Project Directors
Eve Wurtele (ISU) - Genetics, Development and Cell Biology
Peter Lammers (NMSU) - Chemistry and Biochemistry

Summary. Growth and development involve the regulated expression of many genes in a temporal order. The advent of DNA microarrays provides new and expanded opportunities to examine patterns of gene expression in cells and developing organisms. The expression of proteins, which carry out many of the vital functions in eukaryotic cells, is strongly influenced by post-transcriptional events. The emerging field of proteomics is defining protein expression profiles and post-transcriptional modifications. This is especially exciting, as proteomics may allow description of complex systems at the molecular level in real-time. As described below, CMB faculty are developing tools to visualize and statistically analyze various types of gene expression data. These include software tools for the analysis of combined metabolomics, microarray, and proteomic data, text mining curation aids for biologists, and unique visualization tools that can be combined with statistical analysis. These activities provide a framework for formulating testable hypotheses regarding gene function, and serve as the basis for understanding how metabolic and regulatory networks control complex cell functions and dictate developmental programs.

MetNet. Large data sets detailing many aspects of the molecular composition of a biological sample are leading to changes in the ways we look at biology. Ideally, these data sets could be analyzed globally to determine how the cell is regulated. However, precise information on the kinetics of interactions within the biological system as well as a significant proportion of the actual interactions themselves is mostly missing. ISU faculty Wurtele, Julie Dickerson, Leslie Miller and Dianne Cook are developingMetNet , a publicly available software package designed to integrate genome-wide mRNA, protein, and metabolite profiling data from Arabidopsis into an interaction map. Gene expression data can be explored with the aid of a metabolic and regulatory network map and an interactive graph display with visualization, statistical analysis, and modeling tools. The ultimate aim is to use these tools to provide the basis to identify metabolic and regulatory networks that control plant composition and development. These efforts are greatly enhanced by the recently established W.A. Keck Plant Metabolomics Research Laboratory, which is home to highly sophisticated separation and detection equipment that allows high-throughput microanalysis of metabolites in plants and identification of molecular changes that occur at the RNA, protein and metabolite levels in a living organism.

Visualization of global expression data. An important component of MetNet is that expression data can be evaluated in the context of metabolic and regulatory networks. A multivariate graphic capability of the statistical data analysis and visualization software (exploRase) has been developed by CMB faculty member Cook. Metabolic or regulatory flow in the network can be explored by capture of input from MetNetDB, in graphical form, and enable the user to identify pathways between entities. Dynamic relationships between the pathways can be captured in three-dimensional virtual reality systems, such as ISU’s Virtual Reality Applications Center C6 facility, a 6-wall, stereoscopic and fully immersive virtual environment. CMB faculty Dickerson and Wurtele are using the 3D virtual environment to visualize interactions between metabolic pathways and gene expression data, and are developing bioinformatics tools for extracting and modeling signal transduction networks.

Host-pathogen interactions. The complex regulatory networks invoked during host-pathogen interactions are being explored by CMB faculty at several levels of integration. ISU faculty Daniel Nettleton, Adam Bogdanove and Roger Wise are focused on understanding gene expression during plant response to pathogen attack. Similarly, the Lammers lab at NMSU is using microarray analyses to identify genes responsible for pathogen resistance in peppers. Douglas Jones, Thomas Peterson, de Macedo and Vasant Honavar at ISU are investigating immune signaling network patterns and associated functionality during parasite infections in mice. Karen Dorman (ISU) is developing mathematical models of virus-host interactions during persistent lentivirus infections in vivo. Collectively, these activities aim to identify important changes within the host systems or networks that are critical for reduction of pathogen load and disease control.

The research on regulatory pathways triggered by host-pathogen interactions is complemented by work being carried out at NMSU by Brook Milligan, Mary M. Ballyk, Enrico Pontelli, Son Cao Tran, and Karen Villaverde. This NMSU research team is designing and implementing an information management system to integrate molecular, environmental, ecological, and geographic information to improve our understanding of the spatial and temporal patterns of emerging pathogens. These data are critical to develop predictive models and to discover general principles for relationships between anthropogenic environmental change and the transmission and evolution of infectious agents. Data will be housed in a relational database, and a set of tools will be developed to identify patterns and connections between different elements of the data that will lead to hypotheses concerning the ecology of infectious diseases that could be then be tested through modeling.

Developmental Networks. Embryo implantation is a critical stage in vertebrate reproduction and, surprisingly, appears to involve proinflammatory immunomodulators as part of the successful implantation cascade. ISU faculty member Nettleton, whose research focuses on statistical methods for the design and analysis of gene expression data, is collaborating with Tuggle and Honavar on a project to study expression profiling of genes and proteins involved in maternal-fetal communication during implantation. This project integrates RNA and protein patterns expressed from the developing conceptus and the maternal endometrium, to understand both the underlying regulatory logic as well as the reason for enormous loss of embryos at this critical stage. In a separate project, Patrick Schnable's lab (ISU) is developing experimental and computational tools for analysis of developmental and regulatory networks in maize. They pioneered the use of microarray-coupled laser capture microdissection for the global analyses of gene expression patterns in specific types of plant cells and are using this technology to identify genes that control the development of the maize shoot apical meristem, leaf initiation and the formation of the tapetal cell layer of anthers. The Schnable lab is also using a combination of global mRNA, proteomic and metabolic profiling technologies to help understand the molecular mechanisms responsible for heterosis, which is the increased vigor that occurs in the F1 progeny of specific inbred lines. Although this trait is widely exploited in the development of crop cultivars and has been a foundation of US agriculture for over 50 years, the molecular basis of this biological process is not understood.

The work by ISU scientists on metabolic and developmental networks is complemented by several projects at NMSU that focus on plant models – a clear emphasis of both participating institutions. Mary O’Connell's lab (NMSU) investigates the regulation of capsaicinoid biosynthesis. Capsaicinoids are alkaloids produced by peppers that are responsible for heat or pungency. Transcript levels of capsaicinoid biosynthetic genes are correlated with the degree of pungency in the fruit, and understanding mechanisms of coordinate regulation of gene expression can lead to informed means of modulating the synthesis of these compounds. In a separate project, Champa Sengupta-Gopalan's lab (NMSU) studies mechanisms of nitrate utilization. Nitrogen is the most frequent factor limiting the productivity of agricultural systems. The Sengupta-Gopalan lab is characterizing mechanisms that integrate nitrate assimilation and other metabolic and developmental pathways. There is clearly a rich opportunity to apply tools developed at ISU, such as MetNet, to questions being addressed in the O’Connell and Sengupta-Gopalan labs.