Detecting sequence dependent transcriptional pauses from RNA and protein number time series

Background: Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses a?ect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identi?ed from in vitro measurements of transcription elongation kinetics.

Results: Using a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three di?erent but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is su?cient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classi?er. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site.

Conclusions: This method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.

Max separation clustering for feature extraction from Optical Emission Spectroscopy Data

This paper proposes max separation clustering (MSC), a new non-hierarchical clustering method used for feature extraction from optical emission spectroscopy (OES) data for plasma etch process control applications. OES data is high dimensional and inherently highly redundant with the result that it is difficult if not impossible to recognize useful features and key variables by direct visualization. MSC is developed for clustering variables with distinctive patterns and providing effective pattern representation by a small number of representative variables. The relationship between signal-to-noise ratio (SNR) and clustering performance is highlighted, leading to a requirement that low SNR signals be removed before applying MSC. Experimental results on industrial OES data show that MSC with low SNR signal removal produces effective summarization of the dominant patterns in the data.

Present orientation, future orientation and alcohol use in Northern Irish adolescents

Earlier initiation into more problematic drinking behaviour has been found to be associated with more problematic drinking later in life. Research has suggested that a lower future time perspective (and higher present time perspective) is associated with health-compromising behaviours such as problematic alcohol use in college student, University undergraduate and general population samples. This study used a cross-sectional design to examine whether consideration of future consequences (CFC), assessed by the Consideration of Future Consequences Scale, was significantly related to drinking behaviour in a large sample (n=707) of Northern Irish adolescents. Alcohol use was self-reported by means of a composite measure of drinking behaviour. Demographic data were also gathered. After controlling for year in school (proxy for age), sex and for clustering at school level, lower future orientation and higher present orientation were found to be significantly associated with more problematic self-reported drinking behaviour. These results extend recent findings of a significant relationship between a foreshortened future time perspective and more problematic self-reported drinking behaviour in a UK sample of University undergraduates, to a large UK sample of adolescents. Given the relationship between early-onset drinking and more problematic use in later life, health promotion interventions might explore using the CFC construct in targeting adolescent drinkers.

A pseudo-transient solution strategy for the analysis of delamination by means of interface elements

Recent efforts in the finite element modelling of delamination have concentrated on the development of cohesive interface elements. These are characterised by a bilinear constitutive law, where there is an initial high positive stiffness until a threshold stress level is reached, followed by a negative tangent stiffness representing softening (or damage evolution). Complete decohesion occurs when the amount of work done per unit area of crack surface is equal to a critical strain energy release rate. It is difficult to achieve a stable, oscillation-free solution beyond the onset of damage, using standard implicit quasi-static methods, unless a very refined mesh is used. In the present paper, a new solution strategy is proposed based on a pseudo-transient formulation and demonstrated through the modelling of a double cantilever beam undergoing Mode I delamination. A detailed analysis into the sensitivity of the user-defined parameters is also presented. Comparisons with other published solutions using a quasi-static formulation show that the pseudo-transient formulation gives improved accuracy and oscillation-free results with coarser meshes

TlCu1.73Fe0.27Se2 studied by means of Mössbauer spectroscopy and SQUID magnetometry

TlCu2-xFexSe2 is a p-type metal for x < 0.5 which crystallizes in a body-centred tetragonal structure. The metal atoms are situated in ab-planes, similar to 7 angstrom apart, while the metal - metal distance within the plane is similar to 2.75 angstrom. Due to the large difference in cation distances, the solid solutions show magnetic properties of mainly two-dimensional character. The SQUID measurements performed for x = 0.27 give the c-axis as the easy axis of magnetization, but also show clear hysteresis effects at 10 K, indicating a partly ferromagnetic coupling. The magnetic ordering temperature T-c is 55( 5) K as found from both SQUID and Mossbauer spectra. At T << Tc the magnetic hyperfine fields are distributed with a maximum at about 30 T, which are compared to the measured magnetic moment per iron atom, which is 0.97 mu(B)/Fe as found from SQUID measurements. The experimental results are compared to results using other methods on isostructural Tl selenides.

