Marcadores moleculares de tipo inserción en bacterias de las familias Moraxellaceae y Helicobacteraceae (phylum Proteobacteria) / Molecular markers of insertion type in bacterias of the Moraxellaceae and Helicobacteraceae (phylum Proteobacteria) families

Se efectuó un estudio con el empleo de la metodología de Gupta, en el Departamento de Biología y Geografía de la Universidad de Oriente en Santiago de Cuba, para determinar marcadores moleculares de tipo inserción en secuencias de las proteínas ADN polimerasa I y ADN polimerasa III (subunidad alfa), obtenidas de bases de datos internacionales y posteriormente alineadas con el programa ClustalX2. Las familias Moraxellaceae y Helicobacteraceae han sido ampliamente estudiadas, porque comprenden agentes patógenos causantes de numerosas enfermedades en humanos, pero pocas investigaciones han estado dirigidas a la identificación de las características moleculares que puedan distinguir a sus miembros de otros grupos de bacterias; de manera que los presentes resultados constituyen un aporte al conocimiento de la genética y la bioquímica de estas familias y proveen herramientas moleculares para la clasificación taxonómica y el diagnóstico de especies patógenas

A study with the use of Gupta methodology was carried out in the Biology and Geography Department of Oriente University in Santiago de Cuba, to determine molecular markers of insertion type in sequences of the DNA polimerase I proteins and DNA polimerase III (alpha subunity), obtained from international databases and later on aligned with the ClustalX2 program. The Moraxellaceae and Helicobacteraceae families have been broadly studied, because they comprise pathogen agents that cause numerous diseases in humans, but few investigations have been directed to the identification of the molecular characteristics that can distinguish their members from other groups of bacterias; so these results constitute a contribution to the knowledge of genetics and biochemistry of these families and provide molecular tools for the taxonomic classification and the diagnosis of pathogen species

Optimización de la Reacción en Cadena de la Polimerasa para la Detección del gen B1 de T. gondii / Optimization of Polymerase Chain Reaction for the detection of the B1 gene of T. gondii

Optimizar las condiciones de amplificación del gen B1 (35 copias en el genoma) para la detección de ADN de T.gondii en casos probables de toxoplasmosis cerebral. Materiales y métodos: Se realizó extracción de ADN a partir de exudado peritoneal de ratones inoculados con la cepa RH de T. gondii obteniendo 17 ml con una concentración inicial de 1x107 parásitos/ml. Se optimizaron las condiciones de PCR del gen B1. Resultados: Se obtuvo amplificación de un fragmento de 132 pb a partir de ADN obtenido de diluciones seriadas desde 1x106 a 1x10-1 parásitos por ml, estableciéndose un límite de detección de 1 taquizoíto de T. gondii...

This study aimed at optimizing the amplification conditions of the B1 gene (35 copies in the ge­nome) of T. gondii in cases of possible brain toxoplasmosis. Materials and methods: DNA was extracted from the peritoneal exudate of mice inoculated with the RH strain of T. gondii. Total exudate volume was 17 mL with a concentration of 1x107 parasites/mL. PCR conditions for the B1 gene were further optimized.Results: Serial dilutions from 1x106 to 1x10-1 parasites/mL were needed for amplifying a fragment of 132 bp . This set the detection limit for 1 T. gondii tachyzoite...

Rastreo genético del streptococcus mutans / Streptococcus mutans genetic tracking

Las técnicas moleculares para recuperar DNA antiguo brindan la posibilidad de comparar la evolución molecular a través del tiempo, ya que constituye una herramienta para aclarar el diagnóstico de posibles enfermedades infecciosas del pasado. Aislar y secuenciar un fragmento de DNA de Streptococcus mutans fosilizado, considerado el principal agente infeccioso implicado en la formación de la placa bacteriana y el desarrollo de la caries dental, utilizando la reacción en cadena de polimerasa (PCR). La muestra estuvo conformada por caries y tártaro dental proveniente de dientes de diferentes colecciones de México, Barcelona e Islas Baleares. La metodología fue adaptada a las condiciones de conservación de este tipo de muestra para obtener DNA y los primers fueron específicos para la amplificación de un fragmento de 124 pb del gen de la Dextranasa del S. mutans. De las 24 muestras analizadas, 9 resultaron positivas para la amplificación y en 6 se lograron las secuencias correspondientes. Para la alineación de las secuencias obtenidas, se empleó la base de datos BLAST encontrándose una homología del 95% con el genoma del S. mutans UA159. Este estudio demuestra la primera evidencia de obtención de la secuencia de un fragmento de DNA de Streptococcus mutans recuperados a partir de caries y cálculo dental de restos humanos antiguos, presentando un 95% de homología con el DNA de S. mutans de la subespecie UA159 moderno

