Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats.

Cladophialophora exuberans is a filamentous fungus related to black yeasts in the order Chaetothyriales. These melanized fungi are known for their 'dual ecology', often occurring in toxic environments and also being frequently involved in human infection. Particularly Cladophialophora exuberans, C. immunda, C. psammophila, and Exophiala mesophila have been described with a pronounced ability to degrade aromatic compounds and xenobiotic volatiles, such as benzene, toluene, ethyl-benzene, and xylene, and are candidates for bioremediation applications. The objective of the present study is the sequencing, assembly, and description of the whole genome of C. exuberans focusing on genes and pathways related to carbon and toxin management, assessing the tolerance and bioremediation of lead and copper, and verifying the presence of genes for metal homeostasis. Genomic evaluations were carried out through a comparison with sibling species including clinical and environmental strains. Tolerance of metals was evaluated via a microdilution method establishing minimum inhibitory (MIC) and fungicidal concentrations (MFC), and agar diffusion assays. Heavy metal bioremediation was evaluated via graphite furnace atomic absorption spectroscopy (GFAAS). The final assembly of C. exuberans comprised 661 contigs, with genome size of 38.10 Mb, coverage of 89.9X and a GC content of 50.8%. In addition, inhibition of growth was shown at concentrations of 1250 ppm for copper and at 625 ppm for lead, using the MIC method. In the agar tests, the strain grew at 2500 ppm of copper and lead. In GFAAS tests, uptake capacities were observed of 89.2% and 95.7% for copper and lead, respectively, after 21 experimental days. This study enabled the annotation of genes involved in heavy metal homeostasis and also contributed to a better understanding of the mechanisms used in tolerance of and adaptation to extreme conditions.

Hemodynamic responses during inspiratory muscle exercise in healthy young adults / Respuestas hemodinámicas durante el ejercicio de los músculos inspiratorios en adultos jóvenes sanos / Respostas hemodinâmicas durante exercício muscular inspiratório em jovens saudáveis

ABSTRACT The literature on hemodynamic responses during inspiratory muscle exercise (IME) lacks a consensus. To evaluate and compare hemodynamic responses during an IME session with and without resistive load, 15 sedentary men were subjected to two randomized IME sessions: one with 40% of maximal inspiratory pressure (IME 40%) and another without a resistive load (Sham), both of which were performed for two minutes over eight sessions with one-minute intervals. Systolic blood pressure (SBP), diastolic blood pressure (DBP), mean blood pressure (MBP), total peripheral resistance (TPR), stroke volume (SV), cardiac output (CO), and heart rate (HR) were measured by infrared digital photoplethysmography during five basal minutes and during the IME sessions. One-way analysis of variance and the Student's t test for paired data were used to analyze hemodynamic response and delta values between sessions. Effect size was evaluated by Cohen's D. A 5% significance level was adopted. SBP responses (sham: ∆−1±2 vs. 40%: ∆−4±2mmHg, p=0.27), DBP (sham: ∆2±1 vs. 40%: ∆1±2mmHg, p=0.60) and MBP (sham: ∆2±1 vs. 40%: ∆0±2mmHg, p=0.28) were similar between sessions. HR increases were higher in the 40% IME session than in the sham session (sham: ∆9±2 vs. 40%: ∆3±2bpm, p=0.001). SV only decreased during the sham session but responses were similar between sessions (sham: ∆−2±2 vs. IME 40%: ∆−6±2ml, p=0.13). Both sessions did not change SBP, DBP, MBP, CO, and TPR, but we observed a greater increase in HR in the IME 40% session. Only the Sham session decreased SV.

