Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota).

The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.

Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Certain trypanosomatids co-evolve with an endosymbiotic bacterium in a mutualistic relationship that is characterized by intense metabolic exchanges. Symbionts were able to respire for up to 4 h after isolation from Angomonas deanei. FCCP (carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone) similarly increased respiration in wild-type and aposymbiotic protozoa, though a higher maximal O2 consumption capacity was observed in the symbiont-containing cells. Rotenone, a complex I inhibitor, did not affect A. deanei respiration, whereas TTFA (thenoyltrifluoroacetone), a complex II activity inhibitor, completely blocked respiration in both strains. Antimycin A and cyanide, inhibitors of complexes III and IV, respectively, abolished O2 consumption, but the aposymbiotic protozoa were more sensitive to both compounds. Oligomycin did not affect cell respiration, whereas carboxyatractyloside (CAT), an inhibitor of the ADP-ATP translocator, slightly reduced O2 consumption. In the A. deanei genome, sequences encoding most proteins of the respiratory chain are present. The symbiont genome lost part of the electron transport system (ETS), but complex I, a cytochrome d oxidase, and FoF1-ATP synthase remain. In conclusion, this work suggests that the symbiont influences the mitochondrial respiration of the host protozoan.

Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity.

AIMS: To evaluate the diversity of endophytic fungi from the leaves of the common bean and the genetic diversity of endophytic fungi from the genus Colletotrichum using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism) analyses. METHODS AND RESULTS: The fungi were isolated by tissue fragmentation and identified by analysing the morphological features and sequencing the internal transcribed spacer (ITS) regions and the rDNA large subunit (LSU). Twenty-seven different taxa were identified. Colletotrichum was the most commonly isolated genera from the common bean (32.69% and 24.29% of the total isolates from the Ouro Negro and Talismã varieties, respectively). The IRAP and REMAP analyses revealed a high genetic diversity in the Colletotrichum endophytic isolates and were able to discriminate these isolates from the phytopathogen Colletotrichum lindemuthianum. CONCLUSIONS: Fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris endophytic community, and the IRAP and REMAP markers can be used to rapidly distinguish between C. lindemuthianum and other Colletotrichum members that are frequently found as endophytes. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of the diversity of endophytic fungi present in the common bean and the use of IRAP and REMAP markers to assess the genetic diversity of endophytic fungi from the genus Colletotrichum.

Environmental factors in benign migratory glossitis and psoriasis: retrospective study of the association of emotional stress and alcohol and tobacco consumption with benign migratory glossitis and cutaneous psoriasis.

BACKGROUND: The association between benign migratory glossitis (BMG) and psoriasis (PS) has been reported in the literature. OBJECTIVE: This study aimed to determinate the environmental factors related to BMG and PS and to investigate their interactions. METHODS: The study population included 129 patients with PS, 399 patients with BMG and a control group (CG) of 5472 individuals with neither PS nor BMG. The environmental factors evaluated in this study included alcohol and tobacco consumption and emotional stress. The Pearson's chi-squared test was used for analysing the association of the environmental factors with PS and BMG. RESULTS: The prevalence of alcohol consumption in the PS group was significantly higher than that in the CG. Tobacco consumption had a weak negative association with the BMG group. With respect to the PS group, no statistically significant association was observed. Emotional stress was the most important factor in the two study groups. Emotional stress and alcohol use together presented a higher incidence in the study groups than in the CG. Emotional stress and tobacco consumption together had a three times higher incidence in the PS group than in the BMG group. The association of emotional stress, alcohol and tobacco consumption in the PS group was four times higher than that in the CG. LIMITATIONS: This study was limited by the lack of the information about frequency, type and length time of use of tobacco and alcohol, and by difficult to measure stress thought self-report questionnaire. CONCLUSION: The interactions between PS and environmental factors differ from those between BMG and environmental factors. These differences among interactions may be responsible for different forms of manifestations of these diseases, considering being both the same disease.

