RESUMO
Bacteria blight is one of the most serious bacterial diseases of rice worldwide. The identification of genetic potential against bacterial blight in the existing rice resources is a prerequisite to develop multigenic resistance to combat the threat of climate change. This investigation was conducted to evaluate alleles variation in 38 Malaysian cultivars using thirteen Simple Sequences Repeats markers and one Sequence Tagged Sites (STS) marker which were reported to be linked with the resistance to bacterial blight. Based on molecular data, a dendrogram was constructed which classified the rice cultivars into seven major clusters at 0.0, 0.28 and 0.3 of similarity coefficient. Cluster 5 was the largest group comprised of ten rice cultivars where multiple genes were identified. However, xa13 could not be detected in the current rice germplasm, whereas xa2 was detected in 25 cultivars. Molecular analysis revealed that Malaysian rice cultivars possess multigenic resistance.
A ferrugem bacteriana é uma das doenças bacterianas mais graves do arroz em todo o mundo. A identificação do potencial genético contra a ferrugem bacteriana nos recursos de arroz existentes é um pré-requisito para desenvolver resistência multigênica no combate à ameaça da mudança climática. Esta investigação foi conduzida para avaliar a variação de alelos em 38 cultivares da Malásia usando 13 marcadores Simple Sequences Repeats (SSR) e 1 marcador Sequence Tagged Sites (STS), que foram relatados como associados à resistência à ferrugem bacteriana. Com base em dados moleculares, foi construído um dendrograma que classificou as cultivares de arroz em sete grandes agrupamentos a 0,0, 0,28 e 0,3 de coeficiente de similaridade. O Cluster 5 foi o maior grupo composto por 10 cultivares de arroz, no qual múltiplos genes foram identificados. No entanto, xa13 não pôde ser detectado no germoplasma atual de arroz, enquanto xa2 foi detectado em 25 cultivares. A análise molecular revelou que as cultivares de arroz da Malásia possuem resistência multigênica.
Assuntos
Oryza/imunologia , Oryza/microbiologia , Ferrobactérias , Sitios de Sequências Rotuladas , Repetições de Microssatélites , MalásiaRESUMO
The content and composition of seed storage proteins is largely responsible for wheat end-use quality. They mainly consist of polymeric glutenins and monomeric gliadins. According to their electrophoretic mobility, gliadins and glutenins are subdivided into several fractions. Glutenins are classified as high molecular weight or low molecular weight glutenin subunits (HMW-GSs and LMW-GSs, respectively). LMW-GSs are encoded by multigene families located at the orthologous Glu-3 loci. We designed a set of 16 single-nucleotide polymorphism (SNP) markers that are able to detect SDS-PAGE alleles at the Glu-A3 and Glu-B3 loci. The SNP markers captured the diversity of alleles in 88 international reference lines and 27 Mexican cultivars, when compared to SDS-PAGE and STS markers, however, showed a slightly larger percent of multiple alleles, mainly for Glu-B3. SNP markers were then used to determine the Glu-1 and Glu-3 allele composition in 54 CIMMYT historical lines and demonstrated to be useful tool for breeding programs to improve wheat end product properties.
Assuntos
Glutens/genética , Triticum/genética , Alelos , Sequência de Bases , Pão , DNA de Plantas/genética , Genes de Plantas , Marcadores Genéticos , Glutens/química , Peso Molecular , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Subunidades Proteicas , Sitios de Sequências RotuladasRESUMO
We investigated azoospermia region microdeletions in male infertility patients with Klinefelter syndrome (KFS), as well as the association between azoospermia symptoms in patients with KFS and Y chromosome microdeletion polymorphisms. A total of 111 cases with male infertility confirmed to have KFS (47, XXY) and 94 fertile men were included in this study. Peripheral blood was drawn and DNA was extracted from these samples. Multiplex polymerase chain reaction was performed to screen the partial deletions of 25 sequence-tagged sites on the Y chromosome. In 111 cases with KFS, 1 case contained the AZFb+d+c deletion. The Gr/Gr deletion was identified in 12 KFS cases and 5 control cases. In addition, the b2/b3 deletion was identified in 13 KFS cases and 6 control cases. There were no significant differences in phenotype and genotype of the 2 partial AZFc deletions between patients and controls (P > 0.05). Our results suggest that patients with KFS may also have Y chromosome microdeletions to varying degrees and that the gr/gr deletion and b2/b3 deletion may not play a role in the susceptible genetic background of azoospermia in patients with KFS in the Sichuan population.
