Planar Lipid Bilayer Analysis of Candidate Rotavirus Antivirals

Case rates of rotavirus, the leading viral cause of severe acute diarrhea in children under the age of 5, have been steadily declining in countries that have had access to effective mitigation strategies. In children experiencing nutritional insecurity, however, there is a significant decrease in vaccine efficacy. With vaccination and oral rehydration remaining the only rotavirus interventions (preventative and clinical) in place, significant inquiry is required to make antiviral treatment a reality. The NSP4 protein in rotavirus is a viroporin responsible for disturbing the stability of the rough ER membrane of epithelial cells, forming pores that disrupt calcium ion homeostasis. This viral pathway is a prime candidate for target in antiviral drug design, both because of its critical nature towards the function and replication of rotavirus and the myriad of preexisting drugs that block ordinary calcium ion channels. As the Banks lab and its collaborators continue to develop targeted antiviral drugs, an analytical review of existing, FDA-approved ion channel blockers that may cross-react with NSP4 is necessary to determine biophysical drug characteristics that are favorable for inhibiting this protein. After performing an extensive literature review, we selected amlodipine, diltiazem, and verapamil as calcium channel blockers to analyze as NSP4 antagonists. We utilized planar lipid bilayer electrophysiology to determine the binding kinetics and efficacy of selected viroporin inhibitors in lipid bilayer. In addition, we will assess the ability of computational modeling systems to confirm these findings

Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways.

The NF-κB protein RelB controls dendritic cell (DC) maturation and may be targeted therapeutically to manipulate T cell responses in disease. Here we report that RelB promoted DC activation not as the expected RelB-p52 effector of the noncanonical NF-κB pathway, but as a RelB-p50 dimer regulated by canonical IκBs, IκBα and IκBɛ. IκB control of RelB minimized spontaneous maturation but enabled rapid pathogen-responsive maturation. Computational modeling of the NF-κB signaling module identified control points of this unexpected cell type-specific regulation. Fibroblasts that we engineered accordingly showed DC-like RelB control. Canonical pathway control of RelB regulated pathogen-responsive gene expression programs. This work illustrates the potential utility of systems analyses in guiding the development of combination therapeutics for modulating DC-dependent T cell responses

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.

The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.

The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper

Phosphoproteomics-Based Systems Analysis of Signal Transduction Networks

Signal transduction systems coordinate complex cellular information to regulate biological events such as cell proliferation and differentiation. Although the accumulating evidence on widespread association of signaling molecules has revealed essential contribution of phosphorylation-dependent interaction networks to cellular regulation, their dynamic behavior is mostly yet to be analyzed. Recent technological advances regarding mass spectrometry-based quantitative proteomics have enabled us to describe the comprehensive status of phosphorylated molecules in a time-resolved manner. Computational analyses based on the phosphoproteome dynamics accelerate generation of novel methodologies for mathematical analysis of cellular signaling. Phosphoproteomics-based numerical modeling can be used to evaluate regulatory network elements from a statistical point of view. Integration with transcriptome dynamics also uncovers regulatory hubs at the transcriptional level. These omics-based computational methodologies, which have firstly been applied to representative signaling systems such as the epidermal growth factor receptor pathway, have now opened up a gate for systems analysis of signaling networks involved in immune response and cancer

Computational Investigation of Biological Membranes

Lipids are the building blocks of biological membranes, and the types of lipids that compose these cellular envelopes influence the physicochemical properties of the chemicals that can enter or exit the cell across the membrane. This work focuses on the lipid membrane compositions of eukaryotic (red blood cells) and prokaryotic (Pseudomonas aeruginosa) membranes. By analyzing the lipid-lipid and lipid-protein interactions results of the computational simulations, insights into lipid aggregation, bilayer leaflet behavior, membrane asymmetry, and small molecule transport through protein channels were obtained. The differences between prokaryotic and eukaryotic cell membranes are qualitative known; however, this work provides these concepts through quantitative evidence using multiscale molecular dynamics simulations. The results show that membrane leaflet asymmetry affects the membrane properties and protein-lipid interactions. The CLASP algorithm was employed to efficiently simulate the transport of small molecules through a bacterial membrane porin and analyze the resulting contacts of that molecule with the pore-lining residues

An Investigation of Programme Management and Application to a University Research Institute

Programme (or program) management can be regarded as the co-ordination and implementation of a defined set of related projects to achieve an organization’s strategic objectives. This differs from project management (i.e. as detailed in PMBoK and PRINCE2), which focuses on the management processes and activities required to deliver a specific business product or service. Although programme management has been adopted by a number of RTE (research, technology and engineering) organizations, there are different views of the subject as well as a lack of agreement in the literature on best practice. Therefore, this paper will review the discipline of programme management, including discussion of the UK standard for this practice called Managing Successful Programmes (MSPTM). The paper will cover a case study application of programme management to a university research institute, which involved managing the difficult start-up phase of the institute. The initial findings from this application include a need to focus on managing relationships through a consultative approach; a need for effective programme performance measurement and control mechanisms; and the importance of being able to readily adapt and modify the programme to respond to changing external requirements

Computational Biophysics of the Lipidome

Lipids are an essential building block for human life. The amphipathic properties of these molecules enable them to form the cell membranes that act as a barrier between a cell’s interior and exterior. By forming membranes, lipids are directly involved in various cell processes and in the regulation of membrane transport. In this work, we explored the effects of membrane asymmetry on red blood cells and on two types of placental cells. Membranes were analyzed using molecular dynamics simulations after utilizing existing experimental data. Changes in cholesterol partitioning and in membrane properties such as density and area per lipid revealed a clear impact of asymmetry on membrane dynamics. The results of this work provide new insight into membrane asymmetry and provide a framework for future studies to be completed