PATRIC Driving Biological Projects Awarded

Published on 2010-10-29

The Pathosystems Resource Integration Center (PATRIC), a bacterial Bioinformatics Resource Center (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH), is pleased to announce awards for its Driving Biological Projects (DBPs). DBPs are two-year awards that focus on infectious diseases research related to human bacterial pathogens. Research includes the use of high-throughput experimental technologies (HTP) to functionally characterize the genome, proteome or metabolome of bacterial organisms and/or host-pathogen interactions. This research may help elucidate the role of genes, proteins and metabolites with respect to pathogenesis, antimicrobial resistance or other biological processes of interest. The data and information generated by the DBPs will be made accessible to the broad scientific community and will be used to drive PATRIC’s infrastructure development to enable other researchers to perform similar analyses at the PATRIC website using their own data.

The DBP proposals were independently reviewed and evaluated by the PATRIC Scientific Working Group (SWG), and the top two proposals were selected for award.  The awarded DBPs are:

  • Comparative transcriptome and proteome analysis of Clostridium difficile strains: Dr. Yung-Fu Chang, PI, Dept. of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University – The Cornell team will compare five C. difficile strains, generate transcriptome and proteome sequence data for these strains, verify and complement the genome sequence annotations of available sequenced strains and expand the PATRIC data model by joint development, testing and deployment of tools for RNA-Seq analysis that can be used for other bacterial RNA-Seq projects.
  • Fitness Annotation of Bacterial Genomes: Dr. Michael McClelland, PI, Dept. of Pathology and Laboratory Medicine, University of California, Irvine – The goal of this proposal is to provide PATRIC with the information needed to display which genes of non-typhoidal Salmonella serovar Typhimurium (STm) contribute to survival in a variety of environments, including in infections of various hosts. This will be accomplished through a combination of high-throughput screening and sequencing methods and unique resources developed to annotate the STm genome with fitness information.   STm transcriptomes will be generated from bacteria growing in defined environments, including rich and minimal media, at stationary phase, and in conditions that induce virulence pathways. These transcriptomes will provide basal reference profiles to standardize and improve analysis of the impending onslaught of high-throughput transcriptomics data. Decoration of the genome with basal transcriptional data will complement the fitness profile and other existing annotations in this archetypical strain.

PATRIC will use the information learned and workflows identified in these DBPs to develop Web-accessible infrastructure to accept and analyze RNA-Seq data and other associated data types.  The knowledge gained through the experiments will be used to improve annotations for the specific organisms under study and in a broader context where applicable.

Dr. Chang said, “The PATRIC DBP is an excellent opportunity for our laboratory to expand the ongoing genomics research on C. difficile. In this DBP, we will be integrating large scale RNA-Seq, proteome and phenotype array data into the genome annotations of C. difficile. The experimental data generated will further be used for extending the annotations to other draft C. difficile genomes. We will develop experimentally curated pathway maps for several C. difficile genomes. We will also develop a pathway cross-mapping system between popular pathway analysis tools such as KEGG, SEED and Pathway Tools. Dr. Joy Scaria from the Chang laboratory will also work with the PATRIC team at VBI to seamlessly integrate the experimental data into PATRIC system. With the active participation of PATRIC team in the data analysis and software deployment, we anticipate to develop a scalable genomic analysis model extendable to other bacterial pathogens.”

Dr. McClelland said, “It is a privilege to be part of this vitally important NIAID mechanism in which wet labs are funded to link up with bioinformatics resource groups and make their data and analysis tools quickly and easily available to the community. There is a desperate need for many more of these kinds of grants to be funded to keep up with the increasing power of high-throughput data generation and presentation strategies, and to include a wide a range of pathogens and experts.”

Dr. Bruno Sobral, PI of the PATRIC project, offered the following comments on the DBPs: “PATRIC fully supports the concept of driving biological projects with the infectious disease community that performs genomic-scale wet chemistry experiments. The excellent quality of all the proposals received and especially the two selected shows that there is much to be done in support of the thousands of laboratories that work on bacterial infectious diseases. We are grateful to expand the PATRIC team to include such excellent scientists working on two organisms of great importance for hospital-acquired infections and food-borne outbreaks.”

Another solicitation for PATRIC DBPs is expected to occur in 2012.  DBP announcements will be posted on the PATRIC Website.  For individuals who wish to be included on the PATRIC email list for updates to the site, workshop notifications and DBP announcements, please contact us at patric@vbi.vt.edu

About PATRIC

PATRIC, the PathoSystems Resource Integration Center is a comprehensive Web-based resource for bacterial pathogens, biodefense research, and the study of emerging infectious diseases. PATRIC acquires, stores and integrates diverse information from pathogenic bacteria, provides visualization and data analysis tools to scientists, and enables the analysis of genomic, proteomic and various other data arising from, and of relevance to, infectious disease research. PATRIC’s scope includes all bacterial species and near relatives in the selected category A-C pathogens list as defined by NIAID.

The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. The PATRIC project also develops and hosts the Pathogen Portal a gateway and common data repository for the entire NIAID BRC Program.

This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C.

About the Cyberinfrastructure Division

The Cyberinfrastructure (CI) Division at the Virginia Bioinformatics Institute (VBI) of Virginia Tech (VT) is a diverse and highly integrated team of biologists, bioinformaticians, software engineers, and other experts that develops data, methods, infrastructure, and resources that enable scientific discoveries in infectious disease research and increasingly other research fields. The team applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. The CI Division has developed many public resources for curated, diverse molecular and literature data from various systems, and implemented the processes, systems, and databases required to support them. Members of the team also conduct research their own research in a highly coordinated way within the Division and with scientific communities across the globe by applying its methods, data, and infrastructure to make new discoveries.