Reducing false-positive prediction of minimotifs with a genetic interaction filter

Background

Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists.

Methods and Findings

We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target protein pairs have a known genetic interaction. The HomoloGene genetic interaction filter extends these predictions to predicted genetic interactions of orthologous proteins and the node-based filter identifies those minimotifs where proteins that have a genetic interaction with the source or target have a genetic interaction. Each filter was evaluated with a test data set containing thousands of true and false-positives. Based on sensitivity and selectivity performance metrics, the basic filter had the best discrimination for true positives, whereas the node-based filter had the highest sensitivity. We have implemented these genetic interaction filters on the Minimotif Miner 2.3 website. The genetic interaction filter is particularly useful for improving predictions of posttranslational modifications such as phosphorylation and proteolytic cleavage sites.

Conclusions

Genetic interaction data sets can be used to reduce false-positive minimotif predictions. Minimotif prediction in known genetic interactions can help to refine the mechanisms behind the functional connection between genes revealed by genetic experimentation and screens.     

Achieving High Accuracy Prediction of Minimotifs

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network models. The minimotif multi-filter with its excellent accuracy represents the state-of-the-art in minimotif prediction and is expected to be very useful to biologists investigating protein function and how missense mutations cause disease.     

Harpellales in the digestive tracts of Ephemeroptera and Plecoptera nymphs from Veracruz, Mexico

This is the first report of Harpellales (Zygomycota) from Mexico, including herein only the endosymbiotic species of gut fungi in the digestive tracts or shed exuviae of Plecopteran and Ephemeropteran nymphs. Four new species are described: Allantomyces zopilotei, Bojamyces olmecensis, Gauthier-omyces viviparus and Graminella ophiuroidea. Among previously known Harpellales, Lancisporomyces nemouridarum and Zygopolaris ephemeridarum are southern range extremes and new records for Mexico. All species are illustrated and discussed relating to biogeographic implications of the new reports from Mexico, as well as the particular environmental circumstances of the Harpellales in the tropics.     

Production of cachexia mediators by Walker 256 cells from ascitic tumors

In neoplasic cachexia, chemical mediators seem to act as initiators or perpetuators of this process. Walker 256 cells, whose metabolic properties have so far been little studied with respect to cancer cachexia, are used as a model for the study of this syndrome. The main objective of this research was to pinpoint the substances secreted by these cells that may contribute to the progression of the cachectic state. Since inflammatory mediators seem to be involved in the manifestation of this syndrome, the in vitro production of nitric oxide (NO), cytokines (tumor necrosis factor alpha (TNF-alpha) and interleukin-6 (IL-6)), and prostaglandin E2 (PGE2) was evaluated in Walker 256 cells isolated from ascitic tumors. After 4 or 5 h, a significant increase in NO production was observed (2.55 +/- 1.56 and 4.05 +/- 1.99 nmol NO per 10(7) cells, respectively). When isolated from a 6-day-old tumor, a significantly lower production of IL-6 and higher production of TNF-alpha than in cells from a 4-day-old tumor were observed, indicating a relationship between the production of cytokines and the time of tumor development after implantation. Considerable production of PGE(2) by Walker 256 cells isolated from the 6-day-old tumor was also observed. Polyamines were also determined in Walker 256 cells. Levels of putrescine, spermidine, and spermine did not show significant differences in tumors developed during 4 or 6 days. Direct evidence of the release of proinflammatory cytokines and PGE2 by Walker 256 cells suggests that these mediators can drive the cachectic syndrome in the host, the effect being dependent on tumor development time.     

Ecto-Phosphorylation of CD98 Regulates Cell-Cell Interactions

Ecto-phosphorylation plays an important role in many cellular functions. The transmembrane glycoprotein CD98 contains potential phosphorylation sites in its extracellular C-terminal tail. We hypothesized that extracellular signaling through ecto-protein kinases (ePKs) might lead to ecto-phosphorylation of CD98 and influence its multiple functions, including its role in cell-cell interactions. Our results show that recombinant CD98 was phosphorylated in vitro by ePKs from Jurkat cells and by the commercial casein kinase 2 (CK2). Alanine substitutions at serines-305/307/309 or serines-426/430 attenuated CK2-mediated CD98 phosphorylation, suggesting that these residues are the dominant phosphorylation sites for CK2. Furthermore, CD98 expressed in the basolateral membranes of intestinal epithelial Caco2-BBE cells was ecto-phosphorylated by Jurkat cell-derived ePKs and ecto-CK2 was involved in this process. Importantly, cell attachment studies showed that the ecto-phosphorylation of CD98 enhanced heterotypic cell-cell interactions and that the extracellular domain of CD98, which possesses the serine phosphorylation sites, was crucial for this effect. In addition, phosphorylation of recombinant CD98 increased its interactions with Jurkat and Caco2-BBE cells, and promoted cell attachment and spreading. In conclusion, here we demonstrated the ecto-phosphorylation of CD98 by ePKs and its functional importance in cell-cell interactions. Our findings reveal a novel mechanism involved in regulating the multiple functions of CD98 and raise CD98 as a promising target for therapeutic modulations of cell-cell interactions.     

Classification of antituberculosis herbs for remedial purposes by using fuzzy sets

Using fuzzy set theory, we created a system, that assesses a herb's usefulness for the treatment of tuberculosis, based on ethnobotanical data. We analysed two systems which contain different amount of inputs. The first system contains four inputs, the second one contains six inputs. We used the Takagi-Sugeno-Kanga model. Mamdani model is poor at representation as it needs more fuzzy rules than that of TSK to model a real world system where accuracy is demanded. It has been employed a fuzzy controller, and a fuzzy model, in successfully solving difficult control and modelling problems in practice. It is implemented in the Fuzzy Logic Toolbox in Matlab. The data for inputs are gathered in the database named SOPAT (selection of plants against tuberculosis), which is part of a project coordinated by the Oxford International Biomedical Centre. In this database there could be up to one million plant species. It would be cumbersome to select a remedy from one (or some) of these species looking at the data base one-by-one. By means of the fuzzy set theory this remedy can be chosen very quickly.     

Meiotic Structures in the Animal-Parasitic Nematode Ascaris megalocephala: Synaptonemal Complexes,Recombination Nodules,and Centrioles

Two synaptonemal complexes (SCs) were present in the pachytene nuclei of Ascaris megalocephala. The SC was tripartite and comprised of two lateral elements (25 nm) with a striated central element (25 nm) and a central region of 65 nm. Spherical recombination nodules were observed to be associated only with the central element, although they are non-existent in the related A. lumbricoides var. suum (Goldstein, 1977). The SCs were attached to the nuclear envelope at only one end, while the other end was free in the nucleoplasm. This lack of bouquet formation of the chromosomes is consistent with all other nematodes studied. Morphologically distinct sex chromosomes were not observed, which differs from the presence of five Y-chromosomes present in A. lumbricoides var. suum (Goldstein and Moens, 1976). Centrioles (0.2 µm wide) reproduced by budding off the parental centriole. The centrioles consisted of nine singlet microtubules connected by an electron-dense proteinaceous ring. This structure is consistent with centrioles described in other nematodes, yet distinctly different from the centriole structure observed in most organisms in which it consists of nine triplet microtubules without any connecting ring. Multiple synaptonemal complexes, or polycomplexes, are found in A. megalocephala and A. lumbriocoides var. suum. They appear as stacked SC and are present inside the nucleus during zygotene and in the cytoplasm at pachytene.