Assuntos
Síndrome de Klinefelter/genética , Proteínas de Plasma Seminal/genética , Azoospermia/genética , Deleção Cromossômica , Cromossomos Humanos Y/genética , Deleção de Genes , Loci Gênicos/genética , Humanos , Infertilidade Masculina/genética , Masculino , Fenótipo , Sitios de Sequências Rotuladas , Aberrações dos Cromossomos Sexuais , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/genéticaRESUMO
Azoospermia factor (AZF) microdeletion plays a key role in the genetic etiology of male infertility. The relationship between sY152 deletion in the AZFc region and clinical outcomes is still unclear. This study was to determine the effects of sY152 deletion on the sperm parameters and clinical outcomes of non-obstructive azoospermia or oligozoospermia men after intracytoplasmic sperm injection (ICSI) treatment. A total of 61 infertile men with AZFc microdeletion of the Y chromosome from January 2008 to December 2012 were recruited in the present study. They were divided into two groups, the sY152 group (n=12) and the AZFc group (n=49), based upon whether they have deleted single sY152 marker or all AZFc markers. Fifty azoospermia or oligozoospermia patients without Y chromosome microdeletion were included as the control group. The sperm quality and clinical data were compared among the three groups. Retrospective cohort-control study was performed. The sperm concentration and motility in sY152 group were better than AZFc group (P<0.05), and were comparable to the control group (P>0.05); the morphology, seminal zinc, seminal fructose and seminal carnitine were similar among the three groups (P>0.05). Patients in both sY152 and AZFc groups had lower fertilization rates (68.40% and 70.63%, respectively) than those in the control group (74.91%), and the differences were statistically significant (P<0.05). No significant differences were found in terms of MII oocyte, high-grade embryo rate, 2PN zygote, number of available embryos and transferred embryos, clinical pregnancy rate, implantation rate, miscarriage rate, multiple pregnancy rate, delivery rate, preterm rate and the male/female ratio among the three groups (P>0.05). Single sY152 deletion might cause a lower fertilization rate, but no adverse effects on sperm quality and clinical outcomes were found. Our study may provide more information for consultation in these patients.
Assuntos
Azoospermia/genética , Cromossomos Humanos Y/genética , Oligospermia/genética , Adulto , Azoospermia/terapia , Deleção Cromossômica , Feminino , Estudos de Associação Genética , Marcadores Genéticos , Predisposição Genética para Doença , Humanos , Masculino , Oligospermia/terapia , Estudos Retrospectivos , Sitios de Sequências Rotuladas , Injeções de Esperma Intracitoplásmicas , Resultado do TratamentoRESUMO
Y chromosome microdeletions can cause male infertility and are classified as natural transmission and de novo mutations. To examine the source of these deletions in Chinese men and to provide a theoretical and laboratory basis for genetic counseling, patients from Northeast China with primary male infertility (N = 22) and their fathers were investigated. Karyotype analysis was performed on peripheral blood lymphocytes using standard G-banding. Multiplex polymerase chain reaction amplification using 18 specific sequence-tagged sites was selected to detect Y chromosome microdeletions. De novo mutations were observed in 17 father-son pairs, leading to a mutation rate of 77.27% (17/22), while the vertical transmission of Yq AZFc microdeletions was detected in 5 cases of the families investigated (29.41%, 5/17). There were no statistically significant differences between vertically transmitted and de novo mutations in men with AZFc deletions regarding age, testicular volume, and reproductive hormone levels. Most Y chromosome microdeletions in men from Northeast China are the result of de novo mutations via natural conception, and men with Yq AZFc deletions showed no clear differences between vertical transmission and de novo mutations.
