Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restriction, and AMPylating enzymes

Background: The whole-genome sequences of nine Rhizobium species were evaluated using different in silico molecular techniques such as AFLP-PCR, restriction digest, and AMPylating enzymes. The entire genome sequences were aligned with progressiveMauve and visualized by reconstructing phylogenetic tree using NTSYS pc 2.11X. The "insilico.ehu.es" was used to carry out in silico AFLP-PCR and in silico restriction digest of the selected genomes. Post-translational modification (PTM) and AMPylating enzyme diversity between the proteome of Rhizobium species were determined by novPTMenzy. Results: Slight variations were observed in the phylogeny based on AFLP-PCR and PFGE and the tree based on whole genome. Results clearly demonstrated the presence of PTMs, i.e., AMPylation with the GS-ATasE (GlnE), Hydroxylation, Sulfation with their domain, and Deamidation with their specific domains (AMPylating enzymes) GS-ATasE (GlnE), Fic, and Doc (Phosphorylation); Asparagine_hydroxylase and Collagen_prolyl_lysyl_hydroxylase; Sulfotransferase; and CNF (Cytotoxic Necrotizing Factors), respectively. The results pertaining to PTMs are discussed with regard to functional diversities reported in these species. Conclusions: The phylogenetic tree based on AFLP-PCR was slightly different from restriction endonuclease- and PFGE-based trees. Different PTMs were observed in the Rhizobium species, and the most prevailing type of PTM was AMPylation with the domain GS-ATasE (GlnE). Another type of PTM was also observed, i.e., Hydroxylation and Sulfation, with the domains Asparagine_hydroxylase and Collagen_prolyl_lysyl_hydroxylase and Sulfotransferase, respectively. The deamidation type of PTM was present only in Rhizobium sp. NGR234. How to cite: Qureshi MA, Pervez MT, Babar ME, et al. Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restrictions and ampylating enzymes.

Identification of Leptospira serovars by RFLP of the RNA polymerase beta subunit gene (rpoB)

Leptospires are usually classified by methods based on DNA-DNA hybridization and the conventional cross-agglutination absorption test, which uses polyclonal antibodies against lipopolysaccharides. In this study, the amplification of the rpoB gene, which encodes the beta-subunit of RNA polymerase, was used as an alternative tool to identify Leptospira. DNA extracts from sixty-eight serovars were obtained, and the hypervariable region located between 1990 and 2500-bp in the rpoB gene was amplified by polymerase chain reaction (PCR). The 600-bp amplicons of the rpoB gene were digested with the restriction endonucleases TaqI, Tru1I, Sau3AI and MslI, and the restriction fragments were separated by 6% polyacrylamide gel electrophoresis. Thirty-five fragment patters were obtained from the combined data of restriction fragment length polymorphism (PCR-RFLP) analysis and used to infer the phylogenetic relationships among the Leptospira species and serovars. The species assignments obtained were in full agreement with the established taxonomic classifications. Twenty-two serovars were effectively identified based on differences in their molecular profiles. However, the other 46 serovars remained clustered in groups that included more than one serovar of different species. This study demonstrates the value of RFLP analysis of PCR-amplified rpoB as an initial method for identifying Leptospira species and serovars.

Hipermetilación del gen supresor de tumores p53 en pacientes pediátricos con leucemia linfoblástica aguda / Hypermethylation of tumor suppressor gene p53 in Chilean pediatrics patients under 15 years with acute lymphoblastic leukemia

