Tests for Trend in Binary Response

Tests for trend are important in analyzing data where the binary response in ordered categories is of interest. An example is in toxicology where the response in various dose groups is observed. For testing an association between the dose and the response the approach from Cochran and Armitage is widely used. However the result of this test is highly dependent on the scores assigned to the dose groups. Various dose assignments can lead to different outcomes. As an alternative the isotonic regression, a nonparametric method, is proposed. The outcome of this approach is independent of the quantification of the dose. Both methods (Cochran‐Armitage test and isotonic regression) are compared within a simulation study to an isotonic version of the Pearson's Chi‐squared test and the Wilcoxon rank sum test.     

The trophic structure of bark-living oribatid mite communities analysed with stable isotopes (15N, 13C) indicates strong niche differentiation

The aim of the present study was to identify food sources of bark-living oribatid mites to investigate if trophic niche differentiation contributes to the diversity of bark living Oribatida. We measured the natural variation in stable isotope ratios (¹⁵N/¹⁴N, ¹³C/¹²C) in oribatid mites from the bark of oak (Quercus robur), beech (Fagus sylvatica), spruce (Picea abies) and pine (Pinus sylvestris) trees and their potential food sources, i.e., the covering vegetation of the bark (bryophytes, lichens, algae, fungi). As a baseline for calibration the stable isotope signatures of the bark of the four tree species were measured and set to zero. Oribatid mite stable isotope ratios spanned over a range of about 13 δ units for ¹⁵N and about 7 δ units for ¹³C suggesting that they span over about three trophic levels. Different stable isotope signatures indicate that bark living oribatid mites feed on different food sources, i.e., occupy distinct trophic niches. After calibration stable isotope signatures of respective oribatid mite species of the four tree species were similar indicating close association of oribatid mites with the corticolous cover as food source. Overall, the results support the hypothesis that trophic niche differentiation of bark living oribatid mites contributes to the high diversity of the group.     

L-Asparaginase from Erwinia Chrysanthemi 3937: cloning, expression and characterization

Bacterial L-asparaginases (L-ASNases) catalyze the conversion of L-asparagine to L-aspartate and ammonia. In the present work, we report the cloning and expression of L-asparaginase from Erwinia chrysanthemi 3937 (ErL-ASNase) in Escherichia coli BL21(DE3)pLysS. The enzyme was purified to homogeneity in a single-step procedure involving cation exchange chromatography on an S-Sepharose FF column. The enzymatic and structural properties of the recombinant enzyme were investigated and the kinetic parameters (K(m), k(cat)) for a number of substrates were determined. In addition, we found that the enzyme can be efficiently immobilized on epoxy-activated Sepharose CL-6B. The immobilized enzyme retains most of its activity (60%) and shows high stability at 4 degrees C. The approach offers the possibility of designing an ErL-ASNase bioreactor that can be operated over a long period of time with high efficiency, which can be used in leukaemia therapy.     

Wnt5a secretion stimulated by the extracellular calcium-sensing receptor inhibits defective Wnt signaling in colon cancer cells

To understand the role of the colonic extracellular calcium-sensing receptor (CaSR) in calcium chemoprotection against colon cancer, we activated the CaSR with 5 mM Ca(2+) on HT-29 cells, an adenocarcinoma cell line. High Ca(2+) stimulated the upregulation (as assessed by RT-PCR) and the secretion of Wnt5a (assessed by Western blot), a noncanonical Wnt family member. Inhibiting CaSR activity with a short interfering RNA (siRNA) duplex against the CaSR reduced CaSR protein and prevented the secretion of Wnt5a. Dominant negative CaSR (R185Q) or siRNA blocked the high Ca(2+)-mediated inhibition of the beta-catenin reporter TOPflash. The CaSR/Wnt5a inhibition of beta-catenin reporter was prevented by dominant negative ubiquitin ligase seven in absentia homolog 2 (Siah2). In low-calcium medium, overexpressing Wnt5a increased Siah2 amplicons and protein. Inducing the expression of full-length adenomatous polyposis coli (APC) prevented CaSRmediated increases of Siah2 and Wnt5a. Overexpressing the receptor tyrosine kinase-like orphan receptor 2 (Ror2) increased Wnt5a and CaSR-mediated inhibition of TOPflash. Conditioned medium from Wnt5a-transfected cells added to HT-29 cells in low-Ca(2+) medium inhibited the beta-catenin reporter. This inhibition was blocked dose responsively by Frizzled-8/Fc chimeric antibody. Overexpression of Ror2 in HT-29 cells in low-Ca(2+) medium increased the inhibition of beta-catenin reporter caused by recombinant Wnt5a protein compared with addition of Wnt5a protein alone. Our findings demonstrate that APC status plays a key role as a determinant of Wnt5a secretion and suggest that CaSR-mediated secretion of Wnt5a will inhibit defective Wnt signaling in APC-truncated cells in an autocrine manner.     