The molecular techniques for ancient DNA recovering, offers the possibility to compare the molecular evolution through time as these are tools which make clear possible infectious diseases from the ancient times Objective: To isolate and sequence fossilized Streptococcus mutans DNA fragments, considered the infectious agent involved with dental caries and plaque formation and development, by using the polymerase chain reaction (PCR). Dental caries and tartar samples of teeth collections from Mexico, Barcelona and Balearic Islands. The methodology was adapted to the conservation conditions of this type of DNA samples, and primers were specific to amplify a fragment of 124 bp of S. mutans dextranase gene. Results: 24 samples were analyzed, 9 were positive for amplification and 6 were obtained with its corresponding sequences. To alignment the sequences obtained, we used the BLAST database, giving us the 95% homology with the S. mutans UA159 genome. This study shows us the first evidence of Streptococcus mutans DNA sequence fragment recovered from dental caries and tartar from ancient human remains, presenting a 95% homology with S. mutans UA159 modern subspecies DNA

Analysis of DNA polymerase activity in vitro using non-radioactive primer extension assay in an automated DNA sequencer

Although different DNA polymerases have distinct functions and substrate affinities, their general mechanism of action is similar. Thus, they can all be studied using the same technical principle, the primer extension assay employing radioactive tags. Even though fluorescence has been used routinely for many years for DNA sequencing, it has not been used in the in vitro primer extension assay. The use of fluorescence labels has obvious advantages over radioactivity, including safety, speed and ease of manipulation. In the present study, we demonstrated the potential of non-radioactive in vitro primer extension for DNA polymerase studies. By using an M13 tag in the substrate, we can use the same fluorescent M13 primer to study different substrate sequences. This technique allows quantification of the DNA polymerase activity of the Klenow fragment using different templates and under different conditions with similar sensitivity to the radioactive assay.

Implementación de la Técnica Reacción en Cadena de la Polimerasa en el Diagnóstico de Salmonella y Shigella directamente de muestras fecales / Implementation of the Technical Polymerase Chain Reaction in the Diagnosis of `Salmonella` and Shigella directly of fecal samples

Las diarreas causadas por bacterias son las que potencilamente suponene un mayor riesgo vital para el paciente, siendo los patógenos más importantes Shiggella y Salmonella que se ubican entre las causas principales de muerte en niños menores de cinco años, e spor esto que resulta de vital importancia realizar un diagnóstico rápido y preciso, junto a un tratamiento efectivo.

PCR Detection of the DNA Polymerase I Gene of Treponema pallidum from a Case of Atypical Primary Syphilis / 대한진단검사의학회지

Syphilis is easily diagnosed by serologic testing or by identification of the causative organism, Treponema pallidum. Syphilis usually presents a distinct painless primary ulcer or chancre. However, the initial clinical impressions of even the most experienced specialist in sexually transmitted diseases (STDs), may be wrong 40% of the time. We report a case of atypical primary syphilis that was presented with painful ulceration on the penis and showing negative VDRL results. We amplified the DNA polymerase I gene of Treponema pallidum in the penile ulcer lesion to detect syphilis and got the a successful result. The patient was treated with benzathine penicillin G.

Terminal Protein-specific scFv Production by Phage Display

BACKGROUND: One of the important factors in the prognosis of chronic hepatitis B patient is the degree of replication of hepatitis B virus (HBV). It has been known that HBV DNA polymerase plays the essential role in the replication of HBV. HBV DNA polymerase is composed of four domains, TP (Terminal protein), spacer, RT (Reverse transcriptase) and RNaseH. Among these domains, tyrosine, the 65th residue of TP is an important residue in protein-priming reaction that initiates reverse transcription. If monoclonal antibody that recognizes around tyrosine residue were selected, it could be applied to further study of HBV replication. METHODS: To produce TP-specific scFv (single-chain Fv) by phage display, mice were immunized using synthetic TP-peptide contains 57~80th amino acid residues of TP domain. After isolation of mRNA of heavy-variable region (VH) and light-chain variable region (VL) from the spleen of the immunized mouse, DNA of VH and VL were obtained by RT-PCR and joined by a DNA linker encoding peptide (Gly4Ser)3 as a scFv DNA fragments. ScFv DNA fragments were cloned into a phagemid vector. ScFv was expressed in E.coli TG1 as a fusion protein with E tag and phage gIII. To select the scFv that has specific affinity to TP-peptide from the phage-antibody library, we used two cycles of panning and colony lift assay. RESULTS: The TP-peptide-specific scFv was isolated by selection process using TP-peptide as an antigen. Selected scFv had 30 kDa of protein size and its nucleotide sequences were analyzed. Indirect- and competitive-ELISA revealed that the selected scFv specifically recognized both TP-peptide and the HBV DNA polymerase. CONCLUSION: The scFv that recognizes the TP domain of the HBV DNA polymerase was isolated by phage display.