La leucemia linfoblástica aguda (LLA) es la neoplasia maligna hematooncólogica más frecuente en pacientes pediátricos contando hasta 75% de las leucemias y 32-35% del total de cánceres infantiles. Aunque la LLA es considerada una enfermedad con base genética, es cada vez más evidente que alteraciones epigenéticas desempeñan un rol central en su patogénia y progresión. La hipermetilación de regiones promotoras de genes es asociada con la pérdida de función génica. El gen supresor de tumores p53 (GST), es uno de los principales genes en el ciclo celular y apoptosis. El objetivo de este trabajo fue determinar el estado de metilación en la región del promotor-exón 1 del GST p53 y la asociación con la supervivencia en menores de 15 años con LLA. Se analizaron 40 pacientes provenientes de la Región de la Araucanía-Chile. La hipermetilación del p53 se determinó combinando enzimas de restricción sensibles a metilación (HpaII y EcoR II) y reacción en cadena de la polimerasa. Los resultados indicaron que 15/40 casos (37,5%) presentaron hipermetilación. Se encontró una diferencia estadística en la supervivencia según estado de metilación de p53 en el grupo de niñas (p=0,02). Considerando el total de pacientes, una tendencia a mejor supervivencia cuando los recuentos de leucocitos fueron <30.000/mm3 (p=0,08). Se encontró frecuentemente hipermetilado el gen p53 en la región del promotor-exon1. Esto indicaría que la hipermetilación del GST p53 puede ser un evento importante en la patogénesis de la LLA.

Acute lymphoblastic leukemia (ALL) is the most common hematology oncology malignancy in pediatric patients counting up to 75% of leukemias and 32­35% of all childhood cancers. Although ALL is considered a disease with a genetic basis, it is increasingly clear that epigenetic alterations play a central role in the pathogenesis and work was to determine the methylation status in promoter-exon1 of the TSG-p53 and association with survival in children under 15 years with ALL. In our study 40 patients from the Araucanía Region, Chile were analyzed. Hypermethylation of p53 was determined by combining restriction enzymes sensitive to methylation (HpaII and EcoR II) and polymerase chain reaction. Results indicated that 15/40 cases (37.5%) showed hypermethylation. Statistical difference was found in survival according to p53 methylation status in the girls group (p=0.02). Considering all patients, there was a trend to improved survival when leukocyte counts were <30.000/ul (p=0.08). We found the p53 gene frequently hypermethylated in the promoter-exon1 region. This would indicate that TSG p53 hypermethylation may be an important event in the pathogenesis of ALL.

Evaluation of INNO-LiPA mycobacteria v2 assay for identification of rapidly growing mycobacteria

A total of 54 rapidly growing mycobacteria (RGM) isolated from patients attended in the two hospitals of Cádiz Bay (Spain) were selected during a seven-year-period (2000-2006) in order to evaluate the INNO-LiPA Mycobacteria v2 assay for mycobacterial identification, based on the reverse hybridization principle. The strains were cultured in Lõwenstein-Jensen and Middlebrook 7H9 media and identified to the species level by sequencing of the 16S rRNA, PCR-restriction enzyme analysis of the hsp65 gene, conventional tests and INNO-LiPA Mycobacteria v2 assay. By the molecular methods we identified a total of 12 different species: 23 Mycobacterium fortuitum, 11 M. chelonae, 10 M. abscessus, 2 M. senegalense, 1 M. alvei, 1 M. brumae, 1 M. mageritense, 1 M. mucogenicum, 1 M. neoaurum, 1 M. peregrinum, 1 M. septicum and 1 M. smegmatis. Fifty two strains (96.3 percent) were correctly identified by conventional techniques and 47 strains (87.0 percent) by INNO-LiPA Mycobacteria v2 assay. We find INNO-LiPA Mycobacteria v2 assay simple to perform but it provides few advantages in comparison with conventional methods and sometimes needs complementary tests to identify Mycobacterium fortuitum complex, M. chelonae complex and specific species due to the great heterogeneity in the RGM group.

Identificação de micobactérias não tuberculosas isoladas de sítios estéreis em pacientes em um hospital universitário na cidade do Rio de Janeiro / Identification of nontuberculous mycobacteria isolated from clinical sterile sites in patients at a university hospital in the city of Rio de Janeiro, Brazil

OBJETIVO: Identificar micobactérias não tuberculosas (MNT) isoladas de sítios estéreis em pacientes internados no Hospital Universitário Clementino Fraga Filho, Rio de Janeiro (RJ) entre 2001 e 2006. MÉTODOS: Durante o período do estudo, 34 isolados de MNT de sítios estéreis de 14 pacientes, a maioria HIV positivos, foram submetidos a identificação fenotípica e hsp65 PCR-restriction enzyme analysis (PRA, análise por enzimas de restrição por PCR do gene hsp65). RESULTADOS: A maioria dos isolados foi identificada como Mycobacterium avium, seguida por M. monacense, M. kansasii e M. abscessus em menores proporções. CONCLUSÕES: A combinação de PRA, um método relativamente simples e de baixo custo, com algumas características fenotípicas pode fornecer a identificação correta de MNT na rotina de laboratórios clínicos.

