RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Background: Reduced-representation sequencing technology is widely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple genomes is important. It is strongly needed to develop a simulation tool to implement these functions. Results: Here, we introduce a Perl module named RestrictionDigest with more functions and improved performance. It can analyze multiple genomes at one run and generate concise comparison of enzyme performance across the genomes. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process and generate comprehensive information of the simulation including enzyme loci number, fragment number, sequences of the fragments, positions of restriction sites on the genome, the coverage of digested fragments on different genome regions and detailed fragment length distribution. Conclusions: RestrictionDigest is an easy-to-use Perl module with flexible parameter settings. With the help of the information produced by the module, researchers can easily determine the most appropriate enzymes to construct the reduced-representation libraries to meet their experimental requirements.

Bacterial diversity of symptomatic primary endodontic infection by clonal analysis

Abstract The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Samples were collected from 10 patients and submitted to bacterial DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. A bacterial genomic library was constructed and bacterial diversity was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84%) were different species and 29 (38.15%) were taxa reported as yet-uncultivable or as yet-uncharacterized species. Prevotella spp., Fusobacterium nucleatum, Filifactor alocis, and Peptostreptococcus stomatis were the most frequently detected species, followed by Dialister invisus, Phocaeicola abscessus, the uncharacterized Lachnospiraceae oral clone, Porphyromonas spp., and Parvimonas micra. Eight phyla were detected and the most frequently identified taxa belonged to the phylum Firmicutes (43.5%), followed by Bacteroidetes (22.5%) and Proteobacteria (13.2%). No species was detected in all studied samples and some species were identified in only one case. It was concluded that acute primary endodontic infection is characterized by wide bacterial diversity and a high intersubject variability was observed. Anaerobic Gram-negative bacteria belonging to the phylum Firmicutes, followed by Bacteroidetes, were the most frequently detected microorganisms.

Overexpression of Salmonella enterica serovar Typhi recA gene confers fluoroquinolone resistance in Escherichia coli DH5α

A spontaneous fluoroquinolone-resistant mutant (STM1) was isolated from its parent Salmonella enterica serovar Typhi (S. Typhi) clinical isolate. Unlike its parent isolate, this mutant has selective resistance to fluoroquinolones without any change in its sensitivity to various other antibiotics. DNA gyrase assays revealed that the fluoroquinolone resistance phenotype of the STM1 mutant did not result from alteration of the fluoroquinolone sensitivity of the DNA gyrase isolated from it. To study the mechanism of fluoroquinolone resistance, a genomic library from the STM1 mutant was constructed in Escherichia coli DH5α and two recombinant plasmids were obtained. Only one of these plasmids (STM1-A) conferred the selective fluoroquinolone resistance phenotype to E. coli DH5α. The chromosomal insert from STM1-A, digested with EcoRI and HindIII restriction endonucleases, produced two DNA fragments and these were cloned separately into pUC19 thereby generating two new plasmids, STM1-A1 and STM1-A2. Only STM1-A1 conferred the selective fluoroquinolone resistance phenotype to E. coli DH5α. Sequence and subcloning analyses of STM1-A1 showed the presence of an intact RecA open reading frame. Unlike that of the wild-type E. coli DH5α, protein analysis of a crude STM1-A1 extract showed overexpression of a 40 kDa protein. Western blotting confirmed the 40 kDa protein band to be RecA. When a RecA PCR product was cloned into pGEM-T and introduced into E. coli DH5α, the STM1-A11 subclone retained fluoroquinolone resistance. These results suggest that overexpression of RecA causes selective fluoroquinolone resistance in E. coli DH5α.