Genetic variability evaluation in a Moroccan collection of barley, Hordeum vulgare L., by means of storage proteins and RAPDS

The genetic variation existing in a set of barley (Hordeum vulgare L.) landrace samples recently collected in Morocco was estimated. Two kinds of genetic markers, seed storage proteins (hordeins) and random amplified polymorphic DNA (RAPD), were used. Only six out of 31 landraces were subjected to RAPD analysis. Both kinds of markers, RAPD and storage proteins, yielded similar results, showing that the level of variation observed in Moroccan barley was high: all landraces showed variability; 808 different storage protein patterns (multilocus associations) were observed among 1897 individuals (2.32 seeds per association, on average) with an average of 43 multilocus associations per accession. In general, genetic variation within accessions was higher than between accessions. The 100 polymorphic RAPD bands generated by 21 effective primers were able to generate enough patterns to differentiate between uniform cultivars and even between individuals in variable accessions. One of the aims of this work was to compare the effectiveness of RAPD versus storage protein techniques in assessing the variability of genetic resource collections. On average hordeins were more polymorphic than RAPDs: they showed more alternatives per band on gels and a higher percentage of polymorphic bands, although RAPDs supply a higher number of bands. Although RAPD is an easy and standard technique, storage protein analysis is technically easier, cheaper and needs less sophisticated equipment. Thus, when resources are a limiting factor and considering the cost of consumables and work time, seed storage proteins must be the technique of choice for a first estimation of genetic variation in plant genetic resource collections.

Fasciola hepatica:studies on vaccination of rats and mice with a surface antigen prepared from fluke homogenate by means of a monoclonal antibody

T1 tegumental antigen was isolated from a homogenate of eight- to 10-week-old Fasciola hepatica using a T1-specific monoclonal antibody bound to sepharose in an antibody-affinity column. Rats and mice were vaccinated with T1 antigen in Freund's complete adjuvant, and control groups received equivalent amounts of non-T1 antigen (eluted from the antibody-affinity column) or ovalbumin. On completion of the immunisation programme, serum samples were collected for ELISA and IFA testing. The animals were challenged by oral infection with F hepatica metacercariae or, for several vaccinated rats, by intraperitoneal transplantation of live adult flukes. At autopsy, worm-burden and liver damage was assessed for each animal and the condition of transplanted flukes was examined. Comparison of test and control groups of animals showed that neither T1 nor non-T1 antigens provided significant protection against challenge, although specific antibody responses against the appropriate sensitising antigen were engendered. Flukes transplanted to the peritoneal cavity of immunised rats survived without damage, although they became encased in hollow fibrous capsules of host origin. The results lend support to the pre-existing concept that glycocalyx turnover by discharge of T1 secretory bodies at the apical surface of migrating flukes provides an efficient means of protection for the parasite against host immunity.

Regulation of apoptotic protease activating factor-1 oligomerization and apoptosis by the WD-40 repeat region

Apoptotic protease activating factor-1 (Apaf-1) has been identified as a proximal activator of caspase-9 in cell death pathways that trigger mitochondrial damage and cytochrome c release. The mechanism of Apaf-1 action is unclear but has been proposed to involve the clustering of caspase-9 molecules, thereby facilitating autoprocessing of adjacent zymogens. Here we show that Apaf-1 can dimerize via the CED-4 homologous and linker domains of the molecule providing a means by which Apaf-1 can promote the clustering of caspase-9 and facilitate its activation. Apaf-1 dimerization was repressed by the C-terminal half of the molecule, which contains multiple WD-40 repeats, but this repression was overcome in the presence of cytochrome c and dATP. Removal of the WD-40 repeat region resulted in a constitutively active Apaf-1 that exhibited greater cytotoxicity in transient transfection assays when compared with full-length Apaf-1. These data suggest a mechanism for Apaf-1 function and reveal an important regulatory role for the WD-40 repeat region.