Evaluation of Muscardinus avellanarius population density by nest box and by trap checking

Population densities of marked common dormice Muscardinus avellanarius are generally based on nest box checks. As dormice also use natural cavities and leaf nests, we tried to answer the question "what proportion of the population cannot be monitored by nest boy checks", using parallel trapping sessions. We selected a forest of 1.7ha where a 5-year nest box survey revealed an annual mean of 3.4 ± 1.4 dormice per check. The trap design (permanent grid of 77 hanging platforms) was developed in June. During July and August the traps were set every second week (4 sessions of two nights = 8 nights) resulting in a total of 75 captures with mean of 9.4 dormice per night and the presence of 16 different individuals. The grid of 60 nest boxes was checked weekly (8 times) which allowed the recapture of 19 dormice with a mean of 2.4 dormice, per control day and the presence of 6 different individuals. Population density estimated by calendar of capture and the minimal number of dormice alive methods gave for nest-box checks a value of 2.4 animals/ha and the trap checks 6.6 animals/ha with the conclusion that 63% of the population were not being monitored by nest box checks.

Perspectives for Forensic Intelligence in anti-doping: Thinking outside of the box.

Today's approach to anti-doping is mostly centered on the judicial process, despite pursuing a further goal in the detection, reduction, solving and/or prevention of doping. Similarly to decision-making in the area of law enforcement feeding on Forensic Intelligence, anti-doping might significantly benefit from a more extensive gathering of knowledge. Forensic Intelligence might bring a broader logical dimension to the interpretation of data on doping activities for a more future-oriented and comprehensive approach instead of the traditional case-based and reactive process. Information coming from a variety of sources related to doping, whether directly or potentially, would feed an organized memory to provide real time intelligence on the size, seriousness and evolution of the phenomenon. Due to the complexity of doping, integrating analytical chemical results and longitudinal monitoring of biomarkers with physiological, epidemiological, sociological or circumstantial information might provide a logical framework enabling fit for purpose decision-making. Therefore, Anti-Doping Intelligence might prove efficient at providing a more proactive response to any potential or emerging doping phenomenon or to address existing problems with innovative actions or/and policies. This approach might prove useful to detect, neutralize, disrupt and/or prevent organized doping or the trafficking of doping agents, as well as helping to refine the targeting of athletes or teams. In addition, such an intelligence-led methodology would serve to address doping offenses in the absence of adverse analytical chemical evidence.

PchR-box recognition by the AraC-type regulator PchR of Pseudomonas aeruginosa requires the siderophore pyochelin as an effector.

Under iron limitation, the opportunistic human pathogen Pseudomonas aeruginosa produces the siderophore pyochelin. When secreted into the extracellular environment, pyochelin complexes ferric ions and delivers them, via the outer membrane receptor FptA, to the bacterial cytoplasm. Extracellular pyochelin also acts as a signalling molecule, inducing the expression of pyochelin biosynthesis and uptake genes by a mechanism involving the AraC-type regulator PchR. We have identified a 32 bp conserved sequence element (PchR-box) in promoter regions of pyochelin-controlled genes and we show that the PchR-box in the pchR-pchDCBA intergenic region is essential for the induction of the pyochelin biosynthetic operon pchDCBA and the repression of the divergently transcribed pchR gene. PchR was purified as a fusion with maltose-binding protein (MBP). Mobility shift assays demonstrated specific binding of MBP-PchR to the PchR-box in the presence, but not in the absence of pyochelin and iron. PchR-box mutations that interfered with pyochelin-dependent regulation in vivo, also affected pyochelin-dependent PchR-box recognition in vitro. We conclude that pyochelin, probably in its iron-loaded state, is the intracellular effector required for PchR-mediated regulation. The fact that extracellular pyochelin triggers this regulation suggests that the siderophore can enter the cytoplasm.

High expression of the HMG box factor sox-13 in arterial walls during embryonic development.

