Response of heterogeneous ribonuclear proteins (hnRNP) to ionising radiation and their involvement in DNA damage repair.

PURPOSE: To determine the relationship between heterogeneous nuclear ribonucleoproteins (hnRNP) and DNA repair, particularly in response to ionising radiation (IR). MATERIALS AND METHODS: The literature was examined for papers related to the topics of hnRNP, IR and DNA repair. RESULTS: HnRNP orchestrate the processing of mRNA to which they are bound in response to IR. HnRNP A18, B1, C1/C2 and K interact with important proteins from DNA Damage Response (DDR) pathways, binding DNA-dependent protein kinase (DNA-PK), the Ku antigen (Ku) and tumour suppressor protein 53 (p53) respectively. Notably, irregularities in the expression of hnRNP A18, B1, K, P2 and L have been linked to cancer and radiosensitivity. Sixteen different hnRNP proteins have been reported to show either mRNA transcript or protein quantity changes following IR. Various protein modifications of hnRNP in response to IR have also been noted: hnRNP A18, C1/C2 and K are phosphorylated; hnRNP C1/C2 is a target of apoptotic proteases; and hnRNP K degradation is controlled by murine double minute ubiquitin ligase (MDM2). Evidence points to a role for hnRNP A1, A18, A2/B1, C1/C2, K and P2 in regulating double-stranded break (DSB) repair pathways by promoting either homologous recombination (HR) or non-homologous end rejoining (NHEJ) repair pathways following IR. CONCLUSIONS: HnRNP proteins play a pivotal role in coordinating repair pathways following exposure to IR, through protein-protein interactions and transcript regulation of key repair and stress response mRNA. In particular, several hnRNP proteins are critical in coordinating the choice of HR or NHEJ to repair DSB caused by IR.

Diagnostic oligonucleotide microarray fingerprinting of Bacillus isolates.

A genome-independent microarray and new statistical techniques were used to genotype Bacillus strains and quantitatively compare DNA fingerprints with the known taxonomy of the genus. A synthetic DNA standard was used to understand process level variability and lead to recommended standard operating procedures for microbial forensics and clinical diagnostics.

Automated Microarray Image Analysis Toolbox for MATLAB.

UNLABELLED: The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source, microarray image analysis tool that allows the user to customize analyses of microarray image sets. This tool provides several methods to identify and quantify spot statistics, as well as extensive diagnostic statistics and images to evaluate data quality and array processing. The open, modular nature of AMIA provides access to implementation details and encourages modification and extension of AMIA's capabilities. AVAILABILITY: The AMIA Toolbox is freely available at http://www.pnl.gov/statistics/amia. The AMIA Toolbox requires MATLAB 6.5 (R13) (MathWorks, Inc. Natick, MA), as well as the Statistics Toolbox 4.1 and Image Processing Toolbox 4.1 for MATLAB or more recent versions. CONTACT: amanda.white@pnl.gov

Comparing bacterial DNA microarray fingerprints.

Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Biology of TiO2-oligonucleotide nanocomposites.

Emerging areas of nanotechnology hold the promise of overcoming the limitations of existing technologies for intracellular manipulation. These new developments provide approaches for the creation of chemical-biological hybrid nanocomposites that can be introduced into cells and subsequently used to initiate intracellular processes or biochemical reactions. Such nanocomposites would advance medical biotechnology, just as they are improving microarray technology and imaging in biology and medicine, and introducing new possibilities in chemistry and material sciences. Here we describe the behaviour of 45-A nanoparticles of titanium dioxide semiconductor combined with oligonucleotide DNA into nanocomposites in vivo and in vitro. These nanocomposites not only retain the intrinsic photocatalytic capacity of TiO2 and the bioactivity of the oligonucleotide DNA (covalently attached to the TiO2 nanoparticle), but also possess the chemically and biologically unique new property of a light-inducible nucleic acid endonuclease, which could become a new tool for gene therapy.

Sensitivity to low-level radiation in radiosensitive "wasted" mice.

Mice homozygous for the autosomal recessive "wasted" mutation (wst/wst) have abnormalities in T lymphocytes and in the anterior motor neuron cells of the spinal cord, leading to sensitivity to low doses of ionizing radiation, hind limb paralysis, and immunodeficiency. This defect results in a failure to gain weight by 20 days of age and death by 28 days. The wasted mutation (previously mapped to mouse chromosome 2) is shown to be a 3-bp deletion in a T cell-specific (and perhaps motor-neuron-specific) regulatory region (promoter) of the proliferating cell nuclear antigen (PCNA) gene on mouse chromosome 2. A regulatory element is also shown to be important in PCNA expression in T lymphocytes and motor neuron cells affected by the 3-bp deletions in the PCNA promoter. The model is as follows. Absence of PCNA expression in the thymuses (and motor neurons) of wasted mice causes cellular apoptosis. This absence of expression is mediated by a positive transfactor that can bind to the wild-type but not to the wasted mutant PCNA promoter. The bound protein induces late expression of PCNA in T lymphocytes and prevents onset of radiation sensitivity in the cells.