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.     

Regulation and activity of JNK signaling in the wing disc peripodial membrane during adult morphogenesis in Drosophila

Thorax closure in Drosophila is a process during adult morphogenesis in which the anterior ends of the presumptive notum of the two wing imaginal discs fuse to make a seamless thorax. Similar to dorsal closure during embryogenesis, this process is regulated by plegic and JNK signaling pathways. Despite the fact that Peripodial Membrane (PM) cells do not contribute to the formation of any adult structure, they are known to facilitate the process of thorax closure. Here we show that JNK signaling is activated only in a subset of PM cells, known as medial edge cells. While the mechanism that activates JNK signaling specifically in the medial edge cells of the PM is still not understood, the results presented here show that the pair rule gene odd skipped is required to ensure that JNK signaling is not activated anywhere else in the wing disc. Medial edge cells of the PM are elongated in shape, while the remaining PM cells are hexagonal. Down regulation of JNK signaling in the medial edge cells results in defective thorax closure in adult flies. It also causes the transformation of the morphology of medial edge cells into hexagonal shape. Conversely, activation of JNK signaling in hexagonal cells of the PM causes transformation of their morphology to elongated shape. Thus, similar to dorsal closure during embryogenesis, JNK-mediated elongation of medial edge cells is functionally correlated to the process of thorax closure.     

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.     

Novel delta2-isoxazolines as group II phospholipase A2 inhibitors

The synthesized imidazolyl substituted delta2-isoxazolines were subjected to Phospholipase A(2) (PLA(2)) enzyme inhibitory activity against snake venom source and their structure-activity relationship with respect to different groups attached to this moiety is reported for the first time. The crystal structure of the compound 2-butyl-5-chloro-3H-imidazolyl-4-carbaldehyde oxime 2, an intermediate for the construction of isoxazolines is reported. These compounds exerted a significant PLA(2) enzyme inhibitory activity against group II PLA(2). The in vivo activity on mice of selected compounds 3bI and 3bIV shows the comparable anti-inflammatory activity with the known standard ursolic acid.     

Negative regulation ofUltrabithorax expression byengrailed is required for proper specification of wing development inDrosophila melanogaster

In both vertebrates and invertebrates, homeotic selector genes confer morphological differences along the antero-posterior axis. However, insect wing development is independent of all homeotic gene functions, reflecting the ground plan of an ancestral pterygote, which bore wings on all segments. Dipteran insects such asDrosophila are characterized by a pair of wings in the mesothoracic segment. In all other segments, wing development is essentially repressed by different homeotic genes, although in the metathorax they are modified into a pair of halteres. This necessitates that during development all homeotic genes are to be maintained in a repressed state in wing imaginal discs. In this report we show that (i) the function of the segment polarity geneengrailed (en) is critical to keep the homeotic selector geneUltrabithorax (Ubx) repressed in wing imaginal discs, (ii) normal levels of En in the posterior compartment of haltere discs, however, are not enough to completely repressUbx, and (iii) the repression ofUbx byen is independent of Hedgehog signalling through which the long-range signalling ofen is mediated during wing development. Finally we provide evidence for a possible mechanism by whichen repressesUbx. On the basis of these results we propose thaten has acquired two independent functions during the evolution of dorsal appendages. In addition to its well-known function of conferring posterior fate and inducing long-range signalling to pattern the developing appendages, it maintains wing fate by keepingUbx repressed.