Bioinformatics of the Paracoccidioides brasiliensis EST Project

Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an endemic mycosis of Latin America. This fungus presents a dimorphic character; it grows as a mycelium at room temperature, but it is isolated as yeast from infected individuals. It is believed that the transition from mycelium to yeast is important for the infective process. The Functional and Differential Genome of Paracoccidioides brasiliensis Project - PbGenome Project was developed to study the infection process by analyzing expressed sequence tags - ESTs, isolated from both mycelial and yeast forms. The PbGenome Project was executed by a consortium that included 70 researchers (professors and students) from two sequencing laboratories of the midwest region of Brazil; this project produced 25,741 ESTs, 19,718 of which with sufficient quality to be analyzed. We describe the computational procedures used to receive process, analyze these ESTs, and help with their functional annotations; we also detail the services that were used for sequence data exploration. Various programs were compared for filtering and grouping the sequences, and they were adapted to a user-friendly interface. This system made the analysis of the differential transcriptome of P. brasiliensis possible

CARACTERIZAÇÃO DA PRODUÇÃO DO PEIXE-VOADOR, Hirundichthys affinis EM CAIÇARA DO NORTE, RIO GRANDE DO NORTE, BRASIL: DURANTE 1993 A 2010.

The flying fish, Hirundichthys affinis, has great socioeconomic importance, constituting a source of food and income for fishing communities in Caiçara do Norte, in the State of Rio Grande do Norte. The production of H. affinis is responsible for 41.9% of the local fishing, representing the main fishery resource of this municipality. Production data of the flying fish in the years 1993 to 2010 analyzed indicated that its production showed fluctuations impacting the total fishery production of Caiçara do Norte. The production of H. affinis in Caiçara do Norte in general was increasing over the period of 17 years. The number of fishing vessels is not related to the variation in production of H. affinis. The variation of the production of H. affinis could possibly be related to the environmental factors. It was observed that there was no relation between the production of the prey H. affinis and the predator dolphinfish, Coryphaena hippurus during the verified period. This information subsidizes the sustainable management of this species since this fishery resource alone contributes to 38% of the fish production in Rio Grande do Norte.Keywords: artesanal fishery; fishery resources; flying fish; coastal waters.O peixe-voador, Hirundichthys affinis, apresenta enorme importância socioeconômica, constituindo fonte de alimento e renda para comunidades pesqueiras em Caiçara do Norte, no Estado do Rio Grande do Norte. A produção de H. affinis é responsável por 41,9% da produção pesqueira local, representado o principal recurso pesqueiro desse município. Dados analisados da produção do peixe-voador nos anos de 1993 a 2010 indicaram que sua produção apresentou variações, impactando a produção pesqueira total de Caiçara do Norte. A produção de H. affinis em Caiçara do Norte ao longo de 17 anos em geral foi crescente. O número de embarcações pesqueiras não esta relacionado com as variações da produção do peixe-voador, H. affinis. As variações da produção de H. affinis estão possivelmente relacionadas com os fatores ambientais. Observou-se que não teve relação entre a produção de presa H. affinis e do predador peixe dourado, Coryphaena hippurus durante o período verificado. Essas informações subsidiam o manejo sustentável da espécie uma vez que este recurso pesqueiro isoladamente contribui com 38% da produção pesqueira do Rio Grande do Norte .Palavras-chave: pesca artesanal, recursos pesqueiros, peixe-voador, águas costerias