Assuntos
Povo Asiático/genética , Infertilidade Masculina/genética , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/genética , China , Bandeamento Cromossômico , Deleção Cromossômica , Cromossomos Humanos Y/genética , Deleção de Genes , Humanos , Cariótipo , Cariotipagem , Masculino , Linhagem , Análise de Sequência de DNA , Sitios de Sequências Rotuladas , Aberrações dos Cromossomos SexuaisRESUMO
Microdeletions in the AZF region of the Y chromosome are among the most frequent genetic causes of male infertility, although the specific role of the genes located in this region is not fully understood. AZFa and AZFb deletions impair spermatogenesis since no spermatozoa are found in the testis. Deletions of the AZFc region, despite being the most frequent in azoospermic patients, do not correlate with spermatogenic failure. Therefore, the aim of this work was to develop a screening method to ascertain the presence of the main spermatogenesis candidate genes located in the AZFc region in the light of the identification of those responsible for spermatogenic failure. DAZ, CDY, BPY2, PRY, GOLGA2LY and CSGP4LY genes were selected on the basis of their location in the AZFc region, testis-only expression, and confirmed or predicted protein codification. AMEL and SRY were used as amplification controls. The identification of Real Time PCR products was performed by High Resolution Melting analysis with SYTO 9 as intercalating dye. The herein described method allows a rapid, simple, low-cost, high-throughput screening for deletions of the main AZFc genes in patients with spermatogenic failure. This provides a strategy that would accelerate the identification of spermatogenesis candidate genes in larger populations of patients with non-obstructive idiopathic azoospermia.
Assuntos
Cromossomos Humanos Y/genética , Espermatogênese/genética , Azoospermia/genética , Linhagem Celular , Deleção Cromossômica , Humanos , Infertilidade Masculina/genética , Masculino , Reação em Cadeia da Polimerase em Tempo Real/métodos , Proteínas de Plasma Seminal/genética , Deleção de Sequência/genética , Sitios de Sequências Rotuladas , Testículo/metabolismoRESUMO
Background At present, species known as camote de cerro (Dioscorea spp.) are found only in the wilderness in Mexico, but their populations are extremely depleted because they are indiscriminately collected, it is urgent to evaluate the conservation status of these plants in order to design conservation genetics programs. In this study, genetic diversity parameters along with cluster analysis based on Jaccard's coefficient were estimated with the objective to assess the efficiency of Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR), Amplified Fragment Length Polymorphism (AFLP) and Inverse Sequence Tagged Repeat (ISTR) molecular DNA markers in the Dioscorea genus. Results The polymorphic information contents were quite similar for all markers (≈0.48). Genetic variation of Dioscorea spp., in terms of average heterozygosity was lower with ISTR (0.36), and higher when other markers were used (RAPD = 0.43; ISSR = 0.45 and AFLP = 0.47). Conclusion This indicates an important level of genetic differences despite the fact that the plant is asexually propagated. Based on the diversity statistics, any marker tested in present work can be recommended for use in large-scale genetic studies of populations. However, the low correlations among different molecular marker systems show the importance of the complementarity of the information that is generated by different markers for genetic studies involving estimation of polymorphism and relationships.
Assuntos
Polimorfismo Genético , Variação Genética , Dioscorea/genética , DNA/isolamento & purificação , Marcadores Genéticos , Sitios de Sequências Rotuladas , Técnica de Amplificação ao Acaso de DNA Polimórfico , Repetições de Microssatélites , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Heterozigoto , MéxicoRESUMO
Anthracnose (ANT) and angular leaf spot (ALS) are devastating diseases of common bean (Phaseolus vulgaris L.). Ouro Negro is a highly productive common bean cultivar, which contains the Co-10 and Phg-ON genes for resistance to ANT and ALS, respectively. In this study, we performed a genetic co-segregation analysis of resistance to ANT and ALS using an F2 population from the Rudá × Ouro Negro cross and the F2:3 families from the AND 277 × Ouro Negro cross. Ouro Negro is resistant to races 7 and 73 of the ANT and race 63-39 of the ALS pathogens. Conversely, cultivars AND 277 and Rudá are susceptible to races 7 and 73 of ANT, respectively. Both cultivars are susceptible to race 63-39 of ALS. Co-segregation analysis revealed that Co-10 and Phg-ON were inherited together, conferring resistance to races 7 and 73 of ANT and race 63-39 of ALS. The Co-10 and Phg-ON genes were co-segregated and were tightly linked at a distance of 0.0 cM on chromosome Pv04. The molecular marker g2303 was linked to Co-10 and Phg-ON at a distance of 0.0 cM. Because of their physical linkage in a cis configuration, the Co-10 and Phg-ON resistance alleles are inherited together and can be monitored with great efficiency using g2303. The close linkage between the Co-10 and Phg-ON genes and prior evidence are consistent with the existence of a resistance gene cluster at one end of chromosome Pv04, which also contains the Co-3 locus and ANT resistance quantitative trait loci. These results will be very useful for breeding programs aimed at developing bean cultivars with ANT and ALS resistance using marker-assisted selection.