Estudo de variações genômicas para a identificação de biomarcadores personalizados e novos alvos terapêuticos em tumores colorretais / Study of genomic variation to identify biomarkers and novel therapeutic targets in colorectal tumors

O câncer colorretal é um dos tipos de tumores mais frequentes no mundo. A atual dificuldade na avaliação correta da resposta ao tratamento torna necessário o desenvolvimento de novas abordagens de detecção tumoral. Atualmente, o sequenciamento genômico em larga escala permite um estudo mais compreensivo das alterações estruturais e de sequência presentes no tumor. A aplicação destas abordagens de maneira personalizada permite o desenvolvimento de biomarcadores tumor específicos que podem facilitar a avaliação de resposta ao tratamento e a presença de doença residual, bem como revelar alterações de sequência em genes capazes de servir de novos alvos terapêuticos. Neste estudo foi desenvolvida uma metodologia eficiente para a identificação de biomarcadores baseados na existência de variações estruturais em genomas de tumores de reto, eliminando a necessidade de sequenciamento do genoma normal do mesmo paciente e diminuindo portanto o custo da abordagem. Os biomarcadores encontrados para cada um dos seis pacientes foram utilizados para avaliar a presença de doença residual após o tratamento através da detecção de DNA tumoral circulante nas amostras de plasma coletadas em momentos diferentes do tratamento. O sequenciamento em baixa cobertura personalizado é portanto uma alternativa viável e promissora para avaliar a resposta ao tratamento em pacientes com tumores de reto. Na segunda parte do estudo, a análise de linhagens celulares de tumores colorretais revelou uma grande quantidade de mutações pontuais somáticas (SNVs e InDels) em genes codificadores para proteínas de superfície celular (surfaceoma). Estas alterações no surfaceoma indicam potenciais novos alvos para drogas e vias regulatórias alteradas neste tipo de tumor. Além disso, estas mutações pontuais também são responsáveis pela geração de epítopos com potencial imunogênico e estes novos epítopos podem ser aplicados como vacinas antitumorais personalizadas e já haviam sido propostos como uma alternativa terapêutica. A presença de novos epítopos, principalmente nas linhagens com elevadas taxas de mutação (resultante da instabilidade de microssatélites e mutações em genes de reparo de DNA tipo mismatch ou POLE), sugerem também um potencial uso de drogas moduladoras do sistema imune em pacientes com tumores que apresentam estas mesmas características. Portanto, o estudo de alterações genômicas em tumores primários e linhagens de câncer colorretal permitiu a detecção de variações estruturais que foram utilizadas como biomarcadores personalizados em pacientes com tumores de reto assim como a identificação de genes contendo mutações pontuais em linhagens celulares de câncer colorretal, que revelam potenciais novos alvos terapêuticos a serem explorados na clínica

Colorectal cancer is one of the more frequent tumor types in the world. To select the appropriate treatment course, it is necessary to develop more precise diagnostic approaches. The current availability of high throughput genome sequencing methods allows for a comprehensive characterization of the structural and sequence alterations present in each tumor. The use of tumor genome sequencing in a personalized setting can result in tumor specific biomarkers that help evaluate response to treatment and the presence of residual disease, improving the clinical management of these patients, and also reveal sequence alterations in genes capable of serving as new therapeutic targets. In this study we developed an efficient bioinformatics pipeline to identify biomarkers based on the existing structural alterations in rectal tumor genomes, eliminating the need to sequence the matched normal genome and therefore reducing the cost for this approach. The biomarkers found for each of the six patients were used to evaluate the presence of residual disease after treatment through the detection of circulating tumor DNA in plasma samples collected at different points during the treatment. Sequencing tumor genomes with low coverage is therefore a viable and promising alternative to follow up rectal cancer patient's response to treatment. In the second part of this study, the analysis of colorectal cancer cell lines revealed a large quantity of point mutations (SNVs and InDels) in genes coding for proteins located in the cell surface (surfaceome). These alterations in the surfaceome indicate potential new drug targets and altered pathways in this type of tumor. Furthermore, these point mutations are also responsible for the generation of new epitopes with immunogenic potential and these new epitopes can be applied as personalized tumor vaccines and had previously been proposed as a therapeutic alternative. The presence of new epitopes, especially in the cell lines with elevated mutation rates (resulting from MSI and mutations in DNA mismatch-repair genes or POLE), suggests a potential use of immune checkpoint target drugs in patients with tumors that share these genetic characteristics. With a large-scale bioinformatics approach, we detected new tumor epitopes resulting from point mutations, present in most of the cell lines used. The analysis of gene expression data puts into perspective both the somatic mutations found and which targets are promising as well as the development of therapies based on vaccines derived from tumor epitopes. In conclusion, the study of genomic alterations in primary tumors and colorectal cancer cell lines allowed the detection of structural variations that were used as personalized biomarkers in patients with rectal tumors as well as the identification of genes containing point mutations in colorectal cancer cell lines, that reveal potential new therapeutic targets to be explored in the clinical setting