OBJECTIVE: To identify nontuberculous mycobacteria (NTM) isolated from sterile sites in patients hospitalized between 2001 and 2006 at the Clementino Fraga Filho University Hospital, located in the city of Rio de Janeiro, Brazil. METHODS: During the study period, 34 NTM isolates from sterile sites of 14 patients, most of whom were HIV-positive, were submitted to phenotypic identification and hsp65 PCR-restriction enzyme analysis (PRA). RESULTS: Most isolates were identified as Mycobacterium avium, followed by M. monacense, M. kansasii, and M. abscessus. CONCLUSIONS: The combination of PRA, a relatively simple and inexpensive method, with the evaluation of a few phenotypic characteristics can allow NTM to be accurately identified in the routine of clinical laboratories.

Rotavirus A genotype G1P[8]: a novel method to distinguish wild-type strains from the Rotarix® vaccine strain

Rotaviruses are important enteric pathogens for humans and animals. Group A rotaviruses (RV-A) are the most common agents of severe gastroenteritis in infants and young children and vaccination is the most effective method to reduce RV-A-associated diseases. G1P[8], the most prevalent RV-A genotype worldwide, is included in the RV-A vaccine Rotarix®. The discrimination between wild-type G1P[8] and vaccine G1P[8] strains is an important topic in the study of RV-A epidemiology to manage outbreaks and to define control measures for vaccinated children. In this study, we developed a novel method to segregate the wild-type and vaccine strains using restriction endonucleases. The dsRNA from the Rotarix® vaccine was sequenced and the NSP3 gene was selected as the target gene. The vaccine strain has a restriction pattern that is different than that of wild-type RV-A G1P[8] isolates after digestion with the restriction endonuclease BspHI. This pattern could be used as a marker for the differentiation of wild-type G1P[8] strains from the vaccine strain.

Differentiation of Bovine coronavirus (BCoV) genotypes by a restriction enzyme assay

This article reports the use of the GsuI restriction enzyme to differentiate genotypes of Bovine Coronavirus (BCoV), based on an 18-nucleotide deletion of S1-coding region found in one of the two genotypes. It was concluded that this assay can be used as a rapid tool for BCoV genotypes differentiation.

Antimicrobial resistance and investigation of the molecular epidemiology of Listeria monocytogenes in dairy products / A resistência antimicrobiana e investigação de epidemiologia molecular de Listeria monocytogenes em produtos lácteos

INTRODUCTION: Listeria monocytogenes is a ubiquitous microorganism in nature and is responsible for listeriosis, an infectious disease caused by consumption of contaminated food. METHODS: Molecular characterization was performed on 19 strains of Listeria monocytogenes (serovars 1/2a, 1/2b, 4b and 4c), isolated from dairy products in Rio Grande do Sul, Brazil. The molecular techniques applied were random amplification of polymorphic DNA and restriction enzyme analysis. In addition to the molecular analysis, the antimicrobial resistance profile was determined. RESULTS: The strains studied showed a low degree of diversity. In relation to the antimicrobial resistance profile of those microorganisms from the samples analyzed, all of them were susceptible to the antimicrobials tested. CONCLUSIONS: The molecular techniques that were used presented good discriminatory power for the strains studied. Furthermore, all of the samples that were analyzed were susceptible to the antimicrobials tested.

