Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma.

The aim of this study is to determine the fetus Y-STR haplotype in maternal plasma during pregnancy and estimate, non-invasively, if the alleged father and fetus belong to the same male lineage. The study enrolled couples with singleton pregnancies and known paternity. All participants signed informed consent and the local ethics committee approved the study. Peripheral blood was collected in EDTA tubes (mother) and in FTA paper (father). Maternal plasma DNA was extracted by using NucliSens EasyMAG. Fetal gender was determined by qPCR targeting DYS-14 in maternal plasma and it was also confirmed after the delivery. From all included volunteers, the first consecutive 20 mothers bearing male fetuses and 10 mothers bearing female fetuses were selected for the Y-STR analysis. The median gestational age was 12 weeks (range 12-36). All DNA samples were subjected to PCR amplification by PowerPlex Y23, ampFLSTR Yfiler, and two in-house multiplexes, which together accounts for 27 different Y-STR. The PCR products were detected with 3500 Genetic Analyzer and they were analyzed using GeneMapper-IDX. Fetuses' haplotypes (Yfiler format) were compared to other 5328 Brazilian haplotypes available on Y-chromosome haplotypes reference database (YHRD). As a result, between 22 and 27 loci were successfully amplified from maternal plasma in all 20 cases of male fetuses. None of the women bearing female fetuses had a falsely amplified Y-STR haplotype. The haplotype detected in maternal plasma completely matched the alleged father haplotype in 16 out of the 20 cases. Four cases showed single mismatches and they did not configure exclusions; 1 case showed a mutation in the DYS 458 locus due to the loss of one repeat unit and 3 cases showed one DYS 385I/II locus dropout. All mismatches were confirmed after the delivery. Seventeen fetuses' haplotypes were not found in YHRD and one of them had a mutation, which corresponded to the paternity probability of 99.9812% and 95.7028%, respectively. Three fetuses' haplotypes occurred twice in YHRD, which corresponded to paternity probability of 99.9437%. In conclusion, high discriminatory fetal Y-STR haplotype could be determined from maternal plasma during pregnancy starting at 12 weeks of gestation. All male fetuses could be attributed to the alleged father male lineage early in pregnancy. The high probability of paternity associated with each case suggests that the relationship is not random and this strategy can be use as an alternative for male fetal kinship analysis.

Hybrid capture II and PapilloCheck® tests for detection of anal high-risk human papillomavirus.

INTRODUCTION: This study evaluated the level of concordance between hybrid capture II (HCII) and PapilloCheck® for the detection of high-risk human papillomavirus (HPV) in anal samples. METHODS: Anal cell samples collected from 42 human immunodeficiency virus (HIV)+ patients were analyzed. RESULTS: Considering only the 13 high-risk HPV types that are detectable by both tests, HCII was positive for 52.3% of the samples, and PapilloCheck® was positive for 52.3%. The level of concordance was 80.9% (Kappa = 0.61). CONCLUSIONS: Good concordance was observed between the tests for the detection of high-risk HPV.

A comparative study between conventional and liquid-based cytology in screening for anal intraepithelial lesions in HIV-positive patients.

Anal intraepithelial neoplasia (AIN) is associated with HPV infection and can be detected by cytological screening. While conventional exfoliative cytology (CC) is a low-cost and nonaggressive method, liquid-based cytology (LBC) tends to give clearer readings. Although studies of the efficacy of anal cancer screening methods would be of great importance for groups at high risk for AIN, few such studies have been conducted. The aim of the present study was to assess the concordance of CC and LBC in diagnosing anal pre-neoplastic lesions, and to compare cytological results with anoscopy, histopathological, and molecular biology findings. Comparative study involving 33 HIV-positive patients, who underwent anoscopy and biopsy of suspected lesions. Concordance between the two cytology methods was calculated, as were the associations between cytology results and findings from other screening methods. A total of 54.5% of cases were considered AIN-negative by CC and LBC, and concordance between the two methods was statistically significant (P < 0.05). Anoscopy was negative in 15 of the 18 CC- and LBC-negative cases. CC identified 75% of patients with positive biopsy, while LBC identified 85.71% of these patients. Molecular biology results showed that patients with LSIL tested positive for the highest number of HPV subtypes. The associations between positive biopsy and high grade HPV, HPV 16, and multiple HPV infections were not statistically significant. Conventional and liquid-based cytology are equally effective in screening for anal preneoplastic lesions.

Haplotype diversity of 23 Y-chromosomal STRs in a population sample from the Federal District (Brazil)--a territory that arose from nothing.

