Comparison of a multiplex-PCR assay with mycolic acids analysis and conventional methods for the identification of Mycobacteria

A fast, sensitive and cost-effective multiplex-PCR assay for Mycobacterium tuberculosis complex (MTC) and Mycobacterium avium (M. avium) identification for routine diagnosis was evaluated. A total of 158 isolates of mycobacteria from 448 clinical specimens from patients with symptoms of mycobacterial disease were analyzed. By conventional biochemical methods 151 isolates were identified as M. tuberculosis, five as M. avium and two as Mycobacterium chelonae (M. chelonae). Mycolic acid patterns confirmed these results. Multiplex-PCR detected only IS6110 in isolates identified as MTC, and IS1245 was found only in the M. avium isolates. The method applied to isolates from two patients, identified by conventional methods and mycolic acid analysis, one as M. avium and other as M. chelonae, resulted positive for IS6110, suggesting co-infection with M. tuberculosis. These patients were successfully submitted to tuberculosis treatment. The multiplex-PCR method may offer expeditious identification of MTC and M. avium, which may minimize risks for active transmission of these organisms and provide useful treatment information.

PCR-based detection of Babesia bovis and Babesia bigemina in their natural host Boophilus microplus and cattle

PCR and nested-PCR methods were used to assess the frequency of Babesia bovis and Babesia bigemina infection in Boophilus microplus engorged females and eggs and in cattle reared in an area with endemic babesiosis. Blood and the engorged female ticks were from 27 naturally infested calves and 25 crossbred cows. The frequency of both Babesia species was similar in calves and cows (P > 0.05). Babesia bovis was detected in 23 (85.2%) calves and in 25 (100%) cows and B. bigemina was detected in 25 (92.6%) calves and in 21 (84%) cows. Mixed infections with the both Babesia species were identified in 42 animals, 21 in each age category. Of female ticks engorged on calves, 34.9% were negative and single species infection with B. bigemina (56.2%) was significantly more frequent (P < 0.01) than with B. bovis (4.7%). Most of the females (60.8%) engorged on cows did not show Babesia spp. infection and the frequency of single B. bovis infection (17.6%) was similar (P > 0.05) to the frequency of single B. bigemina infection (15.9%). Mixed Babesia infection was lower (P < 0.01) than single species infection in female ticks engorged either in cows (5.7%) or in calves (4.3%). An egg sample from each female was analysed for the presence of Babesia species. Of the egg samples from female ticks infected with B. bovis, 26 (47.3%) were infected while from those from female ticks infected with B. bigemina 141 (76.6%) were infected (P < 0.01). The results showed that although the frequency of both species of Babesia was similar in calves and cows, the infectivity of B. bigemina was higher to ticks fed on calves while to those ticks fed on cows the infectivity of both Babesia species was similar. © 2004 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Os granitóides brasilianos da faixa de dobramentos paraguai, MS e MT

The Brazilian Granitic Province from southeastern Mato Grosso do Sul and Mato Grosso region, central western Brazil, can be divided into two major groups and/or magmatic events related to the evolution of the Paraguay Fold Belt. The southern portion crops out in Mato Grosso do Sul State and is constituted by the Taboco, Rio Negro, Coxim and Sonora massifs forming NE-SW oriented, elongated small intrusions. The north portion crops out in Mato Grosso State and is constituted by the São Vicente, Araguaiana and Lajinha batholiths. Lithogeochemical aspects of the northern granites point to Type-I granites ranging from K calc-alkaline to high-K, peraluminous to metaluminous in composition, generated in an environment of continental collision and/or post- collision decompression. The southern granites are Type-I, from K calc-alkaline to high-K, peraluminous to subordinate metalummous, in a syn-collision continental arc environment with the exception of some pre-collisional facies from the Rio Negro Massif. The southern granites have less SiO 2 and K 2O, and are less differentiated and evolved than granites from the northern region. The four southern granites can be grouped into two subordinate sets with the degree of differentiation increasing from South (Taboco and Rio Negro) to North (Coxim and Sonora). The granitic rocks are characterized by a magmatism generated by melting of material from the lower crust which suggests that in this province the formation from non-cogenetic magmas with diversified compositions and distinct degrees of fractioning reaching more steady consolidated environments at the end of the collisional event in the southeastern Amazonian Craton.