Evolutionary graph theory: breaking the symmetry between interaction and replacement

We study evolutionary dynamics in a population whose structure is given by two graphs: the interaction graph determines who plays with whom in an evolutionary game; the replacement graph specifies the geometry of evolutionary competition and updating. First, we calculate the fixation probabilities of frequency dependent selection between two strategies or phenotypes. We consider three different update mechanisms: birth-death, death-birth and imitation. Then, as a particular example, we explore the evolution of cooperation. Suppose the interaction graph is a regular graph of degree h, the replacement graph is a regular graph of degree g and the overlap between the two graphs is a regular graph of degree l. We show that cooperation is favored by natural selection if b/c>hg/l. Here, b and c denote the benefit and cost of the altruistic act. This result holds for death-birth updating, weak-selection and large population size. Note that the optimum population structure for cooperators is given by maximum overlap between the interaction and the replacement graph (g=h=l), which means that the two graphs are identical. We also prove that a modified replicator equation can describe how the expected values of the frequencies of an arbitrary number of strategies change on replacement and interaction graphs: the two graphs induce a transformation of the payoff matrix.     

Risk Factors for Contamination of Hotel Water Distribution Systems by Legionella Species

The Legionella colonization frequency at 385 Greek hotel hot and cold water distribution systems was 20.8%. Legionella contamination was associated with the presence of an oil heater (odds ratio [OR] = 2.04, 95% confidence interval [CI] = 1.12 to 3.70), with the sample temperature (OR = 0.26, 95% CI = 0.1 to 0.5), with seasonal operation (OR = 3.23, 95% CI = 1.52 to 6.87), and with the presence of an independent disinfection system (OR = 0.30, 95% CI = 0.15 to 0.62). The same water temperatures, free-chlorine levels, and pHs differently affect the survival of various Legionella spp.     

Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind beta-secretase in a N-terminal 10s-loop down conformation

A series of low-molecular weight 2,6-diamino-isonicotinamide BACE-1 inhibitors containing an amine transition-state isostere were synthesized and shown to be highly potent in both enzymatic and cell-based assays. These inhibitors contain a trans-S,S-methyl cyclopropane P(3) which bind BACE-1 in a 10s-loop down conformation giving rise to highly potent compounds with favorable molecular weight and moderate to high susceptibility to P-glycoprotein (P-gp) efflux.     

Synthesis and in vitro evaluation of leishmanicidal and trypanocidal activities of N-quinolin-8-yl-arylsulfonamides

In the present paper 12 N-quinolin-8-yl-arylsulfonamides synthesized by coupling 8-aminoquinolines with various arylsulfonylchlorides were assayed in vitro against Leishmania amazonensis, Leishmania chagasi and Trypanosoma cruzi strains. This series of new compounds were found to be selective for Leishmania spp. promastigote and amastigote forms. The most active compound was the N-(8-quinolyl)-3,5-difluoro-benzenesulfonamide 10 with an IC₅₀ against L. amazonensis and L. chagasi of 2.12 and 0.45 μM, respectively. The less cytotoxic biphenyl derivative 7 was very effective against intracellular L. amazonensis with a reduction of macrophage cell infection of 82.1% at 25 μM. In addition, a copper complex 17 of an inactive ligand was readily synthesized and showed high leishmanicidal and trypanocidal activity against both extra and intracellular forms.