Members of the Sox gene family of transcription factors are defined by the presence of an 80 amino acid homology domain, the High Mobility Group (HMG) box. Here we report the cloning and initial analysis of murine Sox-13 . The 984 amino acids Sox-13 protein contains a single HMG box, a leucine zipper motif and a glutamine-rich stretch. These characteristics are shared with another member of the Sox gene family, Sox-6. High level embryonic expression of Sox-13 occurs uniquely in the arterial walls of 13.5 days post coitum (dpc) mice and later. Low level expression was observed in the inner ear of 13.5 dpc mice and in a limited number of cells in the thymus of 16.5 dpc mice, from which Sox-13 was originally cloned. At 18.5 dpc, Sox-13 is expressed in the tracheal epithelium below the vocal cord and in the hair follicles. The Sox-13 protein binds to the consensus HMG box motif, AACAAAG, but does not transactivate transcription through a concatamer of this motif. Sox-13, like other members of the Sox family likely plays an important role in development.

Monte Carlo simulation of a clearance box monitor used for nuclear power plant decommissioning.

When decommissioning a nuclear facility it is important to be able to estimate activity levels of potentially radioactive samples and compare with clearance values defined by regulatory authorities. This paper presents a method of calibrating a clearance box monitor based on practical experimental measurements and Monte Carlo simulations. Adjusting the simulation for experimental data obtained using a simple point source permits the computation of absolute calibration factors for more complex geometries with an accuracy of a bit more than 20%. The uncertainty of the calibration factor can be improved to about 10% when the simulation is used relatively, in direct comparison with a measurement performed in the same geometry but with another nuclide. The simulation can also be used to validate the experimental calibration procedure when the sample is supposed to be homogeneous but the calibration factor is derived from a plate phantom. For more realistic geometries, like a small gravel dumpster, Monte Carlo simulation shows that the calibration factor obtained with a larger homogeneous phantom is correct within about 20%, if sample density is taken as the influencing parameter. Finally, simulation can be used to estimate the effect of a contamination hotspot. The research supporting this paper shows that activity could be largely underestimated in the event of a centrally-located hotspot and overestimated for a peripherally-located hotspot if the sample is assumed to be homogeneously contaminated. This demonstrates the usefulness of being able to complement experimental methods with Monte Carlo simulations in order to estimate calibration factors that cannot be directly measured because of a lack of available material or specific geometries.

High mobility group box 1 protein (HMGB1) : a pathogenic role in preeclampsia

Introduction : la Physiopathologie maternelle de la prééclampsie s'associe typiquement à un état inflammatoire systémique modéré. La protéine "high mobility group box 1" (HMGB-1) est une protéine nucléaire ubiquitaire. En cas de stress cellulaire, elle est relâchée dans le milieu extrace llua li re et peut ainsi exercer son activité pro-inflammatoire. En cas de prééclampsie, le liquide amniotique et le cytoplasme des cellules trophoblastiques contiennent des quantités anormalement élevées de HMGB-1, mais il n'est toujours pas universellement admis que ces concentrations se retrouvent dans le sang maternel. Méthodes : nous avons recruté 32 femmes au troisième trimestre de grossesse, 16 avec et 16 sans prééclampsie. Nous avons également observé 16 femmes non enceintes et en bonne santé, appariées selon l'âge avec les femmes enceintes. Nous avons mesuré la concentration sérique de HMGB-1 chez les femmes enceintes avant, puis 24-48 heures après leur accouchement, en utilisant un kit ELISA commercial. Le même dosage a été réalisé chez les femmes non enceintes, mais à une seule reprise, au moment de leur inclusion dans l'étude. Résultats : le jour de leur inclusion dans l'étude, la concentration médiane [intervalle interquartile] de HMGB-1 chez les femmes enceintes prééclamptiques était de 2.1 ng/ml [1.1 - 3.2], de 1.1 [1.0-1.2] chez les grossesses saines (p < 0.05 vs groupe prééclamptiques) et de 0.6 [0.5 - 0.8] chez les patientes non enceintes (p < 0.01 vs deux autres groupes). Pour les deux groupes de femmes enceintes, les concentrations mesurées en post-partum ne variaient pas significativement de celles mesurées avant l'accouchement. Conclusion : avec ou sans prééclampsie, le troisième triemstre de la grossesse est associé à une élévation des taux circulants de HMGB-1. Cette augmentation est exagérée en cas de prééclampsie. L'origine de ces concentrations élevées reste à déterminer, mais elle semble impliquer d'autres organes que le placenta lui-même.

CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.

In mammalian circadian clockwork, the CLOCK-BMAL1 complex binds to DNA enhancers of target genes and drives circadian oscillation of transcription. Here we identified 7,978 CLOCK-binding sites in mouse liver by chromatin immunoprecipitation-sequencing (ChIP-Seq), and a newly developed bioinformatics method, motif centrality analysis of ChIP-Seq (MOCCS), revealed a genome-wide distribution of previously unappreciated noncanonical E-boxes targeted by CLOCK. In vitro promoter assays showed that CACGNG, CACGTT, and CATG(T/C)G are functional CLOCK-binding motifs. Furthermore, we extensively revealed rhythmically expressed genes by poly(A)-tailed RNA-Seq and identified 1,629 CLOCK target genes within 11,926 genes expressed in the liver. Our analysis also revealed rhythmically expressed genes that have no apparent CLOCK-binding site, indicating the importance of indirect transcriptional and posttranscriptional regulations. Indirect transcriptional regulation is represented by rhythmic expression of CLOCK-regulated transcription factors, such as Krüppel-like factors (KLFs). Indirect posttranscriptional regulation involves rhythmic microRNAs that were identified by small-RNA-Seq. Collectively, CLOCK-dependent direct transactivation through multiple E-boxes and indirect regulations polyphonically orchestrate dynamic circadian outputs.

Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines.

CD8 T cells play a key role in mediating protective immunity against selected pathogens after vaccination. Understanding the mechanism of this protection is dependent upon definition of the heterogeneity and complexity of cellular immune responses generated by different vaccines. Here, we identify previously unrecognized subsets of CD8 T cells based upon analysis of gene-expression patterns within single cells and show that they are differentially induced by different vaccines. Three prime-boost vector combinations encoding HIV Env stimulated antigen-specific CD8 T-cell populations of similar magnitude, phenotype, and functionality. Remarkably, however, analysis of single-cell gene-expression profiles enabled discrimination of a majority of central memory (CM) and effector memory (EM) CD8 T cells elicited by the three vaccines. Subsets of T cells could be defined based on their expression of Eomes, Cxcr3, and Ccr7, or Klrk1, Klrg1, and Ccr5 in CM and EM cells, respectively. Of CM cells elicited by DNA prime-recombinant adenoviral (rAd) boost vectors, 67% were Eomes(-) Ccr7(+) Cxcr3(-), in contrast to only 7% and 2% stimulated by rAd5-rAd5 or rAd-LCMV, respectively. Of EM cells elicited by DNA-rAd, 74% were Klrk1(-) Klrg1(-)Ccr5(-) compared with only 26% and 20% for rAd5-rAd5 or rAd5-LCMV. Definition by single-cell gene profiling of specific CM and EM CD8 T-cell subsets that are differentially induced by different gene-based vaccines will facilitate the design and evaluation of vaccines, as well as enable our understanding of mechanisms of protective immunity.

Multifractal portrayal of the Swiss population

Fractal geometry is a fundamental approach for describing the complex irregularities of the spatial structure of point patterns. The present research characterizes the spatial structure of the Swiss population distribution in the three Swiss geographical regions (Alps, Plateau and Jura) and at the entire country level. These analyses were carried out using fractal and multifractal measures for point patterns, which enabled the estimation of the spatial degree of clustering of a distribution at different scales. The Swiss population dataset is presented on a grid of points and thus it can be modelled as a "point process" where each point is characterized by its spatial location (geometrical support) and a number of inhabitants (measured variable). The fractal characterization was performed by means of the box-counting dimension and the multifractal analysis was conducted through the Renyi's generalized dimensions and the multifractal spectrum. Results showed that the four population patterns are all multifractals and present different clustering behaviours. Applying multifractal and fractal methods at different geographical regions and at different scales allowed us to quantify and describe the dissimilarities between the four structures and their underlying processes. This paper is the first Swiss geodemographic study applying multifractal methods using high resolution data.