In this study, the genetic variations of 23 short tandem repeats on the Y-chromosome were analyzed in a sample of 201 males from the Federal District (Brazil). The Federal District (Brazil) was built in 1960 in Brazil's Central West region, where there was no previous population. In 2010, the population of this artificially founded district consisted of 2,500,000 inhabitants. We observed 200 different haplotypes, 199 of which were unique and one of which occurred two times. The haplotype diversity was 0.9999, and the discrimination capacity was 0.995. The data are available in the Y chromosome haplotype reference database under accession number YA003843. The results were compared to the haplotypes from other Brazilian macroregions.

Allele frequencies for 15 autosomal STRs in a population sample from the Federal District (Brazil)-a territory that arose from nothing.

The Federal District (Brazil) was created in 1960 in the Central-West Region of Brazil in a previously unpopulated area. In 2010, this artificially founded district was populated by 2,562,963 inhabitants. In this study, the genetic variations of the 15 Next Generation Multiplex (NGM(TM)) short tandem repeat loci were analyzed. The results indicate that the NGM(TM) is a highly informative genetic system in this population, which is more similar to the southeastern, northeastern, and overall Brazil populations. This conclusion agrees with the population composition reported in the 2010 National Survey Inquiries, in which most of the immigrants were from the northeast and the southeast.

Value of human papillomavirus typing for detection of anal cytological abnormalities.

PURPOSE: The objective of this study was to evaluate anal cytology and human papillomavirus (HPV) typing in patients with human immunodeficiency virus infection. MATERIALS AND METHODS: Anal samples were collected from 61 patients (44 men and 17 women) and analyzed by PapilloCheck test and conventional cytology. RESULTS: Of all anal samples, 37.7% had cytological abnormalities, 47.54% were negative and 14.75% were unsatisfactory. High-risk HPV, multiple high-risk HPV and HPV 16 infection was detected in 91.13%, 78.26% and 47.82% of the samples with cytological abnormalities and in 47.54%, 6.89% and 3.44% of the negative samples, respectively. High-risk HPV infection was significantly more frequent in anal samples with cytological abnormalities than in negative samples (P = 0.0005, Fisher's test), particularly multiple high-risk HPV infection (P < 0.0001) and HPV 16 infection (P = 0.0002). CONCLUSIONS: High-risk HPV, multiple high-risk HPV and HPV 16 infections are significantly associated with anal cytological abnormalities. Furthermore, the frequency of HPV infection in anal cytological samples suggests that high-risk HPV detection has high sensitivity, but low specificity for detection of anal cytological abnormalities, but multiple high-risk HPV typing and HPV 16 typing have a lower sensitivity and high specificity. Results suggest that HPV typing may be useful as an adjunct to cytology to screen patients for high-resolution anoscopy and biopsy.

Antihyperglycemic effect and genotoxicity of Psittacanthus calyculatus extract in streptozotocin-induced diabetic rats / Efecto antihiperglicemico y genotoxico de extractos de Psittacanthus calyculatus en ratas diabeticas inducidas con streptozotocina

Psittacanthus calyculatus (DC.) G. Don (Lorantaceae) is known as “ingerto”. The aerial parts are used in the treatment of diabetes and hypertension. Methanolic extract was tested with streptozotocin-induced diabetic rats. Dose of 200 mg/Kg body weight for acute experiments, as well as 200 and 400 mg/Kg for semi-chronic bioassay were used. In both experiments extract produced significant hypoglycemic activity in streptozotocin-induced rats when compared with diabetic control (p 0.05). To study possible clastogenic effects of methanolic extract a mouse micronucleus test was performed (as part of the genetic toxicology trial). CD-1 white mice were administered with 200 and 400 mg/Kg of methanolic extract of P. calyculatus dissolved in water by intraperitoneal injection. The cytotoxic activity polychromatic erythrocytes/normochromatic erythrocytes (PCE/NCE) and the induction of micronuclei in peripheral blood erythrocytes (MNPCE) was recorded with sampling times of 24, 48 and 72, h after an exposure without killing of mice. The frequency of MNPCE in the circulating blood obtained from the tail of the mouse was statistically not significant compared with its negative control animals (time zero) and the PCE/NCE ratio showed evidences of light cytotoxic activity compared with its negative control animals (time zero). Thus, in this test, the methanolic extract of Psittacanthus calyculatus dissolved in water did not induce chromosomal damage resulting in micronucleus formation in peripheral blood erythrocytes and showed light cytotoxic activity.

