Analysing covariates with spike at zero: A modified FP procedure and conceptual issues

In epidemiology and in clinical research, risk factors often have special distributions. A common situation is that a proportion of individuals have exposure zero, and among those exposed, we have some continuous distribution. We call this a ‘spike at zero’. Examples for this are smoking, duration of breastfeeding, or alcohol consumption. Furthermore, the empirical distribution of laboratory values and other measurements may have a semi‐continuous distribution as a result of the lower detection limit of the measurement. To model the dose–response function, an extension of the fractional polynomial approach was recently proposed. In this paper, we suggest a modification of the previously suggested FP procedure. We first give the theoretical justification of this modified procedure by investigating relevant distribution classes. Here, we systematically derive the theoretical shapes of dose–response curves under given distributional assumptions (normal, log normal, gamma) in the framework of a logistic regression model. Further, we check the performance of the procedure in a simulation study and compare it to the previously suggested method, and finally we illustrate the procedures with data from a case–control study on breast cancer.     

Host plant effects on the functional response of Stethorus gilvifrons to strawberry spider mites

The functional response of adult females of the coccinellid beetle Stethorus gilvifrons Mulsant to juveniles of strawberry spider mite, Tetranychus turkestani Ugarov & Nikolski was determined on cowpea, castor bean and cucumber leaves in the laboratory at 25°C and a 14 h L: 10 h D photoperiod. Beetles were isolated singly for 24 h in 9-cm Petri dishes with either 2, 4, 8, 16, 32, 64, or 128 nymphal stages of T. turkestani. Results showed a typical type II response on all plants tested, with up to 110.7, 100.8, and 53.0 prey attacked when 128 nymphal stages were provided on cowpea, castor bean, and cucumber leaves, respectively. Based on the Rogers random attack equation, the highest estimated attack rate and the lowest handling time were obtained on cowpea. It was therefore concluded that the host plant species can affect the predation rate and functional response components of S. gilvifrons, a specific and effective predator of spider mites.     

Molecular classification of scrapie strains in mice using gene expression profiling

Transmissible spongiform encephalopathy strains demonstrate specific prion characteristics, each with specific incubation times, and strain-specific patterns of deposition of the misfolded isoform of prion, PrPSc, in the brains of infected individuals. Different biochemical properties, including glycosylation profiles and the degree of proteinase resistance, have been shown to be strain-specific. However, no relationship between these properties and the phenotypic differences in the subsequent diseases has as yet been determined. Here we explore the utility of gene expression profiles to identify differences in the host response to different strains of prion agent. We identify 114 genes that exhibit significantly different levels of expression in mice infected with three strains of scrapie. These genes represent a pool of genes involved in a strain-specific response to prion disease. We have identified the most discriminatory genes from this list utilizing a wrapper-based feature selection algorithm with external cross-validation.     

The habitat disruption induces immune-suppression and oxidative stress in honey bees

The honey bee is a major insect used for pollination of many commercial crops worldwide. Although the use of honey bees for pollination can disrupt the habitat, the effects on their physiology have never been determined. Recently, honey bee colonies have often collapsed when introduced in greenhouses for pollination in Japan. Thus, suppressing colony collapses and maintaining the number of worker bees in the colonies is essential for successful long-term pollination in greenhouses and recycling of honey bee colonies. To understand the physiological states of honey bees used for long-term pollination in greenhouses, we characterized their gene expression profiles by microarray. We found that the greenhouse environment changes the gene expression profiles and induces immune-suppression and oxidative stress in honey bees. In fact, the increase of the number of Nosema microsporidia and protein carbonyl content was observed in honey bees during pollination in greenhouses. Thus, honey bee colonies are likely to collapse during pollination in greenhouses when heavily infested with pathogens. Degradation of honey bee habitat by changing the outside environment of the colony, during pollination services for example, imposes negative impacts on honey bees. Thus, worldwide use of honey bees for crop pollination in general could be one of reasons for the decline of managed honey bee colonies.     

Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time

 The vernalization gene Vrn-A1 on chromosome 5A is the predominant gene determining the spring/winter habit difference in bread wheat. Vrn-A1 was physically mapped using a set of deletion lines which located it to the region of chromosome 5A flanked by deletion breakpoints 0.68 and 0.78. This interval was shown to be homoeologous to a region of rice chromosome 3 that contains the flowering-time QTL Hd-6, previously mapped in a Nipponbare×Kasalath cross, and FLTQ1, a novel QTL identified by analysis of 78 F₃ families derived from a cross of ‘IR20’ב63–83’. Possible relationships between Vrn-A1 and rice QTL are discussed. Analysis of the chromosome 5A deletion lines showed evidence for a second, more proximal flowering-time effect located between deletion breakpoints 0.56 and 0.64. The proximal part of chromosome 5A is homoeologous to rice chromosome 9, on which two QTL were detected in the ‘IR20ב63–83’ cross. The possible relationship between these effects is also discussed. Received: 23 December 1997 / Accepted: 12 January 1998     

Xanthomonas campestris sensor kinase HpaS co-opts the orphan response regulator VemR to form a branched two-component system that regulates motility

Xanthomonas campestris pv. campestris (Xcc) controls virulence and plant infection mechanisms via the activity of the sensor kinase and response regulator pair HpaS/hypersensitive response and pathogenicity G (HrpG). Detailed analysis of the regulatory role of HpaS has suggested the occurrence of further regulators besides HrpG. Here we used in vitro and in vivo approaches to identify the orphan response regulator VemR as another partner of HpaS and to characterize relevant interactions between components of this signalling system. Bacterial two-hybrid and protein pull-down assays revealed that HpaS physically interacts with VemR. Phos-tag SDS-PAGE analysis showed that mutation in hpaS reduced markedly the phosphorylation of VemR in vivo. Mutation analysis reveals that HpaS and VemR contribute to the regulation of motility and this relationship appears to be epistatic. Additionally, we show that VemR control of Xcc motility is due in part to its ability to interact and bind to the flagellum rotor protein FliM. Taken together, the findings describe the unrecognized regulatory role of sensor kinase HpaS and orphan response regulator VemR in the control of motility in Xcc and contribute to the understanding of the complex regulatory mechanisms used by Xcc during plant infection.     

Potential cotton aphid,Aphis gossypii,population suppression by arthropod predators in upland cotton

The cotton aphid, Aphis gossypii Glover, predation rate of convergent lady beetle, Hippodamia convergens Guerin‐Meneville, was determined by assigning a single predator randomly to each of four prey density treatments in the laboratory. Prey densities included 25, 50, 100, and 200 aphids per Petri dish arena. Predation response was recorded at 1, 4, 8, 16, 24, and 48 h after assigning predators to their prey treatments. Rate of consumption increased through time, with all 25 aphids consumed during the first 4 h of the experiment. At the highest density, adult lady beetle consumed on average 49, 99, 131, 163, 183, and 200 aphids within 1, 4, 8, 16, 24 and 48 h, respectively. Predators showed a curvilinear feeding response in relation to total available time, indicating that convergent lady beetles have the potential to suppress larger populations of aphids through continuous feeding by regulating their predation efficiency during feeding. The analysis of age‐specific mortality in absence of prey revealed that lady beetles could survive for an extended period of time (more than 2 weeks) without prey. The ability of a predator to survive without prey delays or prevents the rebound of pest populations that is a significant factor in natural biological control. A two‐year field sampling of 10 cotton arthropod predator species showed that spiders (27%) were the most dominant foliage dwelling predators in the Texas High Plains cotton followed by convergent lady beetles (23.5%), hooded beetles (13.5%), minute pirate bugs (11%), green lacewings (9.5%), bigeyed bugs (7.5%), scymnus beetles (3%), soft‐winged flower beetles (2%), damsel bugs (1.5%), and assassin bugs (1.5%). A field cage study showed that one H. convergens adult per plant released at prey density of one aphid per leaf kept the aphid population below economic threshold for the entire growing season.     

Effects of UV-B on motility and photobehavior in the green flagellate,Euglena gracilis

UV-B inhibits the motility of the green flagellate, Euglena gracilis, at fluences rates higher than those expected to occur in the natural sunlight even when the stratospheric ozone layer is partially reduced by manmade pollutants. The phototactic orientation of the cells, however, is drastically impaired by only slightly enhanced levels of UV-B irradiation. Since only negative phototaxis (movement away from a strong light source) is impaired while positive phototaxis (movement toward a weak light source) is not, the delicate balance by which the organisms adjust their position in their habitat is disturbed. Under these conditions the cells are unable to retreat from hazardous levels of radiation and are eventually killed not by the UV-B irradiation but by photobleaching of their photosynthetic pigments in the strong daylight at the surface.