Principles of homeostasis in governing virus activation and latency

Phylogenetic analysis of microbial CP-lyase cluster genes for bioremediation of phosphonate

The ever-increasing use of phosphonates and their derivatives has resulted in the discharge of large quantities of these materials into the ecosystem, causing pollution and harmful shifts in microbiome composition. We conducted an extensive phylogenetic analysis to address this mounting problem and to help determine suitable microbes for bioremediation in specific environments. The 84 microorganisms included in our study span the gamut of species and occupied habitats. They degrade phosphonates by expressing an enzyme complex; CP-Lyase transcribed from 14 cistrons. Of the organisms studied, 12, 39, and 25 are singularly suitable for mostly freshwater, marine, or terrestrial habitats, respectively. Others adapted to multihabitats include Calothrix sp. PCC 7507 (both freshwater and marine habitats), Escherichia coli, Kaistia soli, Limoniibacter endophyticus, Marivita sp. and Virgibacillus dokdonensis (both marine and terrestrial habitats), Acidithiobacillus ferrooxidans (both freshwater and terrestrial habitats), with Paenibacillus contaminans suitable for freshwater, marine, and terrestrial habitats. All organisms were statistically rooted to glutathione peroxidase for phylogenetic perspective with tree topology dependent upon 50% or greater support. Clustered genes have been shown to have co-evolved based on striking nucleotide similarity and clade groupings within the tree topologies generated.

Coevolution of hytrosaviruses and host immune responses

BACKGROUND

Hytrosaviruses (SGHVs; Hytrosaviridae family) are double-stranded DNA (dsDNA) viruses that cause salivary gland hypertrophy (SGH) syndrome in flies. Two structurally and functionally distinct SGHVs are recognized; Glossina pallidipes SGHV (GpSGHV) and Musca domestica SGHV (MdSGHV), that infect the hematophagous tsetse fly and the filth-feeding housefly, respectively. Genome sizes and gene contents of GpSGHV (~ 190 kb; 160-174 genes) and MdSGHV (~ 124 kb; 108 genes) may reflect an evolution with the SGHV-hosts resulting in differences in pathobiology. Whereas GpSGHV can switch from asymptomatic to symptomatic infections in response to certain unknown cues, MdSGHV solely infects symptomatically. Overt SGH characterizes the symptomatic infections of SGHVs, but whereas MdSGHV induces both nuclear and cellular hypertrophy (enlarged non-replicative cells), GpSGHV induces cellular hyperplasia (enlarged replicative cells). Compared to GpSGHV's specificity to Glossina species, MdSGHV infects other sympatric muscids. The MdSGHV-induced total shutdown of oogenesis inhibits its vertical transmission, while the GpSGHV's asymptomatic and symptomatic infections promote vertical and horizontal transmission, respectively. This paper reviews the coevolution of the SGHVs and their hosts (housefly and tsetse fly) based on phylogenetic relatedness of immune gene orthologs/paralogs and compares this with other virus-insect models.

RESULTS

Whereas MdSGHV is not vertically transmitted, GpSGHV is both vertically and horizontally transmitted, and the balance between the two transmission modes may significantly influence the pathogenesis of tsetse virus. The presence and absence of bacterial symbionts (Wigglesworthia and Sodalis) in tsetse and Wolbachia in the housefly, respectively, potentially contributes to the development of SGH symptoms. Unlike MdSGHV, GpSGHV contains not only host-derived proteins, but also appears to have evolutionarily recruited cellular genes from ancestral host(s) into its genome, which, although may be nonessential for viral replication, potentially contribute to the evasion of host's immune responses. Whereas MdSGHV has evolved strategies to counteract both the housefly's RNAi and apoptotic responses, the housefly has expanded its repertoire of immune effector, modulator and melanization genes compared to the tsetse fly.

CONCLUSIONS

The ecologies and life-histories of the housefly and tsetse fly may significantly influence coevolution of MdSGHV and GpSGHV with their hosts. Although there are still many unanswered questions regarding the pathogenesis of SGHVs, and the extent to which microbiota influence expression of overt SGH symptoms, SGHVs are attractive 'explorers' to elucidate the immune responses of their hosts, and the transmission modes of other large DNA viruses.

