Christopher J. Rawlings

Prepublication data sharing.

Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

Graph-based analysis and visualization of experimental results with ONDEX

MOTIVATION Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise. RESULTS This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function.

PHI-base: a new database for pathogen host interactions

To utilize effectively the growing number of verified genes that mediate an organisms ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogs 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene/transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of the predicted proteins function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, Enzyme Commission Numbers and so on), and provide links to other external data sources (e.g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at .

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/.

Quantitative aspects of the formation and loss of DNA interstrand crosslinks in Chinese hamster cells following treatment with cis-diamminedichloroplatinum(II) (cisplatin) II. Comparison of results from alkaline elution, DNA renaturation and DNA sedimentation studies

The formation of interstrand crosslinks in the DNA of cis-diamminedichloroplatinum(II) (cisplatin)-treated Chinese hamster cells has been demonstrated by three independent, highly sensitive techniques: namely those of alkaline elution, renaturation of crosslinked DNA and alkaline sucrose gradient velocity sedimentation. Simultaneous measurement of DNA break frequency by the first two methods and a computer model combined with the third enabled the calculation of crosslink frequency after application of low doses of cisplatin. Good agreement was found between the values obtained by the three methods used here, and also with those obtained by direct measurement of the amount of crosslinked hybrid DNA in density-labelled cells treated with higher doses of cis-platin (Roberts, J.J. and Friedlos, F. (1981) Biochim. Biophys, Acta 655, 146--151). When measured by all three methods described here, crosslinking was found to increase during several hours after treatment and then to decrease with a half-life of between 12 and 24 h. For low initial levels of crosslinking, this was largely attributed to an excision repair process, since the formation of breaks in DNA was only minimal.

The Pathogen-Host Interactions Database (PHI-base) Provides Insights into Generic and Novel Themes of Pathogenicity

Fungal and oomycete pathogens of plants and animals are a major global problem. In the last 15 years, many genes required for pathogenesis have been determined for over 50 different species. Other studies have characterized effector genes (previously termed avirulence genes) required to activate host responses. By studying these types of pathogen genes, novel targets for control can be revealed. In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions. Here, we focus on the biology that underlies this computational resource: the nature of pathogen-host interactions, the experimental methods that exist for the characterization of such pathogen-host interactions as well as the available computational resources. Based on the data, we review and analyze the specific functions of pathogenicity genes, the host-specific nature of pathogenicity and virulence genes, and the generic mechanisms of effectors that trigger plant responses. We further discuss the utilization of PHI-base for the computational identification of pathogenicity genes through comparative genomics. In this context, the importance of standardizing pathogenicity assays as well as integrating databases to aid comparative genomics is discussed.

Reasoning about protein topology using the logic programming language PROLOG

Abstract The logic programming language PROLOG was used to represent and reason about the topology of protein structures. prolog descriptions of the relative positions of protein secondary structural features (protein topology) were generated from information in the Brookhaven data-bank. β-structural motifs (hairpin, meander, Greek key and jelly roll) were then defined using PROLOG rules. The PROLOG program was able to infer the presence of these structures in the prolog representation of the protein. A key feature of this approach is the facility to reason about complex topological motifs in protein structure in terms of primitive spatial relationships. Through the ability to represent logical reasoning. prolog could be used to develop flexible, high-level methods for controlling a graphics facility or front ends to more conventional databases.

Walker rat carcinoma cells are exceptionally sensitive to cis-diamminedichloroplatinum(II) (cisplatin) and other difunctional agents but not defective in the removal of platinum-DNA adducts

Cisplatin binds to cellular macromolecules (DNA, RNA and protein) to the same extent in wild-type Walker rat carcinoma cells and a variant sub-line of these cells resistant to cisplatin and to other difunctional, but not monofunctional cytotoxic agents. Wild-type Walker cells exhibit a unique sensitivity to DNA-bound cisplatin, while the resistant cells have a sensitivity that approximates to that of many normal and other tumour cell lines. Total DNA-bound adducts were lost from both sensitive and resistant Walker cells at similar rates. Equal numbers of DNA interstrand crosslinks and DNA-protein crosslinks were formed in both cell lines, and the rate of loss of both types of crosslinks was similar in the two lines. Therefore the unusual sensitivity of Walker cells to cisplatin is not due to a defect in their ability to remove these platinum-DNA adducts.

Computational gene discovery and human disease

Bioinformatics is now an essential tool in many aspects of human molecular genetics research. Methods for the prediction of gene structure are essential components in genomic sequencing projects and provide the key to deriving protein sequence and locating intron/exon junctions. Sequence comparison and database searching are the pre-eminent approaches for predicting the likely biochemical function of new genes, although sequence profiles derived from families of aligned sequences have advantages in the detection of remote sequence relationships. The use of sequence database analysis for large-scale comparative analysis of genome sequence data from model organisms is emerging as the most important recent development in the application of bioinformatics methods for characterizing candidate disease genes.

The unique sensitivity of Walker rat tumour cells to difunctional agents is associated with a failure to recover from inhibiton of DNA synthesis and increased chromosome damage

The rate and mode of DNA synthesis was examined by thymidine uptake and by flow cytometry in Walker tumour cells highly sensitive to difunctional agents (WS), and in a derived subline of resistant cells (WR) (Rawlings and Roberts, 1986), following their treatment with sulphur mustard. Both cell lines exhibited the same dose-dependent and progressive depression in rate of DNA synthesis for up to 4 h after treatment. Thereafter the depression in rate of synthesis was partially reversed in the WR cells but DNA synthesis continued to decrease in the WS cells resulting in their slower transit through the S phase and a persistent block in the G2/M phase of the cell cycle. Sensitive cells which finally escaped the block in G2 carried more chromosome aberrations than the corresponding resistant cells. Neither cell line was defective in daughter strand-gap repair. In their sensitivity to difunctional but not to monofunctional compounds, their failure to recover from the early depression of DNA synthesis, their apparent lack of a defect in excision repair and their sensitivity to chromosome aberration induction, the Walker cell phenotype closely resembles that of the human Fanconis anaemia cell.