Isolation and characterization of 5S rDNA sequences in catfishes genome (Heptapteridae and Pseudopimelodidae): perspectives for rDNA studies in fish by C0t method.

Sequences of 5S ribosomal RNA (rRNA) are extensively used in fish cytogenomic studies, once they have a flexible organization at the chromosomal level, showing inter- and intra-specific variation in number and position in karyotypes. Sequences from the genome of Imparfinis schubarti (Heptapteridae) were isolated, aiming to understand the organization of 5S rDNA families in the fish genome. The isolation of 5S rDNA from the genome of I. schubarti was carried out by reassociation kinetics (C0t) and PCR amplification. The obtained sequences were cloned for the construction of a micro-library. The obtained clones were sequenced and hybridized in I. schubarti and Microglanis cottoides (Pseudopimelodidae) for chromosome mapping. An analysis of the sequence alignments with other fish groups was accomplished. Both methods were effective when using 5S rDNA for hybridization in I. schubarti genome. However, the C0t method enabled the use of a complete 5S rRNA gene, which was also successful in the hybridization of M. cottoides. Nevertheless, this gene was obtained only partially by PCR. The hybridization results and sequence analyses showed that intact 5S regions are more appropriate for the probe operation, due to conserved structure and motifs. This study contributes to a better understanding of the organization of multigene families in catfish's genomes.

Molecular analysis of Aspergillus section Flavi isolated from Brazil nuts.

Brazil nuts are an important export market in its main producing countries, including Brazil, Bolivia, and Peru. Approximately 30,000 tons of Brazil nuts are harvested each year. However, substantial nut contamination by Aspergillus section Flavi occurs with subsequent production of aflatoxins. In our study, Aspergillus section Flavi were isolated from Brazil nuts (Bertholletia excelsa), and identified by morphological and molecular means. We obtained 241 isolates from nut samples, 41% positive for aflatoxin production. Eighty-one isolates were selected for molecular investigation. Pairwise genetic distances among isolates and phylogenetic relationships were assessed. The following Aspergillus species were identified: A. flavus, A. caelatus, A. nomius, A. tamarii, A. bombycis, and A. arachidicola. Additionally, molecular profiles indicated a high level of nucleotide variation within ß-tubulin and calmodulin gene sequences associated with high genetic divergence from RAPD data. Among the 81 isolates analyzed by molecular means, three of them were phylogenetically distinct from all other isolates representing the six species of section Flavi. A putative novel species was identified based on molecular profiles.

Strain-specific polyketide synthase genes of Aspergillus niger.

In silico comparison of 34 putative pks genes in Aspergillus niger strain CBS 513.88 versus A. niger strain ATCC 1015 genome revealed significant nucleotide identity (>95% covering a minimum of 99% of the gene sequence) for 31 of these genes (approximately 91%). A. niger CBS 513.88 harbors three putative pks genes (An01g01130, An11g05940, and An15g07920), for which nucleotide identity was not found in A. niger ATCC 1015. To compare the results of the in silico analysis with the in vivo situation, experimental data were obtained for a large number of A. niger strains obtained from different substrates and geographical regions. Three putative pks genes that were found to be variable between the two A. niger strains using bioinformatics tools were in fact strain-specific genes based on experimental data. The PCR amplification signals for the An01g01130, An11g05940, and An15g07920 pks genes were detected in only 97%, 71%, and 26% of the strains, respectively. Southern blot analyses confirmed the PCR data. Because one of the strain-specific pks genes (An15g07920) is located in a putative ochratoxin cluster, we focused our investigation on that region. We assessed the ochratoxin production capability of the 119 A. niger strains and found a positive association between the presence of this pks gene and the capability of the respective strain to produce ochratoxin.

A bovine teat papilloma specimen harboring Deltapapillomavirus (BPV-1) and Xipapillomavirus (BPV-6) representatives

The common occurrence of multiple papillomavirus infections has been shown in several studies involving the human host. However, investigations with the aim of identifying mixed papillomavirus infections in cattle have been conducted only recently. In the current work we describe a co-infection with two different bovine papillomavirus (BPV) types that was identified in a bovine teat papilloma. The skin wart was obtained from a cow belonging to a Brazilian beef herd. A PCR assay was carried out with the FAP primer pair, which amplifies a partial segment of the L1 gene (approximately 478 bp), and the amplicon was submitted to direct sequencing. Because nucleotide sequences with satisfactory quality scores were not obtained, the amplicon was cloned and further sequencing, involving ten selected clones, was performed. The sequence analysis of the cloned inserts revealed the presence of two different BPV types. BPV-1 (Deltapapillomavirus genus) was detected in six clones, while BPV-6 (Xipapillomavirus genus) was detected in four clones. This finding confirms the presence of BPV co-infection associated with cutaneous papillomatosis in cattle.