Avaliação de dois métodos para condicionamento e coleta de sêmen em quatro espécies do gênero Mazama / Assessment of two methods for conditioning and semen collection in four species of Mazama genus

O desenvolvimento de técnicas não invasivas para a obtenção de sêmen de cervídeos facilita a criação de bancos genômicos, que são importantes instrumentos para a conservação ex situ e in situ. Este trabalho teve como objetivo criar uma metodologia não-invasiva de coleta de sêmen e comparar duas técnicas de coleta em quatro espécies do gênero Mazama: M. americana, M. gouazoubira, M. nana e M. nemorivaga. Para tanto, foram utilizados seis machos (M) e duas fêmeas (F) da espécie M. americana, 3M e 2F de M. gouazoubira, 1M e 1F de M. nana e 2M e 1F de M. nemorivaga. Para cada técnica testada, foi realizado um período de habituação dos animais ao manejo. Em seguida, duas técnicas de condicionamento e coleta foram avaliadas. Na primeira delas foi utilizada uma fêmea em estro com desvio lateral do pênis para vagina artificial (FEDL), obtendo-se a coleta de 50% dos indivíduos (100% dos machos de M. gouazoubira e 50% dos machos de M. americana), não obtendo ejaculados das demais espécies. Na segunda técnica, utilizando um manequim taxidermizado com urina de fêmea em estro (MUFE) não foi possível a coleta de nenhum ejaculado. Em todas as fases foi observado o comportamento do macho quanto ao tempo de interesse e aproximação, reflexo de "Flehmen", ato de cheirar ou lamber, exposição do pênis, ereção, número de falsas montas, tentativas de cópula e ocorrência de agressividade entre os animais.

The development of noninvasive techniques for obtaining semen from deer facilitates the creation of genome banks, which are important tools for ex situ and in situ conservation. This study aimed to establish a noninvasive method of semen collection and compare two techniques of collection in four species of the genus Mazama: M. americana, M. gouazoubira, M. nana and M. nemorivaga. To achieve this, 6 males (M) and 2 females (F) of the species M. Americana, 3M and 2F of M. gouazoubira, 1M and 1F of M. nana and 2M and 1F of M. nemorivaga were used. For each technique tested, a period of habituation to animal handling was conducted; then, the two conditioning techniques and collection were evaluated. In the first, a female in estrus was used with lateral deviation of the penis to an artificial vagina (FEDL), yielding collection from 50% of the males (100% from M. gouazoubira and 50% from M. americana), with no ejaculate from the remaining species. In the second technique, using a taxidermized dummy with urine from females in estrus (MUFE), no semen collection was possible. During all stages, male behavior was observed regarding the time of interest and approximation, the "Flehmen" response, the act of sniffing or licking, exposure of the penis, erection, number of false mounts, attempts at copulation and the occurrence of aggression between the deer.

Description of novel microsatellite loci in the Neotropical fish Prochilodus argenteus and cross-amplification in P. costatus and P. lineatus

Prochilodus is one of the most important fish resources of South America, in addition to the important role it plays in nutrient cycling of Neotropical rivers. In the present study, we describe the isolation and characterization of nine novel microsatellite loci in Prochilodus argenteus. The number of alleles per polymorphic locus varied from 5 (Par76) to 21 (Par85), revealing a total of 116 alleles. The values of observed and expected heterozygosities ranged from 0.629 (Par69) to 0.926 (Par85 and Par86) and from 0.643 (Par66) to 0.931 (Par80), respectively. Furthermore, the ability of these and other previously described microsatellite markers to amplify orthologous loci was tested in two related species, Prochilodus costatus and Prochilodus lineatus. These loci will be useful for studies of population genetic structure in this group of fishes, and in aiding future genetic mapping studies of P. argenteus.