RESUMEN No hay consenso en la literatura sobre las respuestas hemodinámicas durante el ejercicio muscular inspiratorio (EMI). El objetivo de este estudio fue evaluar y comparar las respuestas hemodinámicas durante una sesión de EMI con y sin carga resistiva. Para ello, quince hombres sedentarios recibieron dos sesiones aleatorias de EMI: el 40% de la presión inspiratoria máxima (EMI 40%) y sin carga resistiva (sham), realizadas durante dos minutos, ocho sesiones y a intervalos de un minuto. La presión arterial sistólica (PAS), la presión arterial diastólica (PAD), la presión arterial media (PAM), la resistencia periférica total (RPT), el volumen sistólico (VS), el gasto cardíaco (GC) y la frecuencia cardíaca (FC) se midieron mediante fotopletismografía infrarroja digital durante cinco minutos al inicio y durante las sesiones de EMI. Se utilizaron ANOVA unidireccional y la prueba t de Student a datos emparejados para analizar la respuesta hemodinámica y los valores delta entre las sesiones. El tamaño del efecto se evaluó por el d de Cohen. El nivel de significancia adoptado fue de 5%. Las respuestas de PAS (sham: Δ−1±2 vs. 40%: ∆−4±2mmHg, p=0,27), PAD (sham: ∆2±1 vs. 40%: ∆1±2mmHg, p=0,60) y PAM (sham: ∆2±1 vs. 40%: ∆0±2mmHg, p=0,28) fueron similares entre las sesiones. El incremento de la FC fue mayor en la sesión de EMI 40% comparada con la sesión sham (sham: Δ9±2 vs. 40%: ∆3±2bpm, p=0,001). El VS tuvo una disminución exclusiva durante la sesión sham, pero la respuesta fue similar entre las sesiones (sham: Δ−2±2 vs. EMI 40%: ∆−6±2ml, p=0,13). Ambas sesiones no tuvieron cambios en las variables PAS, PAD, PAM, DC y RPT, pero se observó un mayor incremento de la FC en la sesión EMI 40%. Solamente en la sesión sham hubo una reducción del VS.

RESUMO A literatura carece de um consenso sobre respostas hemodinâmicas durante o exercício muscular inspiratório (EMI). Este estudo buscou avaliar e comparar as respostas hemodinâmicas durante uma sessão de EMI com e sem carga resistiva. Para tanto, 15 homens sedentários foram submetidos a duas sessões randomizadas de EMI: 40% da pressão inspiratória máxima (EMI 40%) e sem carga resistiva (sham), realizadas por dois minutos em oito sessões e com intervalos de um minuto. A pressão arterial sistólica (PAS), pressão arterial diastólica (PAD), pressão arterial média (PAM), resistência periférica total (RPT), volume sistólico (VS), débito cardíaco (DC) e frequência cardíaca (FC) foram medidos por fotopletismografia infravermelha digital por cinco minutos basais e durante as sessões de EMI. Anova de uma via e o teste t de Student para dados pareados foram usados para analisar a resposta hemodinâmica e os valores delta entre as sessões. O tamanho do efeito foi avaliado pelo d de Cohen. Adotou-se nível de significância de 5%. As respostas de PAS (sham: ∆−1±2 vs. 40%: ∆−4±2mmHg, p=0,27), PAD (sham: ∆2±1 vs. 40%: ∆1±2mmHg, p=0,60) e PAM (sham: ∆2±1 vs. 40%: ∆0±2mmHg, p=0,28) foram semelhantes entre as sessões. Os aumentos da FC foram maiores na sessão de EMI 40% do que nas sessões sham (sham: ∆9±2 vs. 40%: ∆3±2bpm, p=0,001). O VS diminuiu exclusivamente durante a sessão sham mas a resposta foi semelhante entre as sessões (sham: ∆−2±2 vs. EMI 40%: ∆−6±2ml, p=0,13). Ambas as sessões não causaram alteração nas variáveis PAS, PAD, PAM, DC e RPT, mas notamos um aumento maior da FC na sessão EMI 40%. Apenas a sessão sham reduziu o VS.

New Insights on Environmental Occurrence of Pathogenic Fungi Based on Metagenomic Data from Brazilian Cerrado Biome

Abstract: Cerrado is the second largest biome in Brazil and majorly contributes to the country's grain production. Previous studies on soil metagenomics from the Cerrado revealed an outstanding microbial diversity. In this study, the abundance of pathogenic fungi was analyzed using metagenomic sequences of the Cerrado soils under native vegetation, and under agriculture with no-tillage and conventional tillage. In total, 128,627 sequences of fungi were identified, with 43,439 representing pathogenic fungi and were distributed as follows: native 17,301 (40%), no-tillage 13,780 (32%), and conventional tillage 12,358 (28%). We identified 41 pathogenic fungal species associated with human and animal infections. The data analysis revealed that the native soils had a higher relative abundance of fungal sequences, similar to pathogenic species sequences, in relation to the total eukaryotic sequences, than the conventional tillage and no-tillage treatments, which observed a reduction in fungal abundance because of anthropogenic activities.

Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network.

Chromoblastomycosis (CBM) is a neglected implantation mycosis prevalent in tropical climate zones, considered an occupational disease that affects impoverished rural populations. This retrospective study described clinical aspects of CBM in a hyperendemic area in Brazil and constructed a worldwide haplotype network of Fonsecaea spp. strains. The variables were collected from medical records using a standard report form, reporting 191 patients with CBM from Maranhão, Brazil. The mean age was 56.1 years, 168 (88%) patients were male and predominantly farmers (85.8%). The mean time of evolution of the disease until diagnosis was 9.4 years. Lower limbs (81.2%) and upper limbs (14.2%) were the main sites affected. Most patients exhibited verrucous (55%) and infiltrative plaque (48.2%). Fonsecaea spp. were identified in 136 cases and a haplotype network constructed with ITS sequences of 185 global strains revealed a total of 59 haplotypes exhibiting high haplotypic and low nucleotide diversities. No correlation was observed between the different haplotypes of Fonsecaea species and dermatological patterns, severity of disease or geographic distribution inside Maranhão. Data from this area contributed to better understanding the epidemiology of CBM. For the first time, a robust haplotype network with Fonsecaea strains reveals an evolutionary history with a recent population expansion.

Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology.

Melanized fungi and black yeasts in the family Herpotrichiellaceae (order Chaetothyriales) are important agents of human and animal infectious diseases such as chromoblastomycosis and phaeohyphomycosis. The oligotrophic nature of these fungi enables them to survive in adverse environments where common saprobes are absent. Due to their slow growth, they lose competition with common saprobes, and therefore isolation studies yielded low frequencies of clinically relevant species in environmental habitats from which humans are thought to be infected. This problem can be solved with metagenomic techniques which allow recognition of microorganisms independent from culture. The present study aimed to identify species of the family Herpotrichiellaceae that are known to occur in Brazil by the use of molecular markers to screen public environmental metagenomic datasets from Brazil available in the Sequence Read Archive (SRA). Species characterization was performed with the BLAST comparison of previously described barcodes and padlock probe sequences. A total of 18,329 sequences was collected comprising the genera Cladophialophora, Exophiala, Fonsecaea, Rhinocladiella and Veronaea, with a focus on species related to the chromoblastomycosis. The data obtained in this study demonstrated presence of these opportunists in the investigated datasets. The used techniques contribute to our understanding of environmental occurrence and epidemiology of black fungi.

Comparative Genomic Analysis of Capsule-Producing Black Yeasts Exophiala dermatitidis and Exophiala spinifera, Potential Agents of Disseminated Mycoses.

The two black yeasts Exophiala dermatitidis and Exophiala spinifera that are clinically considered as the most virulent species potentially causing disseminated infections are both producing extracellular capsule-like material, are compared. In this study, 10 genomes of E. spinifera and E. dermatitidis strains, including both clinical and environmental isolates, were selected based on phylogenetic analysis, physiology tests and virulence tests, sequenced on the Illumina MiSeq sequencer and annotated. Comparison of genome data were performed between intraspecific and interspecific strains. We found capsule-associated genes were however not consistently present in both species by the comparative genomics. The prevalent clinical species, E. dermatitidis, has small genomes containing significantly less virulence-associated genes than E. spinifera, and also than saprobic relatives. Gene OG0012246 and Myb-like DNA-binding domain and SANT/Myb domain, restricted to two strains from human brain, was shared with the neurotropic species Rhinocladiella mackenziei. This study indicated that different virulence profiles existed in the two capsule-producing black yeasts, and the absence of consistent virulence-associated profiles supports the hypothesis that black yeasts are opportunists rather than primary pathogens. The results also provide the key virulence genes and drive the continuing research forward pathogen-host interactions to explore the pathogenesis.

Genome Sequence of the Human Opportunistic Fungus Arthrocladium fulminans (CBS 136243).