Assuntos
Mapeamento Cromossômico , Resistência à Doença/genética , Phaseolus/genética , Phaseolus/microbiologia , Doenças das Plantas/genética , Alelos , Cruzamento , Colletotrichum , Cruzamentos Genéticos , DNA de Plantas/genética , Genes de Plantas , Ligação Genética , Marcadores Genéticos , Interações Hospedeiro-Patógeno/genética , Família Multigênica , Doenças das Plantas/microbiologia , Folhas de Planta/genética , Folhas de Planta/microbiologia , Locos de Características Quantitativas , Sitios de Sequências RotuladasRESUMO
We investigated the frequency and types of Y-chromosome microdeletions and chromosomal anomalies in non-obstructive azoospermic and severely oligozoospermic infertile males in northeastern China. The sample consisted of 519 infertile males (456 azoospermic, 63 severely oligozoospermic). PCR assays for Y-chromosome microdeletions and chromosome analysis were performed on all patients and controls. Array-comparative genomic hybridization was performed for three patients with chromosomal anomalies. Fifty-nine of 519 patients (11.37%) had Y-chromosome microdeletions. Microdeletions were found in 11.18% (51/456) of the non-obstructive azoospermic patients and in 12.7% (8/63) of the severely oligozoospermic patients. Eleven of 51 non-obstructive azoospermic patients with Y-chromosome microdeletions had multiple segmental deletions in the AZFb+c regions; four of these patients had chromosomal anomalies. Our sample from northeastern China had a higher frequency of microdeletions among severely oligozoospermic than among non-obstructive azoospermic males.
Assuntos
Azoospermia/genética , Deleção Cromossômica , Cromossomos Humanos Y/genética , Adulto , China , Hibridização Genômica Comparativa , Humanos , Infertilidade Masculina , Cariotipagem , Masculino , Pessoa de Meia-Idade , Sitios de Sequências Rotuladas , Aberrações dos Cromossomos Sexuais , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/genética , Adulto JovemRESUMO
Khat (Catha edulis Forsk.) is a flowering perennial shrub cultivated for its neurostimulant properties resulting mainly from the occurrence of (S)-cathinone in young leaves. The biosynthesis of (S)-cathinone and the related phenylpropylamino alkaloids (1S,2S)-cathine and (1R,2S)-norephedrine is not well characterized in plants. We prepared a cDNA library from young khat leaves and sequenced 4,896 random clones, generating an expressed sequence tag (EST) library of 3,293 unigenes. Putative functions were assigned to > 98 percent of the ESTs, providing a key resource for gene discovery. Candidates potentially involved at various stages of phenylpropylamino alkaloid biosynthesis from L-phenylalanine to (1S,2S)-cathine were identified.
Assuntos
Catha , Fenilpropanolamina , Sequência de Bases , Plantas Medicinais , Sitios de Sequências RotuladasRESUMO
INTRODUÇÃO: A poliquimioterapia (PQT-OMS) para tratamento da hanseníase resultou em drástica redução da sua prevalência, mas em limitado impacto na detecção de casos novos (CN), que se manteve estável em Santa Catarina, estado na fase de pós-eliminação. Casos com altos índices baciloscópicos apresentam risco de recidiva tardia e podem consistir em focos persistentes de transmissão da doença. OBJETIVOS: Avaliar a recidiva da doença em amostra de pacientes virchowianos regularmente tratados com PQT-OMS 24 doses; ensaios de resistência terapêutica em camundongos para os casos suspeitos; resposta imune específica (celular e humoral) e detecção do DNA do M. leprae nos casos-índices (CI) e seus contatos indradomiciliares (CID); e os achados frente aos indicadores epidemiológicos e operacionais de Santa Catarina. CASUÍSTICA E MÉTODOS: A partir da busca no Sistema de Informação de Agravos de Notificação (SINAN), foram selecionados 46 CI, tratados entre 1990-2000, e 187 CID, dos municípios de Itajaí e Joinville. A avaliação constituiu de: exames dermatoneurológico e anatomopatológico da pele; baciloscopia do esfregaço cutâneo; reação de Mitsuda; sorologia para glicolipídeo fenólico-I (IgM-anti-PGL-I); ensaios de resistência terapêutica em camundongos e de detecção do DNA bacilar no muco nasal por reação em cadeia da polimerase (PCR) para as seqüências repetitivas específicas RLEP-130 e RLEP-372. RESULTADOS: Entre os CI após alta por cura (m=11,2 ± 3 anos), a idade média (57,3±14,5 anos) foi superior (p<0,05) comparada aos CID, com predomínio de homens (p=0,001) e Mitsuda-negativos (78,6%). Em quatro casos (8,7%) considerados recidivados, o valor sérico médio (0,365) e as freqüências da positividade do anti-PGL-I e a da RLEP-130 (75%; p=0,03) foram consistentemente elevados, e os testes em camundongos, negativos. Dentre os 187 CID, 22 (11,8%) adoeceram (CIDd), a maioria (10 casos; 45,4%) foi diagnosticada entre 2 a 19 anos; 6 casos (27,3%), no mesmo período do seu...