Development of SRS. php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Isolation and characterization of microsatellite DNA in the piracema fish Prochilodus lineatus (Characiformes)

We described five novel microsatellite loci for the piracema fish species Prochilodus lineatus (Characiformes), endemic to South America and of extreme importance to both commercial and artisanal fisheries across its occurrence area. A primary, unenriched genomic library was constructed and radioactively screened for repetitive motifs. Positive clones were automatically sequenced and based on the design of new primers, polymerase chain reaction assays were carried out to determine optimum reaction and electrophoretic conditions for each characterized locus. We evaluated its usefulness in population genetic studies by determining Hardy-Weinberg equilibrium, FIS and a jackknife estimate of the number of alleles for a sample of fish caught below the Funil Hydroelectric Power Plant dam (N = 95), Grande River, Brazil. The number of alleles varied from 3 to 21 and expected heterozygosities ranged from 0.58 to 0.91. Two of five loci were in Hardy-Weinberg equilibrium. Jackknife estimates of the number of alleles were higher than the observed number of alleles for three loci and could provide a measure of sampling bias. These markers should provide important tools for the determination of genetic structure, stock delimitation and reservoir fish management in the Grande River as well as to improve hatchery practices for environmental mitigation measures and to help sustain fisheries in the river.

Optimal clone identifier for genomic shotgun libraries: "OC Identifier tool"

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray.

A mucin like gene different from the previously reported members of the mucin like gene families is transcribed in Trypanosoma cruzi but not in Trypanosoma rangeli

Trypanosoma cruzi expresses mucin like glycoproteins encoded by a complex multigene family. In this work, we report the transcription in T. cruzi but not in T. rangeli of a mucin type gene automatically annotated by the T. cruzi genome project. The gene showed no nucleotide similarities with the previously reported T. cruzi mucin like genes, although the computational analysis of the deduced protein showed that it has the characteristic features of mucins: a signal peptide sequence, O-glycosylation sites, and glycosylphosphatidylinositol (GPI) anchor sequence. The presence in this gene of N- terminal and C- terminal coding sequences common to other annotated mucin like genes suggests the existence of a new mucin like gene family.

Biodiversidad y patrimonio genético: importancia y proposiciones del Consejo de Desarrollo Sustentable (CDS) de Chile / Biodiversity and genetic patrimony: importance and chilean Sustainable Development Council (SDC) propositions

Este documento presenta información básica que avala la importancia de la preservación de la biodiversidad en Chile y del usufructo de las especies que lo constituyen, para asegurar el desarrollo sustentable de nuestro país, permitiendo una mejor calidad de vida para las futuras generaciones. Resume los acuerdos concretos adoptados por consenso en las reuniones plenarias del Consejo de Desarrollo Sustentable de Chile (CDS), con la participación del Colegio Médico de Chile. Estos están dirigidos para asegurar la preservación de la biodiversidad chilena y defender el patrimonio genético de Chile. Estos acuerdos constituyen las recomendaciones del CDS dirigidas al Presidente de la República, con el propósito de lograr dichos objetivos.

Partial characterization of ribosomal operons of Lactobacillus delbrueckii UFV H2b20

Operons ribossomais têm sido instrumentos importantes na caracterizacão de comunidades microbianas e no estudo de relacionamentos entre microrganismos, principalmente em bactérias do ácido láctico. Operons ribossomais da linhagem probiótica, Lactobacillus delbrueckii UFV H2b20, foram parcialmente caracterizados. Um banco genômico da linhagem foi construído e os clones, contendo parte do operon ribossomal, foram subclonados pelo método de "shot gun", para em seguida serem seqüenciados com primer "forward". As seqüências indicaram a presenca da extremidade 3' do rDNA 16S seguida da região espacadora curta 1 (16S-23S) e a presenca da extremidade 3' do rDNA 23S seguido da região espacadora 2 (23S-5S), que por sua vez precedia o rDNA 5S. Adjacente ao gene rDNA 5S deste operon rrn uma região codificadora de 6 tRNAs foi detectada.

