Mais G. Ammari

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

HPIDB 2.0: a curated database for host–pathogen interactions

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html

Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences.

BackgroundBovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune suppression if animals are infected with an ncp biotype during early gestation, followed by a subsequent infection of the cp biotype. The molecular mechanisms that underscore the complex disease etiology leading to immune suppression in cattle caused by BVDV are not well understood.ResultsUsing proteomics, we evaluated the effect of cp and ncp BVDV infection of bovine monocytes to determine their role in viral immune suppression and uncontrolled inflammation. Proteins were isolated by differential detergent fractionation and identified by 2D-LC ESI MS/MS. We identified 137 and 228 significantly altered bovine proteins due to ncp and cp BVDV infection, respectively. Functional analysis of these proteins using the Gene Ontology (GO) showed multiple under- and over- represented GO functions in molecular function, biological process and cellular component between the two BVDV biotypes. Analysis of the top immunological pathways affected by BVDV infection revealed that pathways representing macropinocytosis signalling, virus entry via endocytic pathway, integrin signalling and primary immunodeficiency signalling were identified only in ncp BVDV-infected monocytes. In contrast, pathways like actin cytoskeleton signalling, RhoA signalling, clathrin-mediated endocytosis signalling and interferon signalling were identified only in cp BDVD-infected cells. Of the six common pathways involved in cp and ncp BVDV infection, acute phase response signalling was the most significant for both BVDV biotypes. Although, most shared altered host proteins between both BVDV biotypes showed the same type of change, integrin alpha 2b (ITGA2B) and integrin beta 3 (ITGB3) were down- regulated by ncp BVDV and up- regulated by cp BVDV infection.ConclusionsThis study shows that, as we expected, there are significant functional differences in the host proteins that respond to cp or ncp BVDV infection. The combined use of GO and systems biology network modelling facilitated a better understanding of host-pathogen interactions.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

BackgroundSystems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.ResultsThe Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.ConclusionsPSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Understanding the Pathogenesis of Cytopathic and Noncytopathic Bovine Viral Diarrhea Virus Infection Using Proteomics

Bovine Viral Diarrhea Virus (BVDV) is a single-stranded RNA virus in the Pestivirus genus within the Flaviviridae family. BVDV infections are seen in all ages and breeds of cattle worldwide and have significant economic impact due to productive and reproductive losses (Houe 2003). Two antigenically distinct genotypes of BVDV exist, type 1 and 2 (Ridpath et al. 1994). BVDV of both genotypes may occur as cytopathic (cp) or noncytopathic (ncp) biotypes, classified according to whether or not they produce visible changes in cell culture. Data indicate that cp biotypes of BVDV can actually be created through internal deletion of RNA of ncp biotypes, or through RNA recombination between ncp biotypes (Howard et al. 1992). Of the two BVDV biotypes, infection of a fetus by ncp BVDV can result in persistently infected (PI) calf that sheds the virus throughout its life without developing clinical signs of infection. PI animals are the major disseminators of BVDV in the cattle population and have been the cause of severe acute outbreaks (Carman et al. 1998). However cp BVDV is associated predominantly with animals that develop mucosal disease (MD), which can be acute, resulting in death within a few days of onset, or chronic, persisting for weeks or months before the afflicted animal dies (Houe 1999). The interaction of BVDV with its host has several unique features, most notably the capacity to infect its host either transiently or persistently (Liebler-Tenorio et al. 2002; Bendfeldt S 2007). Initially the virus binds to CD46, a complement receptor expressed on lymphoid cells, monocytes, macrophages and dendritic cells and serving as a “magnet” for several viral and bacterial pathogens (Cattaneo 2004). Upon entry, the virus replicates and spreads in the lymphatic system, impairing the immunity of the infected animal, particularly antigen presenting cells (APC) function and production of interferons (IFN). Cytopathic BVDV biotype but not ncp biotype (Schweizer & Peterhans 2001) is implicated in the induction of apoptosis (Zhang et al. 1996; Schweizer & Peterhans 1999; Grummer et al. 2002; Jordan et al.

Leveraging Experimental Details for an Improved Understanding of Host‐Pathogen Interactome

An increasing proportion of curated host‐pathogen interaction (HPI) information is becoming available in interaction databases. These data represent detailed, experimentally‐verified, molecular interaction data, which may be used to better understand infectious diseases. By their very nature, HPIs are context dependent, where the outcome of two proteins as interacting or not depends on the precise biological conditions studied and approaches used for identifying these interactions. The associated biology and the technical details of the experiments identifying interacting protein molecules are increasing being curated using defined curation standards but are overlooked in current HPI network modeling. Given the increase in data size and complexity, awareness of the process and variables included in HPI identification and curation, and their effect on data analysis and interpretation is crucial in understanding pathogenesis. We describe the use of HPI data for network modeling, aspects of curation that can help researchers to more accurately model specific infection conditions, and provide examples to illustrate these principles.

Evaluation of bovine viral diarrhea virus interactions with its host proteome during the course of infection

Identifying viral-host interactions is central in understanding the pathogenesis of intracellular agents, such as bovine viral diarrhea viruses (BVDVs). A high expression level of BVDV NS3 protein is associated with its cytopathic (CP) biotype and is essential in viral replication and viral-induced apoptosis. Although the differences between CP and non-cytopathic BVDV biotypes are well established, especially the importance of the BVDV NS3 viral protein in giving rise to different biotypes, only a few studies identified BVDV-cellular partners. In this study, using a proteomics approach, we identified 71 bovine proteins that interact with the CP NS3 protein at three different time-points post-infection. Our results show that BVDV-host interaction dynamic network involves simultaneously and sequentially interacting proteins in different compartments of the host cells. System analysis of targeted proteins shows that CP BVDVs manipulate multiple and different pathways, primarily the ribosome/translation pathway, specifically at early stages of infection. At later stages of infection, when high levels of NS3 are present, apoptosis can be detected in infected cells. In addition, combining results from this study with previously identified protein interactions adds an extra dimension and higher connectivity to the BVDV strain NADL-host interaction network. Overall, our results indicate correlations among an increase in viral RNA translation, free NS3 level, and cytopathic effect associated with CP biotype infection. Finally, our approach highlights the dynamic interplay between BVDVs and host cells and identifies specific CP BVDV-host interactions that can be used as specific targets for further investigation as BVDV antiviral therapies. Correspondence to: Lesya M. Pinchuk, M.D., Ph.D., Associate Professor, Immunology, College of Veterinary Medicine, P.O. Box 6100, 240 Wise Center Drive, Mississippi State, MS 39762-6100, USA, Tel: (662)325-1130; Fax: (662)325-1031; E-mail: l.pinchuk@msstate.edu