Introduction: Multidrugtherapy (MDT-WHO) resulted in marked reduction of leprosy prevalence in Brazil, without impact on detection of new cases in Santa Catarina (SC) state in the post-elimination phase. Lepromatous cases with high bacilloscopic index have late relapse risk and can consist in the disease transmission focus. Objectives: The aim of this study was to evaluate the disease recurrence and microbiological resistance in lepromatous leprosy patients regularly treated with MDT-WHO/24 doses; specific immune response (cellular and humoral) and M. leprae DNA detection in index cases (IC) and their household contacts (HHC); and the findings face to the epidemiological and operational indicators of Santa Catarina state. Casuistic and methods: After consulting the Brazilian Information System of Notification (SINAN) database, 46 IC successfully diagnosed and treated between 1990 and 2000, and their 187 HHC from Joinville and Itajaí (SC) municipalities were selected. A dermatoneurological examination was performed, as well as the skin biopsies for histopathology and therapy resistance assay in mouse pads, skin smears for bacilloscopy, anti-PGL-I IgM serology, Mitsuda reaction, polymerase chain reaction for M. leprae DNA detection in nasal secretion based on 130bp and 372bp specific repetitive sequences (RLEP). Results: Cured IC (m=11.2±3 years) had mean age higher ((57.3±14.5 years old; p<0.05) than HHC, most of them were males (p=0.001) and Mitsuda negative (78.6%). In 4 relapsed cases (8.7%) the average anti-PGL-I serum levels (0.365), as well as frequency of positive antibody and RLEP-130 (75%; p=0.03) were consistently high and the mouse footpads assays resulted negative. Among 187 HHC, 22 (11.8%) became sick (sHHC), 10 cases (45.4%) were diagnosed between 2 and 19 years, being 6 cases (27.3%) in the same year of their IC; 6 new cases (3 borderline-tuberculoid and 3 tuberculoid) were detected during the study, with high RLEP-130 positive frequency...
Assuntos
Humanos , Masculino , Feminino , Busca de Comunicante , Hanseníase/terapia , Antígeno de Mitsuda , Mycobacterium leprae/isolamento & purificação , Reação em Cadeia da Polimerase , Recidiva , Sitios de Sequências Rotuladas , Testes SorológicosRESUMO
Infertility is a major reproductive health threat; the frequency of male infertility due to Y-chromosome microdeletions is 13-18% in the human population; these microdeletions involve recurrent loss of three non-overlapping regions designated as AZFa, AZFb and AZFc, associated with spermatogenic failure. Several contradictory reports have been published regarding deletion frequency based on sequence-tagged site markers and genotype-phenotype correlation. We examined the prevalence of Yq- deletion in 64 clinically diagnosed infertile male patients. We found a 3% frequency of microdeletion of the AZFc region; hormone profiles (FSH, LH and testosterone) showed significantly (P < 0.001) elevated levels compared to controls. No mutations were observed in the AZFa and AZFb regions, perhaps due to the selective use of sequence-tagged site markers.