The black yeast-like fungus Arthrocladium fulminans is known from strains that cause severe and eventually fatal disseminated infections in immunocompromised patients. Given the dramatic outcome of this clinical case, it is essential to understand the virulence potential of this species. The fungus is a member of the family Trichomeriaceae, at some phylogenetic distance from the Herpotrichiellaceae where most infectious fungi in the order Chaetothyriales are located. Main ecological preferences among Trichomeriaceae include colonization of exposed inert surfaces. Currently, black yeasts genomes that are available in public databases cover members of the families Herpotrichiellaceae and Cyphellophoraceae In the present report, we sequenced the genome of the first member and only clinical representative of the family Trichomeriaceae.

Virulence characteristics and antimicrobial resistance of Aeromonas veronii biovar sobria 312M, a clinical isolate.

Aeromonas are bacteria widely distributed in the environment, and some species are able to cause infections in humans, of which diarrhea is the most common. The objective of this study was to evaluate the presence of virulence and antimicrobial resistance associated characteristics in A. veronii biovar sobria strain 312M isolated from diarrheal stools. For this, the genome sequencing and phenotypical tests were performed. The draft genome annotation revealed several complete pathways associated with carbon metabolism and a mucin-desulfating sulfatase which may contribute to intestine colonization, and a large number of virulence-associated genes encoding structures associated with adhesion, toxins, and secretion systems. The strain exhibited swimming and swarming motility, biofilm formation, and hemolytic activity. It was resistant to ampicillin, ampicillin/sulbactam, and amoxicillin-clavulanic acid. Although a cphA gene encoding a narrow-spectrum carbapenase was identified in the strain genome, no carbapenemase activity was detected in the antimicrobial susceptibility test. When compared with other A. veronii with complete genomes, the main differences in virulence characteristics are related to lateral flagella and type III and VI secretion systems; the antimicrobial resistance spectrum also varied among strains. The results indicated that A. veronii biovar sobria 312M presents high virulence potential and resistance to limited classes of antimicrobials.

Câncer de mama e imagem corporal: impacto dos tratamentos no olhar de mulheres mastectomizadas / Breast cancer and body image: impact of treatments from the point of view of mastectomized females

Esta pesquisa avaliou a percepção da imagem corporal de mulheres mastectomizadas, com ou sem reconstrução mamária, investigando como o adoecimento e os tratamentos impactaram suas vidas. Trata-se de um estudo descritivo, transversal, com abordagem qualitativa. Participaram dez mulheres com diagnóstico de câncer mamário, mastectomizadas, com ou sem reconstrução mamária, atendidas no HU/UFJF, de janeiro a novembro de 2015, por meio de uma entrevista semiestruturada. Para análise qualitativa, aplicou-se a Análise de Conteúdo de Bardin, de onde emergiram as categorias: "Diagnóstico e Enfrentamento", "Rede de Apoio", "Tratamentos e seus Anseios", "Imagem Corporal", e "Papel na Sociedade". Concluiu-se que o cuidado com a saúde das mulheres acometidas pela doença demanda assistência multiprofissional, que auxilie no processo de enfrentamento do câncer e na reabilitação para além das limitações físicas, com o intuito de reconexão do corpo físico, psíquico e espiritual, visando facilitar a adaptação ao "novo corpo" e permitir incremento na autoestima, a reinserção social e melhoria da qualidade de vida.

The perception of body image by mastectomized females, with or without breast reconstruction, is evaluated. Current descriptive, transversal and qualitative research analyzes how illness and treatments impacted their lives. Ten mastectomized females, diagnosed with breast cancer, attended at the University Hospital of UFJF, between January and November 2015, participated through a half-structured interview. Qualitative analysis comprised Bardin´s Content Analysis, from which were derived the categories: "Diagnosis and Coping", "Support Network", "Treatments and Anxiety", "Body Image", and "Role in Society". Results show that health care of ill females require multiprofessional assistance that helps them to cope with cancer and to rehabilitate them beyond physical limitations. The target is the reconnection of the physical, psychic and spiritual body, to facilitate the adaptation to the 'new body' and allow an increase in self-esteem, social reinsertion and improvement in life quality.

Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts.

BACKGROUND: Herbaspirillum seropedicae is an environmental ß-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. RESULTS: Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system. CONCLUSIONS: Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.

Characteristics of an Aeromonas trota strain isolated from cerebrospinal fluid.