Evaluación de la autoinmunidad en ratones BALB/c inmunizados con una biblioteca genómica de expresión de Trypanosoma cruzi / Evaluation of autoimmunuty in Balb/c mice immunized with a genomic library of expression of Trypanosoma cruzi

Uno de los problemas de la seguridad para las vacunas de ADN es la inducción de fenómenos de autoinmunidad. Nosotros examinamos el efecto de la inmunización con ácidos nucleicos de Trypanosoma cruzi en la inducción de diferentes autoanticuerpos en ratones de Balb/c. Los animales fueron divididos en cinco grupos: los primeros cuatro recibieron diferentes esquemas: 25 µg de la biblioteca genómica de expresión (grupo L), 25 µg de antígenos solubles de T. cruzi (grupo T), 25 µg del plásmido pcDNA3 (grupo P), 25 µg de genómica ADN de T. cruzi (grupo G) y un grupo control de animales no inmunizados. Los anticuerpos antinucleares y anticuerpos contra músculo cardíaco fueron evaluados por immunofluorescencia indirecta y los anticuerpos anti ADN de doble, simple cadena y el anti IgG factor reumatoideo fueron determinados semanalmente por ELISA. La vacunación no provocó la inducción de anticuerpos anti ADN de doble o simple cadena, anticuerpos antinucleares ni contra músculo cardíaco. Se observó un aumento transitorio del Factor Reumatoideo IgG en los ratones inmunizados con la biblioteca genómica de expresión de T. cruzi. Nuestros hallazgos sugieren que la inducción de respuestas autoinmunes frente al ADN utilizado en la inmunización es poco probable

Production and immune response of recombinant Hsp60 and Hsp70 from the salmon pathogen Piscirickettsia salmonis

We have isolated and sequenced the genes encoding the heat shock proteins 60 (Hsp60) and 70 (Hsp70) of the salmon pathogen Piscirickettsia salmonis. The sequence analysis revealed the expected two open reading frames that encode proteins with calculated molecular weights of 60,060 and 70,400. The proteins exhibit a 70-80 percent homology with other known prokaryotic Hsp60 and Hsp70 sequences. The coding regions have been expressed in E. coli as thioredoxin fusion proteins. Both recombinant proteins were shown to elicit a humoral response when injected intraperitoneally in Atlantic salmon and also conferred protection to fish challenged with P. salmonis. The present data will facilitate further studies on the involvement of heat shock proteins in protective immunity of fish to infection by P. salmonis and their potential use in recombinants vaccines against this intracellular pathogen.

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

A Pentamidina (PEN) é um composto alternativo para o tratamento de pacientes com leishmaniose que apresentam resistência ao antimônio, cujo alvo celular continua incerto. Uma abordagem para se identificar prováveis alvos seria a identificação e super-expressão de genes capazes de mediar resistência a PEN. A partir de uma genoteca construída com o DNA de Leishmania major em um vetor - cosmídio que se desenvolve tanto em bactérias como nas células do parasita, isolamos um locus que após transfecção é capaz de produzir resistência a PEN às células do parasita. Almejando o mapeamento desse locus de leishmania, o inserto clonado nesse cosmídio foi deletado através de duas digestões parciais sucessivas com enzimas de restrição, seguida de transfecção em células selvagens, super-expressão gênica, indução e testes funcionais na presença de PEN. Para determinar o gene de Leishmania relacionado com a resistência a PEN, o seqüenciamento de nucleotídeos foi executado após inserção de elementos transposicionais de Drosophila melanogaster no interior do inserto deletado para atuar como ilhas de iniciadores. Descrevemos aqui o mapeamento desse locus, após a inserção transposicional, que além de facilitar o seqüenciamento de nucleotídeos de grandes fragmentos de DNA, permite uma rápida identificação do gene relacionado com esse fenótipo. Experimentos posteriores revelaram neste locus a presença do gene de uma Glicoproteína-P de membrana, cujo papel no metabolismo na Leishmania está sendo analisado.