Assuntos
Deleção Cromossômica , Cromossomos Humanos Y/genética , Infertilidade Masculina/genética , Proteínas de Plasma Seminal/genética , Adulto , Primers do DNA/genética , Loci Gênicos , Marcadores Genéticos , Humanos , Masculino , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Sitios de Sequências RotuladasRESUMO
The molecular mechanisms by which trisomy of human chromosome 21 disrupts normal development are not well understood. Global transcriptome studies attempting to analyze the consequences of trisomy in Down syndrome (DS) tissues have reported conflicting results, which have led to the suggestion that the analysis of specific tissues or cell types may be more productive. In the present study, we set out to analyze global changes of gene expression in lymphocytes from children with trisomy 21 by means of the serial analysis of gene expression (SAGE) methodology. Two SAGE libraries were constructed using pooled RNA of normal and Down syndrome children. Comparison between DS and normal profiles revealed that most of the transcripts were expressed at similar levels and functional classes of abundant genes were equally represented. Among the 242 significantly differentially expressed SAGE tags, several transcripts downregulated in DS code for proteins involved in T-cell and B-cell receptor signaling (e.g., PI3Kdelta, RGS2, LY6E, FOS, TAGAP, CD46). The SAGE data and interindividual variability were validated by real-time quantitative PCR. Our results indicate that trisomy 21 induces a modest dysregulation of disomic genes that may be related to the immunological perturbations seen in DS.
Assuntos
Síndrome de Down/genética , Regulação da Expressão Gênica , Criança , Mapeamento Cromossômico , Síndrome de Down/imunologia , Perfilação da Expressão Gênica , Humanos , Linfócitos/imunologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sitios de Sequências RotuladasRESUMO
We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). The core of the server relies on a database of genomic virtual tags built by a recently described method that attempts to reduce the amount of ambiguous assignments for those tags that are not unique in the genome. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. The output of the server consists of a table in HTML format that contains links to a graphic representation of the results and to some external servers and databases, facilitating the tasks of analysis of gene expression and gene discovery. Also, a table in tab delimited text format is produced, allowing the user to export the results into custom databases and software for further analysis. The current server version provides the most accurate and complete SAGE tag mapping source that is available for the yeast organism. In the near future, this server will also allow the accurate mapping of experimental SAGE-tags from other model organisms such as human, mouse, frog and fly. The server is freely available on the web at: http://dna.bio.puc.cl/SAGExplore.html.
Assuntos
Biologia Computacional/métodos , Regulação Fúngica da Expressão Gênica , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Sitios de Sequências Rotuladas , Software , Mapeamento Cromossômico , DNA Complementar/genética , Bases de Dados Genéticas , Etiquetas de Sequências Expressas , Internet , RNA Fúngico/genética , RNA Mensageiro/genética , RNA não Traduzido/genéticaRESUMO
Today infertility is a major health problem affecting about 10-20% of couples. A male factor is assumed to be responsible in about 50% of the infertile couples. The origin of reduced testicular sperm function is unknown in about 60-70% of cases. There are several causes of male infertility such as varicocele, spermatic duct obstruction, and endocrine disorders. Micro-deletions in the Yq are known to represent the pathogenic mechanisms for infertile males. Three different non-overlapping regions designated as AZFa, AZFb, and AZFc are located in interval 5-6 of Yq, and are associated with impaired spermatogenesis in humans. To determine the prevalence of Y chromosomal microdeletions in Venezuelan males with idiopathic infertility, chromosomal, seminal, histological and molecular analyses were carried out in 29 Venezuelan males with idiopathic azoospermia or oligoospermia. Y-microdeletions analyses were performed using a multiplex polymerase chain reaction (PCR)-based technique with 22 sequences-tagged-sites (STSs). One of 29 patients (3.4%) had Yq microdeletions on AZFc. The frequency of AZF microdeletions in Venezuelan patients was similar to other populations with different ethnical or geographical origin.
Assuntos
Deleção Cromossômica , Cromossomos Humanos Y/genética , Infertilidade Masculina/genética , Sitios de Sequências Rotuladas , Azoospermia/genética , Humanos , Masculino , Reação em Cadeia da Polimerase/métodos , VenezuelaRESUMO
Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.
Assuntos
Pesquisa Biomédica/instrumentação , Biologia Computacional/instrumentação , Sistemas de Gerenciamento de Base de Dados/instrumentação , Análise de Sequência de DNA/métodos , Bases de Dados Genéticas , Humanos , Laboratórios , Análise de Sequência de DNA/instrumentação , Sitios de Sequências Rotuladas , Interface Usuário-ComputadorRESUMO
Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.
Assuntos
Humanos , Análise de Sequência de DNA/métodos , Biologia Computacional/instrumentação , Pesquisa Biomédica/instrumentação , Sistemas de Gerenciamento de Base de Dados/instrumentação , Análise de Sequência de DNA/instrumentação , Bases de Dados Genéticas , Laboratórios , Sitios de Sequências Rotuladas , Interface Usuário-ComputadorRESUMO
El objetivo de la presente investigación fue probar la posible asociación de uno o más microsatélites localizados en 4q25-4q33 y FLPNS. Se analizó una muestra de 51 genealogías extensas. A partir de estas genealogías se obtuvieron 51 tríos caso-progenitores, que se estudiaron con el programa extended transmisión disequilibrium test (ETDT). Además se colectó a 51 probandos y 94 controles para un estudio caso-control en población chilena y se postuló comprobar las diferencias entre ambos estudios de asociación. Se analizaron los microsatélites D4S1570, D4S1615, FGA, UCP1 y D4S1597 ubicados en 4q, utilizándose la técnica de la polimerasa en cadena (PCR) para el análisis de ADN, marcandose la hebra líder con un fluorocromo. Los resultados electroforeticos fueron analizados en un secuenciador automático ABIPRISM 377. Observándose que FGA en el grupo control y FGA, D4S1570 y D4S1597 en los pacientes estaban en equilibrio de H-W. Estos resultados implican que un estudio caso-control no es adecuado para el estudio de estos marcadores. Para obviar este problema se utilizó el programa ETDT, observándose que los microsatélites D4S1570, UCP1 y D4S1597 presentaron una asociación tipo alélica en familias multiples. Estos resultados sugiere que estos microsatélites se encontrarían cerca de 1 o más genes candidatos de esta malformación en la región eq24-4q31.
The objective of this investigation is to test the hypothesis of the possible association of one or more microsatellites located on 4q25-4q33 with NSCLP. In this study a sample of 51 extended pedigrees were analyzed. From these pedigrees a sample of 51 case-parents trios was obtained. A novel genetic analysis was carried out using the Extended Transmission Disequilibrium Test (ETDT). Also a case control study was carried out with the 51 probands of the case-parents trios plus a sample of 94 controls of the Chilean population to test if differences were observed resulting from the methods used for the association studies. Microsatellites D4S1570, D4S1615, FGA, UCPI and D4S1597 located in 4q were analyzed. The polymerase chain reaction (PCR) was used for analysis of DNA. Forward primers were marked with fluorescent-dye-Iabel. Electrophoresis and analyses were carried out in an ABI PRISM 377 automatic sequencer. In the case-control study, only FGA was in H-W equilibrium in controls, whereas FGA, D4S1570 y D4S1597 were in H-W equilibrium in cases. These results imply that a case control study does not represent an adequate procedure to carry out an association study between the aforementioned micro satellites and NSCLP. In order to obviate this problem the ETDT program was used. From all of the analyzed microsatellites, D4S1570, UCPl and D4S 1597 presented significant allele wise association in those case-parents trios to multiplex families. This result suggests that these microsatellites would be located close to one or more candidate genes for this malformation in 4q24-4q31.
Assuntos
Humanos , Masculino , Feminino , Doenças Genéticas Inatas/diagnóstico , Fissura Palatina/genética , Fenda Labial/genética , Sitios de Sequências Rotuladas , Marcadores Genéticos , Reação em Cadeia da Polimerase , Repetições de Microssatélites , Estudos de Casos e ControlesRESUMO
Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for approximately 8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.
Assuntos
Perfilação da Expressão Gênica/métodos , Polimorfismo de Nucleotídeo Único , Enzimas de Restrição do DNA/metabolismo , Bases de Dados Genéticas , Humanos , Dados de Sequência Molecular , RNA Mensageiro/química , Análise de Sequência de RNA , Sitios de Sequências RotuladasRESUMO
Microdeletions of the Y chromosome have been observed in some patients with cryptorchidism and severe defects of spermatogenesis. We investigated whether microdeletions of the Y chromosome may be present in patients with cryptorchidism and hypospadias. Peripheral blood was obtained from 20 male patients 5.8 +/- 4.1 years (range: 0.4-14 years) with cryptorchidism and hypospadias for somatic DNA analysis of Y chromosome using multiplex polymerase chain reaction. These patients had no identifiable genetic syndrome, other genitourinary malformations or an abnormal karyotype. We evaluated the presence or absence of amplification using a set of 34 different sequence-tagged sites (STS) in each patient. All patients showed normal length amplifications for each of the regions evaluated, suggesting that microdeletions of the Y chromosome are not a frequent cause of hypospadias associated with cryptorchidism.