Aeromonas are ubiquitous in aquatic habitats. However some species can cause infections in humans, but rarely meningitis. Here we describe the isolation and characterization of an Aeromonas strain from cerebrospinal fluid of a meningitis patient. The isolate, identified as A. trota by biochemical and molecular methods, was susceptible to ampicillin but resistant to cephalothin and cefazolin. Genome sequencing revealed virulence factor genes such as type VI secretion system, aerolysin and lateral flagella. The isolate exhibited swarming motility, hemolytic activity and adhesion and cytotoxicity on HeLa cells. This is the first report of A. trota associated with meningitis and its virulence characteristics.

Protein Function Prediction.

Protein function is a concept that can have different interpretations in different biological contexts, and the number and diversity of novel proteins identified by large-scale "omics" technologies poses increasingly new challenges. In this review we explore current strategies used to predict protein function focused on high-throughput sequence analysis, as for example, inference based on sequence similarity, sequence composition, structure, and protein-protein interaction. Various prediction strategies are discussed together with illustrative workflows highlighting the use of some benchmark tools and knowledge bases in the field.

Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis.

Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species.

Phylogenomic analyses reveal the diversity of laccase-coding genes in Fonsecaea genomes.

The genus Fonsecaea comprises black yeast-like fungi of clinical relevance, including etiologic agents of chromoblastomycosis and cerebral phaeohyphomycosis. Presence of melanin and assimilation of monoaromatic hydrocarbons and alkylbenzenes have been proposed as virulence factors. Multicopper oxidase (MCO) is a family of enzymes including laccases, ferroxidases and ascorbate oxidases which are able to catalyze the oxidation of various aromatic organic compounds with the reduction of molecular oxygen to water. Additionally, laccases are required for the production of fungal melanins, a cell-wall black pigment recognized as a key polymer for pathogenicity and extremotolerance in black yeast-like fungi. Although the activity of laccase enzymes has previously been reported in many wood-rotting fungi, the diversity of laccase genes in Fonsecaea has not yet been assessed. In this study, we identified and characterized laccase-coding genes and determined their genomic location in five clinical and environmental Fonsecaea species. The identification of laccases sensu stricto will provide insights into carbon acquisition strategies as well as melanin production in Fonsecaea.

Genome Sequence of Type Strain Fonsecaea multimorphosa CBS 980.96T, a Causal Agent of Feline Cerebral Phaeohyphomycosis.

A draft genome sequence of type strain Fonsecaea multimorphosa CBS 980.96T was obtained. This species was first isolated from a cat with cerebral phaeohyphomycosis in Queensland, Australia.

Draft Genome Sequence of Fonsecaea nubica Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis.

On the basis of multilocus phylogenetic data, Fonsecaea nubica was described in 2010 as a molecular sibling of F. monophora, an established agent of the human skin disease chomoblastomycosis in tropical zones. Genome analysis of these pathogens is mandatory to identify genes involved in the interaction with host and virulence.

Draft Genome Sequence of Fonsecaea monophora Strain CBS 269.37, an Agent of Human Chromoblastomycosis.

The black yeast Fonsecaea monophora is one of the main etiologic agents of chromoblastomycosis in humans. Its pathogenicity profile is more invasive than that of related Fonsecaea species, causing brain infection in addition to (sub)cutaneous infections.

Draft Genome Sequence of the Ant-Associated Fungus Phialophora attae (CBS 131958).

The black yeast Phialophora attae was isolated from the cuticle of tropical ant gynes. The ant-fungus association is sustained due to symbiotic evolutionary adaptations that allow fungal assimilation and tolerance of toxic compounds produced by the ant. The genome sequence of the first ant-associated fungus, P. attae, is presented here.

Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.

We report the complete genome sequence of Herbaspirillum hiltneri N3 (DSM 17495), a member of the genus Herbaspirillum of the Betaproteobacteria. The genome is contained in a single chromosome, and analysis revealed that N3 lacks the whole nitrogen fixation (nif) gene cluster, confirming its inability to fix nitrogen.

Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin.

Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae. Three hundred and four genes were downregulated and seventy seven were upregulated by naringenin. Data analysis revealed that genes related to bacterial flagella biosynthesis, chemotaxis and biosynthesis of peptidoglycan were repressed by naringenin. Moreover, genes involved in aromatic metabolism and multidrug transport efllux were actived.