Em seres humanos, as infecções múltiplas pelo papilomavírus têm sido demonstradas em vários estudos. Em bovinos, somente recentemente foram conduzidas investigações com o objetivo de avaliar infecções mistas pelo papilomavírus. O presente trabalho teve como objetivo descrever a co-infecção por dois tipos de papilomavírus bovino (BPV) em um papiloma de teto. A amostra clínica foi obtida de uma vaca pertencente a um rebanho de corte localizado na região norte do estado do Paraná, Brasil. Inicialmente, a técnica de PCR foi realizada com o par de oligonucleotídeos iniciadores FAP, que amplificam um segmento do gene L1, sendo que o amplicon gerado foi submetido ao sequenciamento direto. Entretanto, como as sequências obtidas não apresentaram qualidade aceitável, o amplicon foi clonado e dez clones foram selecionados para um novo sequenciamento. A análise das sequências dos insertos revelou a presença de dois diferentes tipos de BPV. O BPV-1 (gênero Deltapapillomavirus) foi detectado em seis clones, enquanto o BPV-6 (gênero Xipapillomavirus) foi detectado em quatro clones. Esse resultado confirma a ocorrência da co-infecção pelo BPV associada a papilomas cutâneos em bovinos.

Genetic relationships among strains of the Aspergillus niger aggregate

We analyzed the genetic relationships between 51 fungal isolates previously identified as A. niger aggregate, obtained from dried fruit samples from worldwide origin and 7 A. tubingensis obtained from Brazilian coffee beans samples. Greater fungal diversity was found in black sultanas. Aspergillus niger sensu stricto was the most prevalent species. It was found in all fruit substrates of all geographical origins. Based on Random Amplification of Polymorphic DNA (RAPD) and β-tubulin sequences data two groups of A. niger were found. In spite of the small number of isolates from Group IV an association between extrolite patterns and molecular clustering is speculated. A. tubingensis were the second most frequent species and this species were clearly subdivided into two groups. The finding of two groups for A. tubingensis strains could not yet explain the contradictions found in the literature about the capability this species for ochratoxin production, because both of them were formed by only non-ochratoxin-producing strains.

Neste trabalho foi analisada a relação genética entre 51 isolados obtidos de amostras de frutas secas provenientes de diferentes regiões do previamente identificados como pertencentes ao agregado A. niger e 7 isolados de Aspergillus tubingensis obtidos de amostras de café do Brasil. Maior diversidade fúngica foi encontrada em uvas passas escuras. Aspergillus niger sensu stricto foi a espécie mais frequente. Esta espécie foi encontrada em todos os substratos e origens geográficas analisadas. Baseando-se nos dados de Polimorfismo de DNA Amplificado ao Acaso (RAPD) e sequências de nucleotídeos do gene da β-tubulina, dois grupos de A. niger foram observados. Apesar do pequeno número de isolados do grupo IV uma associação entre padrão de extrólitos e agrupamento molecular foi encontrada. A. tubingensis foi a segunda espécie mais frequente e foi claramente subdivida em dois grupos. Como os grupos de A. tubingensis são formados somente por linhagens não produtoras de ocratoxina A, a identificação destes grupos não explica a controvérsia encontrada na literatura sobre a capacidade desta espécie em produzir a referida toxina.

Identification of unreported putative new bovine papillomavirus types in Brazilian cattle herds.

The amplification by degenerate primers FAP59/FAP64 and sequencing allowed the detection of 15 putative new BPV types in cutaneous warts as well as in healthy skin. Four of these isolates were recently recognized as new BPV types (BPV-7, -8, -9, and -10) after determination of their complete genome sequences. In Brazil, investigations involving the definition of BPV types present in skin warts are still rare. The aim of the current study was to identify the BPV types associated with cutaneous papillomatosis observed in Brazilian cattle herds. Twenty-two cutaneous papilloma specimens were submitted to PCR assay employing the FAP primer pair. All PCR products with approximately 480 bp were submitted to direct sequencing. Cloning was performed for the amplicons which prior analysis revealed as putative new BPV types. From 16 cutaneous lesions, BPV-1, -2, and -6 were identified in two, six, and eight papilloma specimens, respectively. In addition, four putative new BPV types were identified in other six skin warts, and then designated as BPV/BR-UEL2 to -5. The detection of the BPV-1, -2, and -6 types in skin wart specimens supports the existence of these BPV types throughout the Brazilian cattle herd. In addition, the identification of four putative new BPV types is the first report of the presence of different BPV types in the American continent.