INTRODUÇÃO: Listeria monocytogenes é um microrganismo que se encontra disseminado na natureza, sendo responsável por causar listeriose, uma doença infecciosa causada pelo consumo de alimentos contaminados. MÉTODOS: A análise molecular de 19 linhagens de Listeria monocytogenes, sorovares 1/2a, 1/2b, 4b, 4c, isoladas de produtos lácteos do Rio Grande do Sul, Brasil. As técnicas moleculares aplicadas foram: Amplificação Randômica do DNA Polimórfico e Análise por Enzimas de Restrição. Além da análise molecular foi realizado o perfil de resistência antimicrobiana. RESULTADOS: As linhagens estudadas mostraram baixo grau de diversidade, em relação ao perfil de resistência antimicrobiana desses microrganismos das amostras analisadas todas foram susceptíveis aos antimicrobianos testados. CONCLUSÕES: As técnicas moleculares estudadas apresentaram um bom poder de discriminação para as linhagens estudadas. Além disso, todas as amostras analisadas foram susceptíveis aos antimicrobianos analisados.

RFLP analysis of a PCR-amplified fragment of the 16S rRNA gene as a tool to identify Enterococcus strains

Restriction fragment length polymorphism (RFLP) analysis of a PCR-amplified fragment of the 16S rRNA gene was performed on reference strains belonging to 21 different enterococcal species and on 75 Enterococcus isolates recovered from poultry meat, pasteurised milk and fresh cheese. PCR amplification generated a 275 bp fragment, which was digested with three restriction endonucleases (DdeI, HaeIII, HinfI). The strains were divided into five groups (groups A-E) on the basis of their restriction patterns. Five biochemical tests (arabinose, arginine, manitol, methyl-â-D-glucopyranoside and raffinose) were then performed in addition to RFLP analysis to narrow the identification of enterococcal strains to the species level. PCR-RFLP, in conjunction with the selected biochemical tests, allowed the precise identification of the 21 species of Enterococcus included in the present study. This proposed method is relatively simple and rapid and can be useful as an adjunct tool for accurate identification of Enterococcus.

Conversion of barley SNPs into PCR-based markers using dCAPS method

Molecular genetic research relies heavily on the ability to detect polymorphisms in DNA. Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation in the genome. In combination with a PCR assay, the corresponding SNP can be analyzed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. The dCAPS method exploits the well-known specificity of a restriction endonuclease for its recognition site and can be used to virtually detect any SNP. Here, we describe the use of the dCAPS method for detecting single-nucleotide changes by means of a barley EST, CK569932, PCR-based marker.

Hidden heterochromatin: characterization in the Rodentia species Cricetus cricetus, Peromyscus eremicus (Cricetidae) and Praomys tullbergi (Muridae)

The use of in situ restriction endonuclease (RE) (which cleaves DNA at specific sequences) digestion has proven to be a useful technique in improving the dissection of constitutive heterochromatin (CH), and in the understanding of the CH evolution in different genomes. In the present work we describe in detail the CH of the three Rodentia species, Cricetus cricetus, Peromyscus eremicus (family Cricetidae) and Praomys tullbergi (family Muridae) using a panel of seven REs followed by C-banding. Comparison of the amount, distribution and molecular nature of C-positive heterochromatin revealed molecular heterogeneity in the heterochromatin of the three species. The large number of subclasses of CH identified in Praomys tullbergi chromosomes indicated that the karyotype of this species is the more derived when compared with the other two genomes analyzed, probably originated by a great number of complex chromosomal rearrangements. The high level of sequence heterogeneity identified in the CH of the three genomes suggests the coexistence of different satellite DNA families, or variants of these families in these genomes.

Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa (Oxalidacea) and related species

