions ◽  
Proteomics Data ◽  
Data Types ◽  
Quality Of Data ◽  
Post Translational Modifications ◽  
Systems Modelling ◽  
New Generation

SUMMARYSystems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types.

scholarly journals The Viral Macrodomain Counters Host Antiviral ADP-Ribosylation

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 384 ◽  
Author(s):  
Yousef M. O. Alhammad ◽  
Anthony R. Fehr
Keyword(s):  
Immune Responses ◽  
Protein Interactions ◽  
Innate Immune ◽  
Innate Immune Responses ◽  
Protein Protein Interactions ◽  
Granule Formation ◽  
Inflammatory Cytokine Production ◽  
Adp Ribosylation ◽  
Antiviral Responses ◽  
Host Defense Response

Macrodomains, enzymes that remove ADP-ribose from proteins, are encoded by several families of RNA viruses and have recently been shown to counter innate immune responses to virus infection. ADP-ribose is covalently attached to target proteins by poly-ADP-ribose polymerases (PARPs), using nicotinamide adenine dinucleotide (NAD+) as a substrate. This modification can have a wide variety of effects on proteins including alteration of enzyme activity, protein–protein interactions, and protein stability. Several PARPs are induced by interferon (IFN) and are known to have antiviral properties, implicating ADP-ribosylation in the host defense response and suggesting that viral macrodomains may counter this response. Recent studies have demonstrated that viral macrodomains do counter the innate immune response by interfering with PARP-mediated antiviral defenses, stress granule formation, and pro-inflammatory cytokine production. Here, we will describe the known functions of the viral macrodomains and review recent literature demonstrating their roles in countering PARP-mediated antiviral responses.

scholarly journals Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem

2020 ◽  
Vol 21 (16) ◽  
pp. 5745
Author(s):  
Muhammad Naseem ◽  
Özge Osmanoğlu ◽  
Martin Kaltdorf ◽  
Afnan Ali M. A. Alblooshi ◽  
Jibran Iqbal ◽  
...  
Keyword(s):  
Stem Cells ◽  
Immune Responses ◽  
Shoot Apical Meristem ◽  
Apical Meristem ◽  
Large Scale ◽  
Gene Expression Omnibus ◽  
Immune Defense ◽  
Immune Functions ◽  
Pathogen Infection ◽  
Immune Genes

The growing tips of plants grow sterile; therefore, disease-free plants can be generated from them. How plants safeguard growing apices from pathogen infection is still a mystery. The shoot apical meristem (SAM) is one of the three stem cells niches that give rise to the above ground plant organs. This is very well explored; however, how signaling networks orchestrate immune responses against pathogen infections in the SAM remains unclear. To reconstruct a transcriptional framework of the differentially expressed genes (DEGs) pertaining to various SAM cellular populations, we acquired large-scale transcriptome datasets from the public repository Gene Expression Omnibus (GEO). We identify here distinct sets of genes for various SAM cellular populations that are enriched in immune functions, such as immune defense, pathogen infection, biotic stress, and response to salicylic acid and jasmonic acid and their biosynthetic pathways in the SAM. We further linked those immune genes to their respective proteins and identify interactions among them by mapping a transcriptome-guided SAM-interactome. Furthermore, we compared stem-cells regulated transcriptome with innate immune responses in plants showing transcriptional separation among their DEGs in Arabidopsis. Besides unleashing a repertoire of immune-related genes in the SAM, our analysis provides a SAM-interactome that will help the community in designing functional experiments to study the specific defense dynamics of the SAM-cellular populations. Moreover, our study promotes the essence of large-scale omics data re-analysis, allowing a fresh look at the SAM-cellular transcriptome repurposing data-sets for new questions.

scholarly journals Systems Perspective of Morbillivirus Replication

2016 ◽  
Vol 26 (6) ◽  
pp. 389-400 ◽  
Author(s):  
Naveen Kumar ◽  
Sanjay Barua ◽  
Riyesh Thachamvally ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Immune Response ◽  
Disease Resistance ◽  
Systems Biology ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Host Proteins ◽  
Systems Perspective ◽  
Host Pathogen Interaction ◽  
Comprehensive Information

Systems biology refers to system-wide changes in biological components such as RNA/DNA (genomics), protein (proteomics) and lipids (lipidomics). In this review, we provide comprehensive information about morbillivirus replication. Besides discussing the role of individual viral/host proteins in virus replication, we also discuss how systems-level analyses could improve our understanding of morbillivirus replication, host-pathogen interaction, immune response and disease resistance. Finally, we discuss how viroinformatics is likely to provide important insights for understanding genome-genome, genome-protein and protein-protein interactions.

Sign in / Sign up

Export Citation Format

Share Document