Inter-individual variability in the response of human peripheral blood lymphocytes to ionizing radiation: comparison of the dicentric and micronucleus assays.

Ionizing radiation can induce a wide range of DNA damage that leads to chromosomal aberrations. Some of those aberrations (dicentrics and micronuclei) are applied in biodosimetry. Biological dosimetry assumes similar radiosensitivity of each donor, but it does not exclude inter-individual variations in radiation susceptibility. Therefore, for biological reasons, it is always challenging to investigate inter-individual variability in response to radiation. For mechanistic reasons, it is also interesting to investigate the correlation between dicentric and micronuclei formation in response to radiation. In this experiment, irradiated blood specimens from 14 healthy male and female donors have been used to evaluate inter-individual variability in response to the genotoxic effects of X-ray radiation, as well as the dose-response relationship and test sensitivity using two endpoints (dicentrics and micronuclei). The results showed similar patterns of cytogenetic biomarker distribution between donors, but differences in the response of some donors at some doses. Data also showed that responses of male donors were better detected using the dicentric test, while for females, micronucleus frequencies were higher in response to the same dose of radiation. No influence of smoking status or age on specific responses was observed. Group variability in response to radiation was evaluated using coefficient of variation for each group of individuals irradiated with the same doses; as the dose increases, group variability becomes substantially lower. Despite sporadic inter-individual variability, trend of radiation-induced changes was similar. Produced calibration curves for both types of damage revealed dicentrics as genetic damage more typical for radiation than micronuclei.

Towards a database for genotype-phenotype association research: mining data from encyclopaedia.

To associate phenotypic characteristics of an organism to molecules encoded by its genome, there is a need for well-structured genotype and phenotype data. We use a novel method for extracting data on phenotype and genotype characteristics of microorganisms from text. As a resource, we use an encyclopedia of microorganisms, which holds phenotypic and genotypic data and create a structured, flexible data resource, which can be exported to a range of database formats, containing genotype and phenotype data for 2412 species and 873 genera of microbes. This data source has great potential as a resource for future biological research on genotype-phenotype associations. In this paper, we focus on describing the structure and content of the resulting database and on evaluating the method used for extracting the data. We conclude that the resulting database can be used as a reliable complementary resource for research into genotype-phenotype association.

Putting encyclopaedia knowledge into structural form: finite state transducers approach.

In biology and functional genomics in particular, understanding the dependence and interplay between different genome and ecological characteristics of organisms is a very challenging problem. There are some public databases which combine this kind of information, but there is still much more information about microbes and other organisms that reside in unstructured and semi-structured documents, such as encyclopaedias. In this paper we present a method for extracting information from semi-structured resources, such as encyclopaedias, based on finite state transducers, consisting of two clearly distinguished phases. The first phase strongly relies on the analysis of the document structure and it is used for locating records of data in the text. The second phase is based on the finite state transducers created for extracting the data, which can be modified so as to achieve the preferred efficiency and it is used for extracting the particular characteristic from the text. We show how the two phase method is applied to the text of the encyclopaedia "Systematic Bacteriology". A fully structured database with genotype and phenotype characteristics of organisms has been created from the encyclopaedia unstructured descriptions.