Geologic e geoquímica do batólito Rapakivi Rio Branco, SW do Craton Amazônico - MT

The Rio Branco Rapakivi Batholith belongs to the Cachoeirinha Tectonic Domain, part of the Rio Negro-Juruena Geochronological Province located on the southwestern portion of the Amazonian Craton in Mato Grosso, Central Brasil. A systematic geological mapping on a 1:100.000 scale, coupled with petrographic and geochemical studies allowed to redefine this batholithic unit, to recognize faciological variations and to characterize the geochemical features of this rapakivi magmatism. The batholith is constituted by two major plutonic suites, the first forming a basic suite of fine-grained, equigranular, mesoto melanocratic gray to black lithotypes, with usually discontinuous porphyritic varieties located near the margins of the intrusion. The second one is characterized by acid to intermediate rocks constituted by porphyritic granites, in part granophyric, with rapakivi textures. They have K-feldspar phenocrysts of up to 4cm. Three distinct petrographic facies are recognized in this suite: 1. equigranular to pegmatitic monzogranites; 2. red rapakivi leuco-monzogranites; 3. dark red rapakivi monzogranites to quartz-monzonites. Rocks present SiO2 contents from 67% to 73%, show peraluminous to metaluminous compositions and define a high-K calc-alkaline to shoshonitic magmatism in an I- and A-type, post-orogenic to anorogenic intraplate environment. The magmatic processes are associated with the end of the collisional event that consolidated and stabilized the SW part of the Amazonian Craton.

Heminested reverse-transcriptase polymerase chain reaction (hnRT-PCR) as a tool for rabies virus detection in stored and decomposed samples

Background. The use of methods, both sensitive and specific, for rabies diagnosis are important tools for the control and prophylaxis of the disease. Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) has been used in rabies diagnosis with good results, even in decomposed materials. Additionally, molecular techniques have been used for epidemiological studies and to gain a better knowledge of viral epidemiology. Findings. The aim of this work was to evaluate the RT-PCR and hnRT-PCR for rabies virus detection in original tissues stored at -20°C for different periods considering their use for rabies virus detection in stored and decomposed samples. RT-PCR and hnRT-PCR were evaluated in 151 brain samples from different animal species, thawed and left at room temperature for 72 hours for decomposition. The RT-PCR and hnRT-PCR results were compared with previous results from Direct Fluorescent Antibody Test and Mouse Inoculation Test. From the 50 positive fresh samples, 26 (52%) were positive for RT-PCR and 45 (90%) for hnRT-PCR. From the 48 positive decomposed samples, 17 (34, 3%) were positive for RT-PCR and 36 (75%) for hnRT-PCR. No false-positives results were found in the negatives samples evaluated to the molecular techniques. Conclusion. These results show that the hnRT-PCR was more sensitive than RT-PCR, and both techniques presented lower sensibility in decomposed samples. The hnRT-PCR demonstrated efficacy in rabies virus detection in stored and decomposed materials suggesting it's application for rabies virus retrospective epidemiological studies. © 2008 Arajo et al; licensee BioMed Central Ltd.

Assessing genetic variability in bat species of Emballonuridae, Phyllostomidae, Vespertilionidae and Molossidae families (Chiroptera) by RFLP-PCR

A PCR-RFLP analysis of the restriction pattern in nuclear (RAG2) and mitochondrial (12S/16S) gene sequences of bat species from the Molossidae, Phyllostomidae, Vespertilionidae, and Emballonuridae families produced a large number of fragments: 107 for RAG2 and 155 for 12S/16S combined in 139 and 402 haplotypes, respectively. The values detected for gene variation were low for both sequences (0.13 for RAG2 and 0.15 for 12S/16S) and reflected their conservative feature, reinforced by high values of inter- and intraspecies genetic identity (70-100%). The species with a high gene divergence were variable in the analyses of RAG2 (Eumops perotis, Artibeus lituratus, and Carollia perspicillata) and of 12S/16S (Nyctinomops laticaudatus, C. perspicillata, and Cynomops abrasus), and furthermore, one of them, C. perspicillata, also showed the highest intraspecific variation. The species that exhibited the lowest variation for both genes was Molossus rufus. In the families, the highest variation was observed in the Molossidae and this can be attributed to variation exhibited by Eumops and Nyctinomops species. The variations observed were interpreted as a natural variability within the species and genus that exhibited a conserved pattern in the two gene sequences in different species and family analyzed. Our data reinforce the idea that the analyses of mitochondrial and nuclear genes contribute to our knowledge of the diversity of New World bats. The genetic variability found in different taxa suggests that an additional diversity, unnoticed by other methods, can be revealed with the use of different molecular strategies. ©FUNPEC-RP.