Factor analysis of sarcoidosis phenotypes at two referral centers in Brazil.

BACKGROUND: In sarcoidosis, clinical presentations and outcomes vary widely. OBJECTIVE: To characterize the clinical phenotypes of sarcoidosis, by factor analysis, in a series of cases with long-term follow-up. METHODS: We conducted a retrospective study involving 137 patients with biopsy-confirmed sarcoidosis, recruited from two referral centers in São Paulo, Brazil. Organ involvement was evaluated in accordance with a previously established protocol. Sarcoidosis phenotypes were characterized by factor analysis. RESULTS: Follow-up ranged from 6 to 144 months. Four factors (phenotypes) were identified: relevant residual pulmonary fibrosis; relapse; residual airflow limitation; and acute disease. The four factors collectively accounted for 66% of the total variance. Patients with relevant residual pulmonary fibrosis were older and presented with the following: greater symptom duration; skin involvement; low forced vital capacity; low forced expiratory volume in one second/forced vital capacity ratio; and more advanced radiographic stages at baseline. The relapse phenotype was associated with chronic disease, greater dyspnea severity, neurologic involvement, and cardiac involvement. Patients with residual airflow limitation more often had airflow obstruction at baseline, chronic disease, and relevant residual pulmonary fibrosis. Acute disease was associated with being younger, weight loss, scoring lower for dyspnea, and having extensive involvement. Abnormal calcium metabolism was associated with acute disease and with relapse. CONCLUSIONS: Sarcoidosis can be categorized into four different clinical phenotypes: three that are chronic; and one that is acute and self-limiting. In many cases, these phenotypes can be easily recognized.

Intrauterine dentistry: an integrated model of prevention.

Intrauterine Dentistry is a highly relevant subject of our time. The use of preventive measures in the intrauterine stage can avoid several diseases, among these, dental caries. The WHO advises that from the 4th month of pregnancy, women should avoid the intake of sugar, so that the fetus, future child, does not develop an exaggerated attraction for these types of foods, thus being susceptible to caries. Through questionnaires sent to gynecologist-obstetricians and dentists, this research investigated the information they have about this subject and how they instruct their patients. Questionnaires were also sent to pregnant women requesting information about the instructions they had received for the prevention of oral diseases of their fetus. Seventy-one percent of the dentists and 80% of the gynecologist-obstetricians reported having instructed the pregnant women to reduce the intake of sugar. However, only 13.6% of the dentists and no gynecologist-obstetrician instructed the reduction of sugar intake between the 12th and 18th week of pregnancy. A total of 42.2% of the pregnant women referred to these instructions, but none received instruction as to the specific period of the 12th and 18th week. An ideal model of treatment for pregnant women must include integrated and multiprofessional treatment, in which general dentists and gynecologist-obstetricians work together with the participation of the patient.

Closure of rRNA related gaps in the Chromobacterium violaceum genome with the PCR-assisted contig extension (PACE) protocol

In the finishing phase of the Chromobacterium violaceum genome project, the shotgun sequences were assembled into 57 contigs that were then organized into 19 scaffolds, using the information from shotgun and cosmid clones. Among the 38 ends resulting from the 19 scaffolds, 10 ended with sequences corresponding to rRNA genes (seven ended with the 5S rRNA gene and three ended with the 16S rRNA gene). The 28 non-ribosomal ends were extended using the PCR-assisted contig extension (PACE) methodology, which immediately closed 15 real gaps. We then applied PACE to the 16S rRNA gene containing ends, resulting in eight different sequences that were correctly assembled within the C. violaceum genome by combinatory PCR strategy, with primers derived from the non-repetitive genomic region flanking the 16S and 5S rRNA gene. An oriented combinatory PCR was used to correctly position the two versions (copy A and copy B, which differ by the presence or absence of a 100-bp insert); it revealed six copies corresponding to copy A, and two to copy B. We estimate that the use of PACE, followed by combinatory PCR, accelerated the finishing phase of the C. violaceum genome project by at least 40 per cent