MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study

Background  

The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quantify the importance of multi-SNP interactions, few of them could handle the genome wide data due to the combinatorial explosive search space and the difficulty to statistically evaluate the high-order interactions given limited samples.     

Diversity of lactic acid bacteria of the bioethanol process

Background  

Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil.     

Examination of the Cytotoxic and Embryotoxic Potential and Underlying Mechanisms of Next-Generation Synthetic Trioxolane and Tetraoxane Antimalarials

Semisynthetic artemisinin-based therapies are the first-line treatment for P. falciparum malaria, but next-generation synthetic drug candidates are urgently required to improve availability and respond to the emergence of artemisinin-resistant parasites. Artemisinins are embryotoxic in animal models and induce apoptosis in sensitive mammalian cells. Understanding the cytotoxic propensities of antimalarial drug candidates is crucial to their successful development and utilization. Here, we demonstrate that, similarly to the model artemisinin artesunate (ARS), a synthetic tetraoxane drug candidate (RKA182) and a trioxolane equivalent (FBEG100) induce embryotoxicity and depletion of primitive erythroblasts in a rodent model. We also show that RKA182, FBEG100 and ARS are cytotoxic toward a panel of established and primary human cell lines, with caspase-dependent apoptosis and caspase-independent necrosis underlying the induction of cell death. Although the toxic effects of RKA182 and FBEG100 proceed more rapidly and are relatively less cell-selective than that of ARS, all three compounds are shown to be dependent upon heme, iron and oxidative stress for their ability to induce cell death. However, in contrast to previously studied artemisinins, the toxicity of RKA182 and FBEG100 is shown to be independent of general chemical decomposition. Although tetraoxanes and trioxolanes have shown promise as next-generation antimalarials, the data described here indicate that adverse effects associated with artemisinins, including embryotoxicity, cannot be ruled out with these novel compounds, and a full understanding of their toxicological actions will be central to the continuing design and development of safe and effective drug candidates which could prove important in the fight against malaria.     

Photosynthetic parameters of birch (Betula pendula Roth) leaves growing in normal and in CO2- and O3- enriched atmospheres

Two silver birch (Betula pendula Roth) clones K1659 and V5952 were grown in open‐top chambers over 3 years (age 7–9 years). The treatments were increased CO₂ concentration (+CO₂, 72 Pa), increased O₃ concentration (+O₃, 2 × ambient O₃ with seasonal AOT40 up to 28 p.p.m. h) and in combination (+CO₂ + O₃). Thirty‐seven photosynthetic parameters were measured in the laboratory immediately after excising leaves using a computer‐operated routine of gas exchange and optical measurements. In control leaves the photosynthetic parameters were close to the values widely used in a model (Farquhar, von Caemmerer and Berry, Planta 149, 78–90, 1980). The distribution of chlorophyll between photosystem II and photosystem I, intrinsic quantum yield of electron transport, uncoupled turnover rate of Cyt b₆f, Rubisco specificity and K_m (CO₂) were not influenced by treatments. Net photosynthetic rate responded to +CO₂ with a mean increase of 17% in both clones. Dry weight of leaves increased, whereas protein, especially Rubisco content and the related photosynthetic parameters decreased. Averaged over 3 years, eight and 17 mechanistically independent parameters were significantly influenced by the elevated CO₂ in clones K1659 and V5952, respectively. The elevated O₃ caused a significant decrease in the average photosynthetic rate of clone V5952, but not of clone K1659. The treatment caused changes in one parameter of clone K1659 and in 11 parameters of clone V5952. Results of the combined treatment indicated that +O₃ had less effect in the presence of +CO₂ than alone. Interestingly, changes in the same photosynthetic parameters were observed in chamberless grown trees of clone V5952 as under +O₃ treatment in chambers, but this was not observed for clone K1659. These results suggest that during chronic fumigation, at concentrations below the threshold of visible leaf injuries, ozone influenced the photosynthetic parameters as a general stress factor, in a similar manner to weather conditions that were more stressful outside the chambers. According to this hypothesis, the sensitivity of a species or a clone to ozone is expected to depend on the growth conditions: the plant is less sensitive to ozone if the conditions are close to optimal and it is more sensitive to ozone under conditions of stress.     

Effects of wax bloom variation in Brassica oleracea on foraging by a vespid wasp

Foraging by individual Polistes dominulus (Christ) (Hymenoptera: Vespidae) was observed and compared on Brassica oleracea L. plants that differed in surface wax bloom. Twenty-six wasps, previously trained to forage on plants for 4th instar Trichoplusia ni (Walker), were presented in the greenhouse with mixtures of plants with normal wax bloom or genetically reduced wax bloom, and on which T. ni caterpillars had been placed. During foraging, the wasps were observed to slip significantly more frequently from the leaf surfaces of normal-wax bloom plants than from reduced-wax bloom plants (129 vs 63 occurrences) and to retrieve significantly fewer pieces of caterpillar after attack on normal-wax bloom plants (151 vs 223 pieces). Altogether the wasps retrieved 333 caterpillar pieces from reduced-wax bloom plants and 248 pieces from normal-wax bloom plants. Despite these differences, the number of caterpillars attacked and killed did not differ between the two wax bloom types (116 vs 121), nor did handling time for individual attacks (time from contact with prey until prey piece was carried to the nest) (170±12.5 s vs 180±10.5 s). Thus, in contrast with previous reports for smaller predators, wax bloom variation in B. oleracea did not influence the effectiveness of P. dominulus as a predator of T. ni.     

