Target highlights in CASP13: Experimental target structures through the eyes of their authors

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.     

Hormone sensitivity and plant adaptations to flooding

Plant hormones play a key role as mediators between environmental signals and adaptive plant responses. Auxin, ethylene and gibberellins are involved in the initiation of adaptive plant responses such as the development of adventitious roots and stimulated shoot elongation upon flooded conditions. These adaptive plastic responses in plants are frequently linked to changes in the concentrations of the hormones involved, but only rarely to shifts in sensitivity. Examples from ecophysiological research performed with species from the genusRumex demonstrate the importance of the hormone sensitivity concept in plant adaptations to flooding: (a)Rumex species can be grouped into three response categories according to the ethylene sensitivity of the youngest petioles: positive, negative and indifferent; (b) Sub-ambient oxygen concentrations sensitize petioles of wetlandRumex species to ethylene; (c) Enhanced ethylene levels sensitize petioles of wetlandRumex species to gibberellin; (d) Auxin is the primary plant hormone responsible for the initiation of adventitious roots in wetlandRumex species. However, a factor related to waterlogging, possibly ethylene, is required to sensitize the root-shoot junction to endogenous auxin.     

Analysis of copia sequence variation within and between Drosophila species

The sequences of the 5' long-terminal repeat (LTR) and adjacent leader regions of 27 full-length copia elements isolated from natural populations of Drosophila melanogaster, D. simulans, and D. mauritiana are presented. Phylogenetic analyses indicate that although D. melanogaster copia elements are distinct from those of D. simulans and D. mauritiana, the elements of these latter two species are not distinguishable from one another. LTRs and adjacent 5' leader regions of elements isolated from D. simulans and D. mauritiana are structurally similar to one another and carry substantial deletional variation mapping to regions previously identified as being of potential importance for copia expression.      

Predicting breast cancer using an expression values weighted clinical classifier

Background

Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. To improve clinical management, these data should be fully exploited. This requires efficient algorithms to integrate these data sets and design a final classifier.LS-SVM classifiers and generalized eigenvalue/singular value decompositions are successfully used in many bioinformatics applications for prediction tasks. While bringing up the benefits of these two techniques, we propose a machine learning approach, a weighted LS-SVM classifier to integrate two data sources: microarray and clinical parameters.

Results

We compared and evaluated the proposed methods on five breast cancer case studies. Compared to LS-SVM classifier on individual data sets, generalized eigenvalue decomposition (GEVD) and kernel GEVD, the proposed weighted LS-SVM classifier offers good prediction performance, in terms of test area under ROC Curve (AUC), on all breast cancer case studies.

Conclusions

Thus a clinical classifier weighted with microarray data set results in significantly improved diagnosis, prognosis and prediction responses to therapy. The proposed model has been shown as a promising mathematical framework in both data fusion and non-linear classification problems.     

Ethylene Biosynthesis and Accumulation under Drained and Submerged Conditions (A Comparative Study of Two Rumex Species)

A model is presented of the regulation of ethylene biosynthesis in relation to submergence and flooding resistance. It is based on time-course measurements of ethylene production, ethylene accumulation, and concentrations of free and conjugated 1-aminocyclo-propane-1-carboxylic acid (ACC) in submerged and drained flooding-resistant Rumex palustris Sm. and flooding-sensitive Rumex acetosella L. plants. From these data, in vivo reaction rates of the final steps in the ethylene biosynthetic pathway were calculated. According to our model, submergence stimulates ACC formation and inhibits conversion of ACC to ethylene in both Rumex species, and as a result, ACC accumulates. This may explain the stimulated ACC conjugation observed in submerged plants. Although submergence inhibited ethylene production, physical entrapment increased endogenous ethylene concentrations in both flooding-resistant R. palustris and flooding-sensitive R. acetosella plants. However, R. palustris plants controlled their internal ethylene levels in the long term by a negative regulation of ACC synthase induced by ethylene. In flooding-sensitive R. acetosella plants, absence of negative regulation increased internal ethylene levels to more than 20 [mu]L L-1 after 6 d of submergence. This may accelerate the process of senescence and contribute to their low level of flooding resistance.     

Iodination by stimulated human neutrophils. Studies on its stoichiometry, subcellular localization and relevance to microbial killing

Myeloperoxidase of phagocytic leucocytes is thought to utilize H2O2 to oxidize halides, which then react with and kill ingested microbes. This hypothesis was based largely on the incorporation of radiolabelled iodide into cells that had phagocytosed bacteria. The present studies investigated the stoichiometry of these reactions and the subcellular localization and electrophoretic pattern of the cellular components that became iodinated. 1. The stoichiometry of the reactions are such that only a small proportion (less than 0.3%) of the total oxygen consumed is utilized for iodination. Iodination after stimulation with the soluble stimulus phorbol myristate acetate (PMA), which is not known to involve the azurophil granules and their contained myeloperoxidase, was comparable with that occurring after bacterial ingestion. 2. Analytical subcellular fractionation of cells that had phagocytosed bacteria localized about 25% of the radioactivity to the membranes, and most of the residual radioactivity distributed with the bacteria and dense granules. In cells stimulated with PMA, more of the radioactivity was associated with the membranes, but about half was still associated with the dense granules. 3. Autoradiographs after dodecyl sulphate/polyacrylamide-gel electrophoresis of cells stimulated with opsonized bacteria gave a similar distribution of iodinated components to that obtained with cells that had been stimulated with PMA or iodinated with Iodogen. These patterns of iodination were very different from those obtained when bacteria alone were iodinated with Iodogen or myeloperoxidase and H2O2. Preparations in which bacteria had been phagocytosed did not show evidence of iodination of bacterial proteins or coating opsonins. Thus positive evidence for the iodination of bacteria has not been produced, and the role of iodination in the microbicidal process of neutrophils remains to be established.     

Stage specific reprogramming of mouse embryo liver cells to a beta cell-like phenotype

We show that cultures of mouse embryo liver generate insulin-positive cells when transduced with an adenoviral vector encoding the three genes: Pdx1, Ngn3 and MafA (Ad-PNM). Only a proportion of transduced cells become insulin-positive and the highest yield occurs in the period E14–16, declining at later stages. Insulin-positive cells do not divide further although they can persist for several weeks. RT-PCR analysis of their gene expression shows the upregulation of a whole battery of genes characteristic of beta cells including upregulation of the endogenous counterparts of the input genes. Other features, including a relatively low insulin content, the expression of genes for other pancreatic hormones, and the fact that insulin secretion is not glucose-sensitive, indicate that the insulin-positive cells remain immature. The origin of the insulin-positive cells is established both by co-immunostaining for α-fetoprotein and albumin, and by lineage tracing for Sox9, which is expressed in the ductal plate cells giving rise to biliary epithelium. This shows that the majority of insulin-positive cells arise from hepatoblasts with a minority from the ductal plate cells.