Contexto tectônico dos granitóides neoproterozóicos da faixa de dobramentos paraguai, MS e MT

The Neoproterozoic Granitic Province from the southeast of Mato Grosso and Mato Grosso do Sul region is constituted by seven distinctive granitic bodies, emplaced in the epimetamorphic rocks of the Cuiabá Group and related to the evolution of Paraguai Folded Belt. The Northern portion crops out in Mato Grosso State and is constituted by São Vicente, Araguaiana and Lajinha batholiths; the Southern portion crops out in the Mato Grosso do Sul State and is represented the Sonora, Coxim Rio Negro and Taboco massifs. The structural evolution is evidenced by the presence of three deformational phases, the first one is characterized by axial planar foliation (S 1), parallel or sub parallel to S 0, with attitude N60E/70NW; the second constitutes the most important phase for the tectonic arrangement and is defined by a slaty and/or crenulation cleavages (S 2), with attitude N10W/30SW and contact metamorphism associated to the emplacement of granitic bodies, the third phase is characterized by a weak retrometamorphic cleavage (S 3) with attitude N10E/ 80NW, that evolves local and gradually to strike-slip shear zones. The geological data suggest that this province was formed syn- to post tectonic to the D2 deformational set associated to the end of the collisional event in the Southeastern of the Amazonian Craton.

Multiplex PCR use for Staphylococcus aureus identification and oxacillin and mupirocin resistance evaluation

Oxacillin-resistant Staphylococcus aureus represents a serious problem in hospitals worldwide, increasing infected patients' mortality and morbidity and raising treatment costs and internment time. In this study, the results of using the Multiplex PCR technique to amplify fragments of the genes femA (specific-species), mecA (oxacillin resistance) and ileS-2 (mupirocin resistance) were compared with those of tests conventionally used to identify S. aureus isolates and ascertain their resistance to drugs. Fifty S. aureus strains were isolated from patients receiving treatment at UNOESTE University Hospital in Presidente Prudente, SP, Brazil. The 686 bp fragment corresponding to the gene femA was amplified and detected in all the isolates. On the other hand, the 310 bp fragment corresponding to the mecA gene was amplified in 29 (58%) of the isolates. All of the isolates showed sensitivity to mupirocin in the agar diffusion test, which was corroborated by the lack of any amplicon of the 456 bp fragment corresponding to the ileS-2 gene, in the PCR bands. The conventional tests to identify S. aureus and detect resistance to oxacillin and mupirocin showed 100% agreement with the PCR Multiplex results. The use of techniques for rapid and accurate identification of bacteria and assessment of their resistance may be valuable in the control of infection by resistant strains, allowing the rapid isolation and treatment of an infected patient. However, the results demonstrate that traditional phenotypic tests are also reliable, though they take more time.

Genetic polymorphism, molecular characterization and relatedness of Macrobrachium species (Palaemonidae) based on RAPD-PCR.

The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.

Magmatismo do batólito rapakivi Rio Branco, sw do Cráton Amazônico (MT)

Rio Branco Rapakivi Batholith is located on the southwestern portion of the Amazonian Craton in Mato Grosso and belongs to the Cachoeirinha Tectonic Domain, part of the Rio Negro-Juruena Geochronological Province, Central Brasil. The batholith is constituted by microgabbros to quartz microgabbros and microdiorites to quartz microdiorites, middle to fine-grained equigranular to porphyritic varieties form the Rio Branco Intrusive Basic Suite, showing a discontinuous distribution and located near the margins of the intrusion.Majorly constituted by porphyritic, granophyric and isotropic facies of Rio Branco Intrusive Acid Suit which is composed by older dark red rapakivi monzogranites to quartz monzonites and quartz sienites (1403±0.6 Ma) and the younger red rapakivi leuco-monzogranites (1382±49 Ma) and late equigranular to pegmatitic monzogranites. The magmatism is constituted by two distinct magmas related to the end of the collisional event of Cachoeirinha Orogeny, one with alkaline basalts generated in an intraplate environment and the other postorogenic to anorogenic with peraluminous to metaluminous compositions and define a high-K calc-alkaline to shoshonitic magmatism in transition among the I- and A-types. The contacts are marked by extensive mafic sills and dikes of alkaline basalts derived from intraplate environment of the Salto do Céu Intrusive Basic Suite (±808 Ma) associate to the Sunsás-Aguapei Orogenic Belt and metasedimentary rocks of the Aguapeí Grup.