AVALIAÇÃO DA EFICIÊNCIA DE REUTILIZAÇÃO DO CIDR® EM PROTOCOLOS DE SUPEROVULAÇÃO DE OVELHAS

Sheep farming is an area of veterinary medicine of great importance at regional and national level, among the easily found breeds of economic relevance in northeastern Brazil are Morada Nova and Santa Inês. In addition, ultrasonography has been used systematically in animals superovulatory response to the sheep supervoulation protocols. In order to assess, based on the number of yellow bodies and number of viable embryos produced, the efficiency of the reuse of CIDR® in superovulation protocols in sheep using ultrasonography in color Doppler mode, a superovulatory protocol was performed in a total 40 sheep, with G-USED when 10 Morada Nova ewes and 10 Santa Inês ewes received reused CIDR® and G-NOVO when 10 Morada Nova ewes and 10 Santa Inês ewes received new CIDR®. The mean and standard error of yellow bodies was 10.35±1.33 for G-USED and 9.25±1.65 for G-NOVO, while the number of viable embryos was 6.50±2, 54 for G-USED and 8.25±1.49 for G-NEW. Thus, the reuse of CIDR® demonstrated efficiency in superovulation and did not interfere with the development of corpus luteum and the production of quality transferable embryos in sheep.A ovinocultura é uma área da medicina veterinária de grande importância a nível regional e nacional, dentre as raças de relevância econômica facilmente encontradas no nordeste do Brasil estão a Morada Nova e a Santa Inês. Além disso, a ultrassonografia tem sido utilizada sistematicamente na resposta superovulatória de animais aos protocolos de supervolução de ovinos. Com o objetivo de avaliar, com base no número de corpos amarelos e no número de embriões viáveis produzidos, a eficiência do reaproveitamento do CIDR® em protocolos de superovulação em ovelhas por ultrassonografia no modo Doppler colorido, foi realizado um protocolo de superovulação em um total de 40 ovelhas, com G-USED quando 10 ovelhas Morada Nova e 10 ovelhas Santa Inês receberam CIDR® reutilizado e G-NOVO quando 10 ovelhas Morada Nova e 10 ovelhas Santa Inês receberam CIDR® novo. A média e erro padrão dos corpos amarelos foi de 10,35±1,33 para G-USED e 9,25±1,65 para G-NOVO, enquanto o número de embriões viáveis foi de 6,50±2, 54 para G-USED e 8,25±1,49 para G-NEW. Assim, a reutilização do CIDR® demonstrou eficiência na superovulação e não interferiu no desenvolvimento do corpo lúteo e na produção de embriões transferíveis de qualidade em ovinos

AnuraSet: A dataset for benchmarking Neotropical anuran calls identification in passive acoustic monitoring

Global change is predicted to induce shifts in anuran acoustic behavior, which can be studied through passive acoustic monitoring (PAM). Understanding changes in calling behavior requires the identification of anuran species, which is challenging due to the particular characteristics of neotropical soundscapes. In this paper, we introduce a large-scale multi-species dataset of anuran amphibians calls recorded by PAM, that comprises 27 hours of expert annotations for 42 different species from two Brazilian biomes. We provide open access to the dataset, including the raw recordings, experimental setup code, and a benchmark with a baseline model of the fine-grained categorization problem. Additionally, we highlight the challenges of the dataset to encourage machine learning researchers to solve the problem of anuran call identification towards conservation policy. All our experiments and resources can be found on our GitHub repository https://github.com/soundclim/anuraset

Transcriptional remodeling patterns in murine dendritic cells infected with Paracoccidioides brasiliensis : more is not necessarily better

Most people infected with the fungus Paracoccidioides spp. do not get sick, but approximately 5% develop paracoccidioidomycosis. Understanding how host immunity determinants influence disease development could lead to novel preventative or therapeutic strategies; hence, we used two mouse strains that are resistant (A/J) or susceptible (B10.A) to P. brasiliensis to study how dendritic cells (DCs) respond to the infection. RNA sequencing analysis showed that the susceptible strain DCs remodeled their transcriptomes much more intensely than those from the resistant strain, agreeing with a previous model of more intense innate immunity response in the susceptible strain. Contrastingly, these cells also repress genes/processes involved in antigen processing and presentation, such as lysosomal activity and autophagy. After the interaction with P. brasiliensis, both DCs and macrophages from the susceptible mouse reduced the autophagy marker LC3-II recruitment to the fungal phagosome compared to the resistant strain cells, confirming this pathway’s repression. These results suggest that impairment in antigen processing and presentation processes might be partially responsible for the inefficient activation of the adaptive immune response in this model