Oxalis tuberosa is an octoploid Andean tuber crop called oca that belongs to the worldwide distributed genus Oxalis. The genus is very heterogeneous and its systematics is still problematic. It has been proposed that O. tuberosa evolved by polyploidization of a still not defined ancestor that belongs to an alliance of species sharing the same basic chromosome number (x = 8). Nuclear rDNA units of O. tuberosa and a selected group of four related diploid species were characterised by RFLP using different restriction endonucleases and southern hybridization probes to produce a restriction map for EcoRI and BamHI. The major rDNA unit length in O. tuberosa was estimated at 10.7 kbp. As expected, restriction site variation was observed mainly in the intergenic spacer (IGS), but was also detected in coding regions. Restriction site mapping organization of the transcribed rDNA unit of O. tuberosa is very similar to O. oblongiformis. Nucleotide sequencing of a region of O. peduncularis IGS generated a complex organization pattern of repeats and subrepeats. Diploid species O. peduncularis, O. tabaconasensis and O. aff. villosula exhibited a ladder pattern that is a consequence of a 170 bp subrepeat unit indicating that these species share organization similarity and sequence homology. The variation pattern provided information to compare among diploid species, although it did not help to clarify taxonomic relationships between O. tuberosa and the putative diploid ancestors analysed in this study. Nonetheless, the RFLP pattern exhibited by O. tuberosa for the IGS region was quite unique and will be a useful tool to prospect in other related species.

Clinical and molecular diagnosis of a Costa Rican family with autosomal recessive myotonia congenita (Becker disease) carrying a new mutation in the CLCN1 gene

Myotonia congenita is a muscular disease characterized by myotonia, hypertrophy, and stiffness. It is inherited as either autosomal dominant or recessive known as Thomsen and Becker diseases, respectively. Here we confirm the clinical diagnosis of a family diagnosed with a myotonic condition many years ago and report a new mutation in the CLCN1 gene. The clinical diagnosis was established using ocular, cardiac, neurological and electrophysiological tests and the molecular diagnosis was done by PCR, SSCP and sequencing of the CLCN1 gene. The proband and the other affected individuals exhibited proximal and distal muscle weakness but no hypertrophy or muscular pain was found. The myotatic reflexes were lessened and sensibility was normal. Electrical and clinical myotonia was found only in the sufferers. Slit lamp and electrocardiogram tests were normal. Two affected probands presented diminution of the sensitive conduction velocities and prolonged sensory distal latencies. The clinical spectrum for this family is in agreement with a clinical diagnosis of Becker myotonia. This was confirmed by molecular diagnosis where a new disease-causing mutation (Q412P) was found in the family and absent in 200 unaffected chromosomes. No latent myotonia was found in this family; therefore the ability to cause this subclinical sign might be intrinsic to each mutation. Implications of the structure-function-genotype relationship for this and other mutations are discussed. Adequate clinical diagnosis of a neuromuscular disorder would allow focusing the molecular studies toward the confirmation of the initial diagnosis, leading to a proper clinical management, genetic counseling and improving in the quality of life of the patients and relatives.

La miotonía congénita es una enfermedad muscular caracterizada por miotonía, hipertrofia y rigidez. Se presenta con dos patrones de herencia, autosómica dominante en cuyo caso recibe el nombre de miotonía de Thomsen, o autosómica recesiva conocida como miotonía de Becker. En este trabajo se confirmó el diagnóstico clínico presuntivo hecho hace algunos años en una familia con una condición miotónica y se reporta una nueva mutación en el gen CLCN1. El diagnóstico clínico se estableció después de estudios oculares, cardíacos, neurológicos y electrofisiológicos. El diagnóstico molecular fue hecho mediante la PCR, SSCP y secuenciación del gen CLCN1. El caso índice y los otros individuos afectados exhibieron debilidad muscular proximal y distal, pero no se encontró hipertrofia ni dolor muscular. Los reflejos miotáticos estuvieron disminuidos y la sensibilidad fue normal. Se encontró miotonía clínica y eléctrica solo en los individuos afectados. Las pruebas de lámpara de hendidura y electrocardiograma resultaron normales. Dos individuos afectados presentaron disminución de las velocidades de conducción sensitiva y latencias distales sensoriales prolongadas. El cuadro clínico concuerda con la miotonía de Becker, lo cual se confirmó con el hallazgo de una mutación responsable de la enfermedad en el gen CLCN1 (Q412P), la cual se encontró en la familia y estuvo ausente en 200 cromosomas provenientes de la población general. No se encontró miotonía latente, por lo que probablemente la habilidad de causar este signo subclínico es intrínsica de cada mutación. Afinar el diagnóstico clínico diferencial de las enfermedades neuromusculares permitiría enfocar los estudios moleculares hacia la confirmación del diagnóstico inicial en forma eficiente, lo cual permitiría un manejo clínico y asesoramiento genético más adecuados y una mejora en la calidad de vida de los pacientes y sus familias.