A Biomolecular Network Driven Proteinic Interaction in HCV Clearance

Hepatitis C virus infection causes chronic liver disease that leads to cancer-related mortality. Presently around 30% of the HCV (infected) affected population get rid of the infection through spontaneous disease clearance. This phenomenon is conducted by a set of reported immune candidate genes. Hence, this study focuses only on these immune-response related genes with aid of network approach, where the idea is to disseminate the network for better understanding of key functional genes and their transcription control activity. Based on the network analysis the IFNG, TNF, IFNB1, STAT1, NFKB1, STAT3, SOCS1, and MYD88 genes are prioritized as hub genes along with their common transcription factors (TFs), IRF9, NFKB1, and STAT1. The dinucleotide frequency of TF binding elements indicated GG-rich motifs in these regulatory elements. On the other hand, gene enrichment report suggests the regulation of response to interferon gamma signaling pathway, which plays central role in the spontaneous HCV clearance. Therefore, our study tends to prioritize the genes, TFs, and their regulatory pathway towards HCV clearance. Even so, the resultant hub genes and their TFs and TF binding elements could be crucial in underscoring the clearance activity in specific populations.

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection

Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. The virus life-cycle is classically described by schematic pictures. Using this ontology, it can be represented by a combination of successive terms: “entry”, “latency”, “transcription”, “replication” and “exit”. Each of these parts is broken down into discrete steps. For example Zika virus “entry” is broken down in successive steps: “Attachment”, “Apoptotic mimicry”, “Viral endocytosis/ macropinocytosis”, “Fusion with host endosomal membrane”, “Viral factory”. To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases.

Infection homeostasis: implications for therapeutic and immune programming of metabolism in controlling infection

Homeostasis underpins at a systems level the regulatory control of immunity and metabolism. While physiologically these systems are often viewed as independent, there is increasing evidence showing a tight coupling between immune and metabolic functions. Critically upon infection, the homeostatic regulation for both immune and metabolic pathways is altered yet these changes are often investigated in isolation. Here, we summarise our current understanding of these processes in the context of a clinically relevant pathogen, cytomegalovirus. We synthesise from the literature an integrative view of a coupled immune-metabolic infection process, centred on sugar and lipid metabolism. We put forward the notion that understanding immune control of key metabolic enzymatic steps in infection will promote the future development of novel therapeutic modalities based on metabolic modifiers that either enhance protection or inhibit infection.

Use of logic theory in understanding regulatory pathway signaling in response to infection

Biological pathways link the molecular and cellular levels of biological activity and perform complex information processing seamlessly. Systems biology aims to combine an understanding of the cause-effect relationships of each individual interaction to build an understanding of the function of whole pathways. Therapies that target the 'host' biological processes in infectious diseases are often limited to the use of vaccines and biologics rather than small molecules. The development of host drug targets for small molecules is constrained by a limited knowledge of the underlying role of each target, particularly its potential to cause harmful side effects after targeting. By considering the combinatorial complexity of pathways from the outset, we can develop modeling tools that are better suited to analyzing large pathways, enabling us to identify new causal relationships. This could lead to new drug target strategies that beneficially disrupt host-pathogen interactions, minimizing the number of side effects. We introduce logic theory as part of a pathway modeling approach that can provide a new framework for understanding pathways and refine 'host-based' drug target identification strategies.

Dynamics of recurrent viral infection

In chronic viral infection, low levels of viral replication and infectious particle production are maintained over long periods, punctuated by brief bursts of high viral production and release. We apply well-established principles of modelling virus dynamics to the study of chronic viral infection, demonstrating that a model which incorporates the distinct contributions of cytotoxic T lymphocytes (CTLs) and antibodies exhibits long periods of quiescence followed by brief bursts of viral production. This suggests that for recurrent viral infections, no special mechanism or exogenous trigger is necessary to provoke an episode of reactivation; rather, the system may naturally cycle through recurrent episodes at intervals which can be many years long. We also find that exogenous factors which cause small fluctuations in the natural course of the infection can trigger a recurrent episode. Our model predicts that longer periods between recurrences are associated with more severe viral episodes. Four factors move the system towards less frequent, more severe episodes: decreased viral infectivity, decreased CTL efficacy, decreased memory T cell response and increased antibody efficacy.

Immune checkpoints in viral latency

The dynamics of the relationship between the immune system and latent viruses are highly complex. Latent viruses not only avoid elimination by the host's primary immune response, they also remain with the host for life in the presence of strong acquired immunity, often exhibiting periodic reactivation and recurrence from the latent state. The continual battle between reemergent infectious virus and immunological memory cells provides an essential virus-host regulatory loop in latency. In this review, we speculate on the critical importance of immune interference mechanisms by viruses contributing to the regulatory loop in viral homeostasis of latency. Central to the notion of viral homeostasis, we further invoke the concept of threshold limits in naive and memory states of immunity to account for the failure of the host to completely eradicate these intracellular parasites.