New genomic resources for the honey bee(Apis mellifera L): development of a deep-coverage BAC library and a preliminary STC database

We have constructed a bacterial artificial chromosome (BAC) library for a European honey bee strain using the cloning enzyme HindIII in order to develop resources for structural genomics research. The library contains 36,864 clones (ninety-six 384-well plates). A random sampling of 247 clones indicated an average insert size of 113 kb (range = 27 to 213 kb) and 2 empty vectors. Based on an estimated genome size of 270 Mb, this library provides approximately 15 haploid genome equivalents, allowing >99 probability of recovering any specific sequence of interest. High-density colony filters were gridded robotically using a Genetix Q-BOT in a 4 x 4 double-spotted array on 22.5-cm2 filters. Screening of the library with four mapped honey bee genomic clones and two bee cDNA probes identified an average of 21 positive signals per probe, with a range of 7-38 positive signals per probe. An additional screening was performed with nine aphid gene fragments and one Drosophila gene fragment resulting in seven of the nine aphid probes and the Drosophila probe producing positive signals with a range of 1 to 122 positive signals per probe (average of 45). To evaluate the utility of the library for sequence tagged connector analysis, 1152 BAC clones were end sequenced in both forward and reverse directions, giving a total of 2061 successful reads of high quality. End sequences were queried against SWISS-PROT, insect genomic sequence GSS, insect EST, and insect transposable element databases. Results in spreadsheet format from these searches are publicly available at the Clemson University Genomics Institute (CUGI) website in a searchable format (http://www.genome.clemson.edu/projects/stc/bee/AM__Ba/)

Significant and transitory control of lesions development in mice immunized with a genomic library of Leishmania amazonensis

DNA from a genomic library of Leishmania amazonensis and from pcDNA3 plasmid were used to immunize BALB/c mice. Three immunizations at two weeks intervals were done, with 50µg/0.1ml of DNA. A control group was also injected with the same volume of saline solution. Afterward, all mice were challenged with infective promastigotes of the parasite, and the development of lesions was followed during 16 weeks by dorsoventral measures of the footpad. Mice previously immunized with the genomic library were capable of controlling lesions at a significant level, with major significance between 9 and 13 weeks post challenge.

Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3 percent) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8 percent) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci

Construcción de una biblioteca genómica de Leishmania amazonensis y su expresión en músculo de ratones BALB/c / Building of a genomic library of Leishmania amazonensis and its expression in BALB/c miceïs muscle

Se construyó una biblioteca genómica de Leishmania amazonensis mediante el vector pcDNA3, con promotor de expresión en células eucariotas, con el objetivo de contribuir a la aplicación de la tecnología de inmunización con ácidos nucleicos en la leishmaniosis. Para demostrar la expresión de la genoteca en el músculo de ratones inmunizados con esta, se realizó la técnica de inmunofluorescencia indirecta. Como anticuerpo primario se utilizó una mezcla de sueros con alto título antileishmania, de una zona donde predomina la infección con L. braziliensis. Se obtuvo una biblioteca con 80 porciento de clones recombinantes. Se demostró la expresión de determinantes antigénicos en el músculo de ratones BALB/c inmunizados, según resultados de la inmunofluorescencia

Evaluación de la respuesta inmune humoral por western blot en ratones inmunizados con una biblioteca genómica de expresión de Trypanosoma cruzi / Evaluation of the humoral immune response by Western Blot test in mice immunized with expression genomic library of Trypanosoma cruzi

Se construyó una biblioteca genómica de expresión de Trypanosoma cruzi con la utilización como vector el plásmido pcDNA3, con la cual se inmunizaron ratones de la línea isogénica BALB/c por vía intramuscular. Se empleó un grupo control positivo al que se le administraron antígenos solubles de T. cruzi y otro grupo que recibió el plásmido utilizado para la construcción de la biblioteca genómica; un grupo no recibió inmunización. A todos los animales se les extrajo sangre del plexo retrorbital 2 semanas posteriores a la tercera inmunización, para estudiar la respuesta de anticuerpos específicos contra los antígenos solubles del parásito mediante la técnica de western blot. Se obtuvo una respuesta de anticuerpos en los animales inmunizados con la biblioteca genómica de expresión y con antígenos solubles del parásito