Adenoviruses C in non-hospitalized Mexican children older than five years of age with acute respiratory infection

Adenoviruses (AdV) are commonly involved in acute respiratory infections (ARI), which cause high morbidity and mortality in children. AdV are grouped in six species (A-F), which are associated with a wide range of diseases. The aim of this study was to identify the AdV species infecting non-hospitalized Mexican children with ARI symptoms, attending to the same school. For that, a PCR/RFLP assay was designed for a region of the hexon gene, which was chosen, based on the bioinformatical analysis of AdV genomes obtained from GenBank. A total of 100 children's nasopharyngeal samples were collected from January to June, 2005, and used for viral isolation in A549 cells and PCR/RFLP analysis. Only 15 samples produced cytopathic effect, and in all of them AdV C was identified. AdV C was also identified in eight additional nasopharyngeal samples which were negative for viral isolation. In summary, this outpatient population showed a rate of AdV infection of 23 percent, and only AdV C was detected.

Caracterización por Ardrea de microorganismos acidófilos aislados en minas de oro de Marmato, Colombia / Ardrea characterisation of acidophilic micro-organisms isolated from gold mines in Marmato, Colombia

La bio-oxidación de minerales mejora la recuperación de metales valiosos y disminuye el impacto negativo causado por los subproductos de las operaciones mineras, pero las interacciones de los microorganismos involucrados son poco conocidas. Con el objeto de avanzar en el estudio de interacciones microbianas de bacterias acidófilas nativas en cultivos mixtos, en este trabajo se utilizó la siembra en medio sólido doble capa y el análisis de enzimas de restricción del ADN ribosomal amplificado (Ardrea)con las enzimas Eco72I, Eco24I, XcmI y BsaAI para caracterizar cuatro aislados tomados de minas de oro de Marmato, Colombia. Los aislados que oxidan hierro y azufre exhibieron patrones de restricción del gen ARNr 16S compatibles con los reportados para Acidithiobacillus ferrooxidans, aunque uno de ellos mostró una morfología de colonia que no ha sido descrita para esta especie; el aislado que oxida azufre mostró un patrón que coincide con el análisis teórico realizado sobre secuencias para Acidithiobacillus thiooxidans incluidas en bases de datos primarias. La técnica Ardrea permitió diferenciar entre At.ferrooxidans y At.thiooxidans, y verificar si la identidad de los aislados correspondía con sus características fisiológicas y la morfología de sus colonias.

Cre-loxP recombination vectors for promoter studies

For promoter studies the cloning, subcloning and transfer to different plasmid vectors usually requires use of restriction enzymes and ligation reactions. One obstacle is the nucleotide polymorphisms of eukaryotic genomic DNA, which has the consequence that a sequence often differs from published sequences. Therefore sequencing, rigorous restriction enzyme analysis or introduction of suitable sites has to be performed prior to cloning and subcloning. In addition, conventional methods using restriction enzymes, insert purifications and ligations is expensive and labour demanding. We have developed a fast, efficient and inexpensive Cre recombinase-loxP based method, which allows cloning of promoter regions and subcloning of these into a variety of vectors in a restriction enzyme independent manner. We here demonstrate that expression of a number of reporter genes and a therapeutic gene from both a viral and 2 mammalian promoters cloned by this recombinase method have activities comparable to conventionally cloned plasmids.

First-trimester prenatal diagnosis of pyruvate kinase deficiency in an Indian family with the pyruvate kinase-Amish mutation

Pyruvate kinase (PK) deficiency is a rare red cell glycolytic enzymopathy. The purpose of the present investigation was to offer prenatal diagnosis for PK deficiency to a couple who had a previous child with severe enzyme deficiency and congenital non-spherocytic hemolytic anemia. PK deficiency was identified in the family by assaying the enzyme activity in red cells. Chorionic villus sampling was performed in an 11-week gestation and the mutation was located in exon 10 of the PKLR gene characterized by polymerase chain reaction and using restriction endonuclease digestion with the MspI enzyme, which was confirmed by DNA sequencing on the ABI 310 DNA sequencer. Both the parents were heterozygous for the 1436G-->A [479 Arg-->His] mutation in exon 10 and the proband was homozygous for this mutation. The fetus was also heterozygous for this mutation and the pregnancy was continued. Prenatal diagnosis allowed the parents with a severely affected child with PK deficiency to have the reproductive choice of having the fetus tested in a subsequent pregnancy.