Activation of morphogenesis and proliferation by low specificity chemical effectors

Activation of highly specific biochemical processes by simple chemical agents is demonstrated for morphogenesis (anlage and development of female gametophyte in cereal) and mitosis (in cell cultures and animal and plant tissues). The effects of these agents are tissue-specific. Structure--activity relationship is analyzed in this group of compounds. Thus, the phenomenon reveals the exact pathways of the influence of allelopathic and anthropogenic chemical agents on evolution of plant biocenoses.     

Ontogenetic shifts within the selfish herd: predation risk and foraging trade-offs change with age in colonial web-building spiders

We tested for the existence of density dependence in annual adult rangeland grasshopper (Orthoptera: Acrididae) data from Montana, USA (1951–1991). Statistical density dependence was, in the sense of a stochastic equilibrium or return tendency, detected in all of the grasshopper mean density time-series from the three major physiographic regions of the state, Northern Glaciated Plains, Southern Unglaciated Plains, and Western Mountains. Parameters were estimated for a model that described the stochastic equilibrium characteristics of regional mean densities. The analyses showed that rangeland grasshopper regional densities fluctuate according to gamma distribution with a mean of 6.1–6.3 grasshoppers per m². Further, when regions exhibit outbreaks, the resulting infestation period (duration of outbreak) is short, spanning only a few generations.     

Relative accuracy of spatial predictive models for lynx Lynx canadensis derived using logistic regression-AIC,multiple criteria evaluation and Bayesian approaches

We compared probability surfaces derived using one set of environmental variables in three Geographic Information Systems (GIS) -based approaches: logistic regression and Akaike's Information Criterion (AIC),Multiple Criteria Evaluation (MCE),and Bayesian Analysis (specifically Dempster-Shafer theory). We used lynx Lynx canadensis as our focal species,and developed our environment relationship model using track data collected in Banff National Park,Alberta,Canada,during winters from 1997 to 2000. The accuracy of the three spatial models were compared using a contingency table method. We determined the percentage of cases in which both presence and absence points were correctly classified (overall accuracy),the failure to predict a species where it occurred (omission error) and the prediction of presence where there was absence (commission error). Our overall accuracy showed the logistic regression approach was the most accurate (74.51% ). The multiple criteria evaluation was intermediate (39.22%),while the Dempster-Shafer (D-S) theory model was the poorest (29.90%). However,omission and commission error tell us a different story: logistic regression had the lowest commission error,while D-S theory produced the lowest omission error. Our results provide evidence that habitat modellers should evaluate all three error measures when ascribing confidence in their model. We suggest that for our study area at least,the logistic regression model is optimal. However,where sample size is small or the species is very rare,it may also be useful to explore and/or use a more ecologically cautious modelling approach (e.g. Dempster-Shafer) that would over-predict,protect more sites,and thereby minimize the risk of missing critical habitat in conservation plans.     

Age-related sequential web building in the colonial spider Metepeira incrassata (Araneidae): an adaptive spacing strategy

Colonial orb-weaving spiders provide insight into the proximate mechanisms by which social animals space themselves within a group. We examined mechanisms for the temporal patterns of web building that determine individual positions in Metepeira incrassata (Araneidae) colonies. The spiders display a characteristic age-related sequence of daily web building, with larger spiders completing their webs significantly earlier than smaller ones. We used data on behavioural interactions, web building, prey capture and predator attacks to evaluate four hypotheses. (1) Larger spiders are better competitors and pre-empt optimal spatial positions. (2) Smaller spiders reduce competition with larger individuals by building webs later. (3) Prey captured by different size classes is available at different times. (4) Differential predation risk determines web-building times. Large individuals dominated behavioural interactions. Disturbances by larger spiders during web construction significantly delayed the completion of smaller individuals' webs and precipitated movements to new web sites. One prediction of the first hypothesis, that spatial needs translate into earlier building, was confirmed by significantly earlier web building by mature females with egg sacs (which are unable to move their egg sacs) compared with same-sized females without eggs (which can change locations freely). Experiments to determine whether the presence of large spiders inhibited the web building of smaller individuals were equivocal. Prey availability and risk of predation are not factors affecting web-building patterns. Sequential web building appears to be a result of both larger spiders competing to pre-empt space from one another and smaller individuals attempting to reduce conflict during web construction. Sequential web building is a proximate mechanism that influences spacing among colonial orb-weaving spiders and helps shape the typical hierarchical size distribution of spiders within the colony. Similar spacing mechanisms may be seen in colonial birds and marine invertebrates. Copyright 2000 The Association for the Study of Animal Behaviour.