The Expression of Aphidicolin Induced Fragile Sites in Human Peripheral Blood Lymphocytes / 대한해부학회지

An aphidicolin is a chemical agent which selectively inhibits DNA polymerase alpha in S phase of cell cycle. The purpose of this study is toinvestigate of chromosomal abnormalities including fragile sites induced by 0.2 microgram/ml and 0.4 ng/ml aphidicolin in lymphocyte cultures of six healthy individuals. The results were follows. 1. A significant decreasing in mitotic indexes in respect to control culture was observed with both aphidicolin concentrations used. 2. The cells showing chromosome aberrations and the total number of cytogeneticic alterations were significantly increased both aphidicolin treated cultures than control cultures. 3. The total numbers of chromosomal aberrations were increased in the concentration of 0.4 microgram/ml aphidicolin compared to 0.2 microgram/ml treated groups. 4. The most frequent type of chromosomal aberration is a gap. 5. A site showing a gap or break was defined as common fragile sites (c-fra) if it appeared more than 1% of cells analyzed and in at least three of six individuals studied with the same culture treatment. Using these criteria, 3p14, 4q12, 5p13, 6q16, 9p13, and 16q23 were induced in different proportions by different concentration of aphidicolin and four of these c-fras, 4q12, 5p13, 6q16, 9p13 have not been reported so far. This results support that aphidicolin induced fragile sites differently according to cultured cell or cultured conditions, and also suggest the mechanism that common fragile sites caused be closely related with the defect of DNA synthesis in the S phase of cell cycle.

Inibiçäo seletiva das atividades das enzimas transcriptase reversa do vírus HIV-1 e DNA polimerases humanas por derivados dipirazolo-piridina / Selective inhibition of reverse transcriptase enzyme activity of HIV-1 virus and human polymerases DNA by dipirazolo-pyridines derivatives

Novos ribonucleosídeos derivados dos sistemas dipirazolo-piridina foram preparados e avaliados quanto à atividade polimerásica das enzimas transcriptase reversa (RT) do vírus HIV-1 e das DNA polimerases humanas alfa e epsilon. Os derivados 1b e 1d inibiram a atividade da transcriptase reversa em concentraçöes de micromolares. Entretanto, as mesmas substâncias näo foram capazes de inibir a atividade polimerase das enzimas DNA-polimerase humana alfa e epsilon.

Nuclear matrix bound DNA polymerase-beta in mouse fibrosarcoma: effect of gamma-radiation.

Nuclear matrices isolated from the mouse fibrosarcoma tumour cells contain the eukaryotic replicative enzyme DNA polymerase-alpha and the presumptive repair enzyme DNA polymerase-beta. Exposure of tumors to various doses of gamma-radiation (1.95 to 6.5 Gy) causes a 2-fold increase in the levels of only DNA polymerase-beta in the nuclear matrix. The increase in the levels of this enzyme is not discernible if the matrices are isolated 24 hr after irradiation. The rise in the levels of the repair enzyme DNA polymerase-beta could be indicative of radiation stress response of the tumour cells and their repair ability.

Comparative evaluation of labelling intensity for detection of enterotoxigenic Escherichia coli.

Twenty four Esch. coli isolates obtained from patients of diarrhoea were tested by DNA hybridization for presence of enterotoxigenic Esch. coli (ETEC). The probe generated for this study was labelled by two different ways using the large Klenow fragment of DNA polymerase-I. It was observed that labelling by sequential harnessing of the exonuclease and polymerase activity of the enzyme was superior to extension of random hexanucleotide primers. This method besides being economic, dispenses with the critical step involved in the thermodynamics of oligoannealing and initiation of DNA synthesis.

In vitro characterization of repair synthesis initiated by T4 endonuclease V on a synthetic DNA substrate.

The size of the repair patch produced by E. coli DNA polymerase (Pol I) following the removal of a pyrimidine dimer from DNA in response to the nicking activity of T4 endonuclease (T4 endo V) was determined. A 48-bp DNA containing a pyrimidine dimer at a defined location was labelled in the damaged strand and incubated with T4 endo V and E. coli endonuclease IV. Subsequently, DNA synthesis by DNA Pol I was carried out in the presence of four dNTPs, ATP and DNA ligase. Analysis of the reaction products on a sequencing gel revealed a ladder of only 4-oligonucleotides, 1-4 nucleotides greater in length than the fragment generated by the combined nicking activities of T4 endo V and E. coli endonuclease IV. Thus we conclude that the in vitro repair patch size of T4 endo V is 4 nucleotides and that in some cases the repaired DNA is not ligated.

Amplificación del gen de la ADN polimerasa I por multiplicación del Lambda polA mediante ciclo lítico en la E. coli WK6: obtención y purificación de la enzima / Amplification of the gene for DNA polimerasa I by the multiplication of Lambda polA in E. coli WK6: obtention and purification of the enzyme

El fago Lambda polA (Qam 73, Sam 7) fue aislado y purificado de un lisógeno de la E. coli 594, y posteriormente se multiplicó en una cepa SupE, SupF. Se obtuvo una cantidad considerable de DNA polimerasa I multiplicándolo por vía ciclo lítico, tras la infección a alto MOI (Multiplicity of Infection) de una cepa libre de supresores amber (E. coli WK6). En este trabajo se muestran los resultados de la estandarización de las condiciones para obtener un nivel adecuado de expresión del gen polA, el esquema de purificación utilizado y se discuten las modificaciones realizadas para la obtención de la DNA polimerasa I a gran escala. La DNA pol I purificada incorporó P32-dATP por Nick translation en fragmentos de DNA entre 800-50 000 bp con un alto marcaje específico