Identificación rápida de micobacterias no tuberculosas mediante análisis de patrones de restricción / Rapid identification of non tuberculous mycobacteria by restriction pattern analysis

Background: The frequency of diseases caused by non tuberculous mycobacteria has increased in the last years. Their clinical diagnosis is difficult, mainly in immunocompromised patients. The identification of these mycobacteria by traditional methods is based on phenotypic characteristics and the results are obtained two to four weeks after their isolation in primary cultures. Aim: To report a new identification method for non tuberculous mycobacteria. Material and methods: The restriction pattern analysis method was implemented. It is based on the amplification, using polymerase chain reaction (PCR), of a polymorphic region of 440 base pairs that codifies Hsp65 protein, followed by a digestion with BstE II and Hae III restriction enzymes. The results were compared with patterns established for each strain. Results: Sixty four strains of mycobacteria obtained from clinical samples and seven reference mycobacteria, were identified using the traditional methods and restriction pattern analysis. The latter method identified the same strain as the former in 87.5% of cases. In the remainder 12.5% of cases there was no agreement between both methods. In these, the sequencing of a fragment of a gene that codifies 16S ribosomal RNA, confirmed the correct identification by restriction patterns. Conclusions: Restriction pattern analysis is a rapid identification method for non tuberculous mycobaterial strains.

Karyotypic characterization of Iheringichthys labrosus (Pisces, Pimelodidae): C-, G- and restriction endonuclease banding

Various chromosomal banding techniques were utilized on the catfish, Iheringichthys labrosus, taken from the Capivara Reservoir. C-banding regions were evidenced in telomeric regions of most of the chromosomes. The B microchromosome appeared totally heterochromatic. The restriction endonuclease AluI produced a banding pattern similar to C-banding in some chromosomes; the B microchromosome, when present, was not digested by this enzyme and remained stained. G-banding was conspicuous in almost all the chromosomes, with the centromeres showing negative G-banding. When the restriction endonuclease BamHI was used, most of the telomeres remained intact, while some centromeres were weakly digested. The B chromosome was also not digested by this enzyme. The first pair of chromosomes showed a pattern of longitudinal bands, both with G-banding and BamHI; this was more evident with G-banding. This banding pattern can be considered a chromosomal marker for this population of I. labrosus.

Polymerase chain reaction and restriction fragment length polymorphism analysis of the ITS2 region for differatiation of Brazilian Biomphalaria intermediate hosts of the Schistosoma mansoni

O sequenciamento da região espaçadora transcrita interna 2 do DNA ribossomal (ITS2-DNAr) das espécies brasileiras gênero Biomphalaria (B. glabrata, B. tenagophila and B. straminea) hospedeiras intermediárias do Schistosoma mansoni no Brasil, permitiu a análise dos sítios de restrição presentes nestas seqüências. A análise do mapa de restrição obtido dessas seqüências nos permitiu selecionar enzimas mais promissoras que gerassem perfis de restrição capazes de identificar essas espécies. Foram testadas 4 enzimas e a enzima HpaII foi selecionada por produzir perfis espécie específicos de fácil visualização em gel de poliacrilamida. A utilização da região ITS2 tem como vantagens a obtenção de um fragmento pequeno de 460bp, o qual pode ser facilmente amplificado por PCR. Neste trabalho, nos demonstramos que a amplificação da região ITS2-DNAr e a restrição deste com a enzima HpaII é uma ferramenta molecular auxiliar a identificação morfológica desses moluscos, bem como para estudos taxonômicos e filogenéticos de planorbídeos neotropicais.