Dothideales

The type specimens or representative specimens of the potentially dothidealean genera Bagnisiella, Botryochora, Coccostromella, Columnosphaeria, Delphinella, Dictyodothis, Discosphaerina, Dothidea, Dothiora, Endodothiora, Jaffuela, Mycoporis, Omphalospora, Pachysacca, Plowrightia, Saccothecium, Stylodothis, Sydowia and Yoshinagaia were examined while, fresh specimens of Aureobasidium pullulans, Dothidea insculpta, Plowrightia ribesia and Saccothecium sepincola were made from Italy and Thailand. An introduction and the history of these genera, their family placement, morphology, and molecular phylogeny are provided. Morphology plus GenBank data are used to provide a systematic treatment of Dothideales. Phylogenetic analysis of LSU, SSU and ITS gene regions was carried out and in the resulting phylogenetic tree the taxa cluster in two clades with high bootstrap support. Clade A comprises Dothideaceae, the family type of Dothideales. The family Dothioraceae is not recognized as a distinct family and is synonymized under Dothideaceae. Neocylindroseptoria is introduced to accommodate Cylindroseptoria pistaciae as it forms a well-supported distinct clade in Dothideaceae. Clade B comprises Aureobasidium, Kabatiella, Pseudoseptoria, Saccothecium and Selenophoma species and Columnosphaeria fagi, for which we propose a new family, Aureobasidiaceae. The recently introduced Sydowia eucalypti also clustered within Clade B and therefore based on morphology and molecular phylogeny a new genus Pseudosydowia is introduced for Sydowia eucalypti. Celosporium laricicola is separated in a distinct clade, and therefore it is placed in Dothideales, genera, incertae sedis. The genera Bagnisiella, Botryochora, Coccostromella, Jaffuela, Lucidascocarpa, Mycoporis, Omphalospora, Pachysacca and Yoshinagaia are excluded from Dothideales and their placements are discussed.     

Trichomeriaceae, a new sooty mould family of Chaetothyriales

Trichomerium is a genus of foliar epiphytes with the appearance of sooty moulds, mostly occurring on the surface of living leaves and apparently gaining their nutrients from insect exudates. Species have ascostromata with setae and develop on a loosely interwoven mycelial mass of dark brown hyphae, while asci have a bitunicate appearance with hyaline ascospores. In this study, we made 16 collections of Trichomerium from Thailand. All were isolated, and the LSU and ITS rDNA gene regions sequenced. Phylogenetic analysis indicated that the Trichomerium species form a monophyletic clade within Chaetothyriales and warrant the introduction of a new family Trichomeriaceae. Bootstrap support for the Chaetothyriales is 100?% and clearly separates Trichomeriaceae from Capnodiales which are morphologically very similar. A detailed account of Trichomerium is provided and we describe and illustrate three new species based on morphological and molecular data. We propose that T. foliicola is adopted as the generic type of Trichomerium because it has been impossible to obtain the holotype specimen of T. coffeicola and also no molecular data exists in worldwide databases for this species or genus.     

Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach

Emergence of drug resistance remains one of the most challenging issues in the treatment of HIV-1 infection. Here we focus on resistance to HIV-1 protease inhibitors (PIs) at a molecular level, which can be analysed genotypically or phenotypically. Genotypic assays are based on the analysis of mutations associated with reduced drug susceptibility, but are problematic because of the numerous mutations and mutational patterns that confer drug resistance. Phenotypic resistance or susceptibility can be experimentally evaluated by measuring the amount of free drug bound to HIV-1 protease molecules, but this procedure is expensive and time-consuming. To overcome these problems, we have developed a docking protocol that takes protein-inhibitor flexibility into account to predict phenotypic drug resistance. For six FDA-approved Pls and a total of 1792 HIV-1 protease sequence mutants, we used a combination of inhibitor flexible docking and molecular dynamics (MD) simulations to calculate protein-inhibitor binding energies. Prediction results were expressed as fold changes of the calculated inhibitory constant (Ki), and the samples predicted to have fold-increase in calculated Ki above the fixed cut-off were defined as drug resistant. Our combined docking and MD protocol achieved accuracies ranging from 72-83% in predicting resistance/susceptibility for five of the six drugs evaluated. Evaluating the method only on samples where our predictions concurred with established knowledge-based methods resulted in increased accuracies of 83-94% for the six drugs. The results suggest that a physics-based approach, which is readily applicable to any novel PI and/or mutant, can be used judiciously with knowledge-based approaches that require experimental training data to devise accurate models of HIV-1 Pl resistance prediction.     

Public familiarity with,knowledge of,and predictors of negative attitudes toward epilepsy in Thailand

The purpose of this nationwide survey was to assess familiarity with and knowledge of epilepsy, as well as to identify predictors of negative attitudes toward people with epilepsy, in Thailand. Of the 1581 people interviewed, 80.8% were familiar with the word epilepsy, but few knew anyone with the condition. The main reason given for avoiding helping a seizure victim was a lack of proper first-aid knowledge, not a negative attitude toward the person. The factors predicting negative attitudes in the Thai population were low educational level, unfamiliarity with epilepsy, and the misconception that epilepsy is a form of insanity. Different from most previous studies worldwide, the attitudes of friends and parents toward people with epilepsy were strongly positive. Social awareness of the public organization Epilepsy Society of Thailand was low; only 4.6% of the respondents knew about it. These data should be considered in a nationwide strategy to alleviate social discrimination against people with epilepsy.