Use of reverse transcriptase polymerase chain reaction (RT-PCR) in molecular screening of Newcastle disease virus in poultry and free-living bird populations

The aim of this study was to evaluate a simple molecular method of reverse transcriptase polymerase chain reaction (RT-PCR) to differentiate Newcastle disease virus strains according to their pathogenicity, in order to use it in molecular screening of Newcastle disease virus in poultry and free-living bird populations. Specific primers were developed to differentiate LaSota-LS-(vaccine strain) and Sao Joao do Meriti-SJM-strain (highly pathogenic strain). Chickens and pigeons were experimentally vaccinated/infected for an in vivo study to determine virus shedding in feces. Validation of sensitivity and specificity of the primers (SJM and LS) by experimental models used in the present study and results obtained in the molecular analysis of the primers by BLAST made it possible to generalize results. The development of primers that differentiate the level of pathogenicity of NDV stains is very important, mainly in countries where real-time RT-PCR is still not used as a routine test. These primers were able to determine the presence of the agent and to differentiate it according to its pathogenicity. © 2012 Springer Science+Business Media B.V.

Exequibility of differential gene expression analysis by DDRT-PCR in murine bone marrow cells

Model of study: Experimental study. Introduction: Recently, stem cell research has generated great interest due to its applicability in regenerative medicine. Bone marrow is considered the most important source of adult stem cells and the establishment of new methods towards gene expression analysis regarding stem cells has become necessary. Thus Differential Display Reverse Transcription Polymerase Chain Reaction (DDRT-PCR) may be an accessible tool to investigate small differences in the gene expression of different stem cells in distinct situations. Aim: In the present study, we investigated the exequibility of DDRT-PCR to identify differences in global gene expression of mice bone marrow cells under two conditions. Methods: First, bone marrow cells were isolated fresh and a part was cultivated during one week without medium replacement. Afterwards, both bone marrow cells (fresh and cultivated) were submitted to gene expression analyses by DDRT-PCR. Results: Initially, it was possible to observe in one week-cultured bone marrow cells, changes in morphology (oval cells to fibroblastic-like cells) and protein profile, which was seen through differences in band distribution in SDS-Page gels. Finally through gene expression analysis, we detected three bands (1300, 1000 and 225 bp) exclusively expressed in the fresh bone marrow group and two bands (400 and 300 bp) expressed specifically in the cultivated bone marrow cell group. Conclusions: In summary, the DDRT-PCR method was proved efficient towards the identification of small differences in gene expression of bone marrow cells in two defined conditions. Thus, we expect that DDRT-PCR can be fast and efficiently designed to analyze differential gene expression in several stem cell types under distinct conditions.

A PCR/RFLP methodology to identify non-Amazonian Brazilian deer species

Due to the necessity of using noninvasive samples to study animals as elusive as the deer that occur in Brazil, we realized it was important to develop a PCR/RFLP protocol to assist in identifying such samples. Thus we developed a protocol in which a fragment of the cytochrome b gene is digested with two enzymes: SspI, which distinguishes species of the genus Mazama from Blastocerus dichotomus and Ozotoceros bezoarticus, and TAQα1 which permits differentiation between the species B. dichotomus and O. bezoarticus. © 2013 Springer Science+Business Media Dordrecht.

Use of PCR to estimate the prevalence of Equus caballus papillomavirus in aural plaques in horses

Aural plaques occur on the skin of the medial surface of the pinnae of horses. In this study the presence of Equus caballus papillomavirus (EcPV)-3 and -4 DNA was assessed in 45 such plaques using a 'touchdown' PCR. Papillomaviruses (PVs) were detected in 62.3% (28/45) of samples: EcPV-3 and -4 DNA in 8.89% (4/45) and 37.78% (17/45) of samples, respectively, with 15.56% (7/45) of samples exhibiting co-infection. Viral DNA was not detected in 37.78% (17/45) of samples, suggesting the possible existence of other equine PVs. Neither EcPV-3 nor -4 were detected in negative control skin. This study is the first to evaluate the prevalence of these two viruses in equine aural plaques. © 2013 Elsevier Ltd.