Transcriptional profiles of the human pathogenic fungus paracoccidioides brasiliensis in mycelium and yeast cells

This work was supported by MCT, CNPq, CAPES, FUB, UFG, and FUNDECT-MS. PbGenome Network: Alda Maria T. Ferreira, Alessandra Dantas, Alessandra J. Baptista, Alexandre M. Bailão, Ana Lídia Bonato, André C. Amaral, Bruno S. Daher, Camila M. Silva, Christiane S. Costa, Clayton L. Borges, Cléber O. Soares, Cristina M. Junta, Daniel A. S. Anjos, Edans F. O. Sandes, Eduardo A. Donadi, Elza T. Sakamoto-Hojo, Flábio R. Araújo, Flávia C. Albuquerque, Gina C. Oliveira, João Ricardo M. Almeida, Juliana C. Oliveira, Kláudia G. Jorge, Larissa Fernandes, Lorena S. Derengowski, Luís Artur M. Bataus, Marcus A. M. Araújo, Marcus K. Inoue, Marlene T. De-Souza, Mauro F. Almeida, Nádia S. Parachin, Nadya S. Castro, Odair P. Martins, Patrícia L. N. Costa, Paula Sandrin-Garcia, Renata B. A. Soares, Stephano S. Mello, and Viviane C. B. ReisParacoccidioides brasiliensis is the causative agent of paracoccidioidomycosis, a disease that affects 10 million individuals in Latin America. This report depicts the results of the analysis of 6,022 assembled groups from mycelium and yeast phase expressed sequence tags, covering about 80% of the estimated genome of this dimorphic, thermo-regulated fungus. The data provide a comprehensive view of the fungal metabolism, including overexpressed transcripts, stage-specific genes, and also those that are up- or down-regulated as assessed by in silico electronic subtraction and cDNA microarrays. Also, a significant differential expression pattern in mycelium and yeast cells was detected, which was confirmed by Northern blot analysis, providing insights into differential metabolic adaptations. The overall transcriptome analysis provided information about sequences related to the cell cycle, stress response, drug resistance, and signal transduction pathways of the pathogen. Novel P. brasiliensis genes have been identified, probably corresponding to proteins that should be addressed as virulence factor candidates and potential new drug targets

Comparison of venous plasma glycemia and capillary glycemia for the screening of type 2 diabetes mellitus in the Japanese-Brazilian community of Mombuca (Guatapará-SP)

<p>Abstract</p> <p>Background</p> <p>To identify the most appropriate cut-off points of fasting glycemia for the screening of diabetes mellitus type 2 (DM2) with the comparison of the properties of capillary glycemia (CG) and venous blood plasma glycemia (PG) in a population of Japanese origin from the community of Mombuca, Guatapará - SP, Brazil.</p> <p>Methods</p> <p>This was a population-based descriptive cross-sectional study conducted on a sample of 131 individuals of both genders aged 20 years or more (66.8% of the target population). CG was measured with a glucometer in a blood sample obtained from the fingertip and PG was determined by an enzymatic method (hexokinase) in venous blood plasma, after a 10-14 hour fast in both cases. Data were analyzed by the receiver operating characteristic (ROC) curve in order to identify the best cut-off point for fasting glycemia (CG and PG) for the diagnosis of DM, using the 2-hour plasma glycemia > 200 mg/dl as gold - standard.</p> <p>Results</p> <p>The ROC curve revealed that the best cut-off point for the screening of DM was 110 mg/dl for CG and 105 mg/dl for PG, values that would optimize the relation between individuals with positive and false-positive results. The area under the ROC curve was 0.814 for CG (p < 0.01) and 0.836 for PG (p < 0.01).</p> <p>Conclusions</p> <p>The cut-off points of 105 mg/dl(5.8 mmol/l) for PG and of 110 mg/dl(6.1 mmol/l) for CG appear to be the most appropriate for the screening of DM2 in the population under study, with emphasis on the fact that the value recommended for CG is 5 mg/dl higher than that for PG, in contrast to WHO recommendations.</p

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio