Particulate matter from both heavy fuel oil and diesel fuel shipping emissions show strong biological effects on human lung cells at realistic and comparable in vitro exposure conditions.

Background: Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling.

Objectives: To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols.

Combining metabolomic non-targeted GC×GC-ToF-MS analysis and chemometric ASCA-based study of variances to assess dietary influence on type 2 diabetes development in a mouse model.

Insulin resistance (IR) lies at the origin of type 2 diabetes. It induces initial compensatory insulin secretion until insulin exhaustion and subsequent excessive levels of glucose (hyperglycemia). A high-calorie diet is a major risk factor contributing to the development of this metabolic disease.

An evaluation of the "GGP" personal samplers under semi-volatile aerosols: sampling losses and their implication on occupational risk assessment.

Semi-volatile (SV) aerosols still represent an important challenge to occupational hygienists due to toxicological and sampling issues. Particularly problematic is the sampling of hazardous SV that are present in both particulate and vapour phases at a workplace. In this study we investigate the potential evaporation losses of SV aerosols when using off-line filter-adsorber personal samplers.

Spatial and temporal variability of source contributions to ambient PM10 during winter in Augsburg, Germany using organic and inorganic tracers.

Daily PM10 samples were collected during a one-month sampling campaign from February 13 to March 12, 2008 at eight different sampling sites in Augsburg, Southern Germany. Source apportionment was performed to identify the main sources and related contributions by analysis of organic and inorganic tracers. Nine factors were separated comprising: solid fuel combustion, traffic-related emissions, secondary inorganics, and mixed sources.

The impact of blood on liver metabolite profiling - a combined metabolomic and proteomic approach.

Metabolomics has entered the well-established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.

BZLF1 governs CpG-methylated chromatin of Epstein-Barr Virus reversing epigenetic repression.

Epigenetic mechanisms are essential for the regulation of all genes in mammalian cells but transcriptional repression including DNA methylation are also major epigenetic mechanisms of defense inactivating potentially harmful pathogens. Epstein-Barr Virus (EBV), however, has evolved to take advantage of CpG methylated DNA to regulate its own biphasic life cycle. We show here that latent EBV DNA has an extreme composition of methylated CpG dinucleotides with a bimodal distribution of unmethylated or fully methylated DNA at active latent genes or completely repressed lytic promoters, respectively.

DOT1A-dependent H3K76 methylation is required for replication regulation in Trypanosoma brucei.

Cell-cycle progression requires careful regulation to ensure accurate propagation of genetic material to the daughter cells. Although many cell-cycle regulators are evolutionarily conserved in the protozoan parasite Trypanosoma brucei, novel regulatory mechanisms seem to have evolved. Here, we analyse the function of the histone methyltransferase DOT1A during cell-cycle progression.

Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus.

Whether or not metazoan replication initiates at random or specific but flexible sites is an unsolved question. The lack of sequence specificity in origin recognition complex (ORC) DNA binding complicates genome-scale chromatin immunoprecipitation (ChIP)-based studies. Epstein-Barr virus (EBV) persists as chromatinized minichromosomes that are replicated by the host replication machinery.

Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.

Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes.

On the causes of outliers in Affymetrix GeneChip data.

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips.

Reducing spatial flaws in oligonucleotide arrays by using neighborhood information.

We address the problem of detection and correction of spatial flaws in oligonucleotide microarrays. We present two similar procedures, of which one is intended solely for use with replicates and the other has wider applicability. By constructing a set of replicates, with one realistically flawed, we are able to examine the extent to which our procedures are capable of repairing the flaw.

The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA.

We are developing a computational pipeline to use surveys of Affymetrix GeneChips as a discovery tool for unravelling some of the biology associated with post-transcriptional processing of RNA. This work involves the integration of a number of bioinformatics resources, from comparing annotations to processing images to determining the structure of transcripts. The rapidly growing datasets of GeneChips available to the community puts us in a strong position to discover novel biology about post-transcriptional processing, and should enable us to determine the mechanisms by which some groups of genes make co-ordinated changes in their production of isoforms.

Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips.

We have developed a computational pipeline to analyse large surveys of Affymetrix GeneChips, for example NCBI's Gene Expression Omnibus. GEO samples data for many organisms, tissues and phenotypes. Because of this experimental diversity, any observed correlations between probe intensities can be associated either with biology that is robust, such as common co-expression, or with systematic biases associated with the GeneChip technology.

An overview of image-processing methods for Affymetrix GeneChips.

We present an overview of image-processing methods for Affymetrix GeneChips. All GeneChips are affected to some extent by spatially coherent defects and image processing has a number of potential impacts on the downstream analysis of GeneChip data. Fortunately, there are now a number of robust and accurate algorithms, which identify the most disabling defects.