Rapid diagnosis of coccidioidomycosis by nested PCR assay of sputum

Coccidioidomycosis is a deep infection caused by two dimorphic fungi, Coccidioides immitis and Coccidioides posadasii. Diagnosis of the disease requires culture of suspicious clinical samples on mycological media. However, as these species are virulent pathogens, handling of their cultures is a high-risk activity, and is limited to Biosafety Level 3 laboratories. This study describes the direct detection of C. posadasii DNA in an inappropriate sputum sample by PCR amplification of the highly specific Ag2/PRA antigen gene. the results obtained suggest that direct detection of the Ag2/PRA sequence in sputum is an excellent method for rapid and specific diagnosis of coccidioidomycosis.Fed Univ Ceara, Med Mycol Specialized Ctr, Fortaleza, Ceara, BrazilFed Univ Ceara, Postgrad Program Med Sci, Fortaleza, Ceara, BrazilState Univ Ceara, Postgrad Program Vet Sci, Fortaleza, Ceara, BrazilState Univ Ceara, Dept Sci Biol, Fortaleza, Ceara, BrazilUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilWeb of Scienc

Prediction of the geographic distribution and conservation of Amazonian palm trees Astrocaryum acaule Mart. and Astrocaryum aculeatum Mart.

ABSTRACT ? Astrocaryum aculeatum Mart. Moreover, Astrocaryum acaule Mart. are palm trees with ecological and extractive importance in the Amazon. These are hearty species that have been associated with archaeological sites and thrive in the presence of humans in certain areas. This work aimed to verify the effect of global climate change on the potential geographic distribution of A. acaule and A. aculeatum in the current period and future climate scenarios using ecological niche modeling in Brazilian phytogeographic domains. The modeling was based on 19 bioclimatic variables obtained from the Worldclim website and four algorithms (Climate space model, Envelope Score, Niche Mosaic, and Environmental Distance). Additionally, the Environmental Distance algorithm showed greater similarity regarding species distribution with potential occurrence in the fi ve Brazilian domains (Amazon, Pantanal, Caatinga, Cerrado, and Atlantic Forest). The dispersion patterns were very similar between the two Astrocaryum palms though A. aculeatum was more sensitive to climatic variations. A. acaule may be more resilient to changes, as demonstrated by being able to recolonize in the southern portion of the Amazon in future scenarios in the year 2070. The modeling helped to delimit potential areas for A. aculeatum and A. acaule, indicating the need for the conservation of the species in more sensitive regions. RESUMO - Astrocaryum aculeatum Mart. e Astrocaryum acaule Mart. são palmeiras que apresentam importância ecológica e para o extrativismo na Amazônia. São espécies rústicas e que foram associadas a sítios arqueológicos e à presença de humanos em determinadas áreas. O objetivo deste trabalho foi verificar o efeito das mudanças climáticas globais na distribuição geográfica potencial de A. acaule e A. aculeatum, no período atual e em cenários climáticos futuros, utilizando a modelagem de nicho ecológico nos domínios fitogeográficos brasileiros. As modelagens foram baseadas em 19 variáveis bioclimáticas, obtidas no site do Worldclim, e quatro algoritmos (Climate space model, Envelope Score, Niche Mosaic e Enviromental Distance), dos quais o algoritmo Environmental Distance apresentou maior similaridade quanto à distribuição das espécies com ocorrência potencial nos cinco domínios brasileiros (Amazônia, Pantanal, Caatinga, Cerrado e Mata Atlântica). Os padrões de dispersão foram muito similares entre as duas palmeiras de Astrocaryum, porém A. aculeatum é mais sensível às variações climáticas. A. acaule tem potencial para ser mais resiliente às mudanças, podendo recolonizar a porção sul da Amazônia em cenários futuros, no ano de 2070. A modelagem auxiliou a delimitar as áreas potenciais de A. aculeatum e A. acaule, indicando a necessidade de conservação das espécies em regiões mais sensíveis.Título em Português: Predição da distribuição geográfica e conservação das palmeiras amazônicas Astrocaryum acaule Mart. e Astrocaryum aculeatum Mart

Genus Paracoccidioides: Species Recognition and Biogeographic Aspects

Background: Paracoccidioidomycosis is a systemic mycosis caused by Paracoccidioides brasiliensis (species S1, PS2, PS3), and Paracoccidioides lutzii. This work aimed to differentiate species within the genus Paracoccidioides, without applying multilocus sequencing, as well as to obtain knowledge of the possible speciation processes. Methodology/Principal Findings: Single nucleotide polymorphism analysis on GP43, ARF and PRP8 intein genes successfully distinguished isolates into four different species. Morphological evaluation indicated that elongated conidia were observed exclusively in P. lutzii isolates, while all other species (S1, PS2 and PS3) were indistinguishable. To evaluate the biogeographic events that led to the current geographic distribution of Paracoccidioides species and their sister species, Nested Clade and Likelihood Analysis of Geographic Range Evolution (LAGRANGE) analyses were applied. The radiation of Paracoccidioides started in northwest South America, around 11–32 million years ago, as calculated on the basis of ARF substitution rate, in the BEAST program. Vicariance was responsible for the divergence among S1, PS2 and P. lutzii and a recent dispersal generated the PS3 species, restricted to Colombia. Taking into account the ancestral areas revealed by the LAGRANGE analysis and the major geographic distribution of L. loboi in the Amazon basin, a region strongly affected by the Andes uplift and marine incursions in the Cenozoic era, we also speculate about the effect of these geological events on the vicariance between Paracoccidioides and L. loboi. Conclusions/Significance: The use of at least 3 SNPs, but not morphological criteria, as markers allows us to distinguish among the four cryptic species of the genus Paracoccidioides. The work also presents a biogeographic study speculating on how these species might have diverged in South America, thus contributing to elucidating evolutionary aspects of the genus Paracoccidioides

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

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans – anteaters, sloths, and armadillos – have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with 24 domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, ten anteaters, and six sloths. Our dataset includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data-paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the south of the USA, Mexico, and Caribbean countries at the northern portion of the Neotropics, to its austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n=5,941), and Cyclopes sp. has the fewest (n=240). The armadillo species with the most data is Dasypus novemcinctus (n=11,588), and the least recorded for Calyptophractus retusus (n=33). With regards to sloth species, Bradypus variegatus has the most records (n=962), and Bradypus pygmaeus has the fewest (n=12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other datasets of Neotropical Series which will become available very soon (i.e. Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans dataset

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016