En la zona del bajío mexicano la planta Psittacanthus calyculatus (DC.) G. Don (Lorantaceae) es conocida popularmente como “ingerto”. Las partes aéreas de este vegetal se utilizan para tratar enfermedades como la diabetes y la hipertensión. Se realizaron experimentos agudos y semi-crónicos en ratas diabéticas inducidas con estreptozotocina. El efecto hipoglucemiante del extracto metanólico se evaluó a dosis de 200 y 400 mg/Kg de peso. En ambos experimentos, el extracto redujo significativamente (p < 0.05) la glucemia en las ratas diabéticas. Para determinar los posibles efectos clastogénicos del extracto metanólico se administraron por vía intraperitoneal a ratones cepa CD-1 las dosis que mostraron actividad hipoglucemiante disueltas en agua y se llevó a cabo el bioensayo de micronúcleos en sangre periférica de ratón. La actividad citotóxica se determinó mediante el cálculo de la relación entre los eritrocitos policromáticos y los eritrocitos normocromáticos (PCE/NCE). La inducción de micronúcleos en eritrocitos de sangre periférica (MNPCE) fue el indicador de gentotoxicidad los cuales se midieron a las 24, 48 y 72 horas después de la administración del extracto. La frecuencia de micronúcleos en eritrocitos policromáticos no fue estadísticamente significativa con relación al control negativo (al tiempo 0) por lo tanto, el extracto no induce daño cromosómico. Asimismo la relación PCE/NCE mostró que el extracto metanólico fue ligeramente citotóxico a la dosis de 400 mg/Kg y a las 48 h posteriores a la administración.

Helix 12 dynamics and thyroid hormone receptor activity: experimental and molecular dynamics studies of Ile280 mutants.

Nuclear hormone receptors (NRs) form a family of transcription factors that mediate cellular responses initiated by hormone binding. It is generally recognized that the structure and dynamics of the C-terminal helix 12 (H12) of NRs' ligand binding domain (LBD) are fundamental to the recognition of coactivators and corepressors that modulate receptor function. Here we study the role of three mutations in the I280 residue of H12 of thyroid hormone receptors using site-directed mutagenesis, functional assays, and molecular dynamics simulations. Although residues at position 280 do not interact with coactivators or with the ligand, we show that its mutations can selectively block coactivator and corepressor binding, and affect hormone binding affinity differently. Molecular dynamics simulations suggest that ligand affinity is reduced by indirectly displacing the ligand in the binding pocket, facilitating water penetration and ligand destabilization. Mutations I280R and I280K link H12 to the LBD by forming salt bridges with E457 in H12, stabilizing H12 in a conformation that blocks both corepressor and coactivator recruitment. The I280M mutation, in turn, blocks corepressor binding, but appears to enhance coactivator affinity, suggesting stabilization of H12 in agonist conformation.

Diagnóstico molecular – passado, presente e futuro / Molecular diagnosis – past, present and future

Este artigo consiste em uma descrição dos fatos históricos relacionados ao diagnóstico molecular, das técnicas disponíveis e do que se espera para o futuro do setor. Inicialmente, foram abordados as descobertas e os avanços originados dentro dos laboratórios de pesquisa das universidades, onde, efetivamente, nasceram as técnicas de análise de ácidos nucleicos. Posteriormente foi descrita a evolução que estas técnicas vêm sofrendo ao longo do tempo até se chegar ao formato atual, passando pela biologiamolecular manual e automatizada, abrangendo, basicamente, a PCR e a PCR tempo real. Além disso, foram discutidas e descritas brevemente outras técnicas de amplificação de ácidos nucleicos, amplificação de sinal e microarranjos. Por fim, foi apresentado um resumo das principais expectativas em relação ao diagnóstico molecular, considerando seu crescimento, o mercado de análises clínicas e as novas áreas e abordagens.

This article is a description of historical events related to molecular diagnosis, the techniques used today, and what thehope for the future of this segment is. First, we turn back to discoveries and advances originated within the research laboratory inside the universities, where the nucleic acid analysis techniques were born and we describe the progress that they have suffered until the current format. Otherwise, this is a brief history from manual molecular biology to automated molecular biology coveringmainly PCR, real time PCR. Moreover, we discuss briefly about other techniques for nucleic acid amplification, signal amplification and microarrays. Finally, we make a summary of the main expectations for the molecular diagnosis covering growth, market, new areas and approaches.

Selenoprotein-related disease in a young girl caused by nonsense mutations in the SBP2 gene.

CONTEXT: Selenoproteins are essential for life, and their biosynthesis requires the incorporation of the rare amino acid selenocysteine (Sec) in a process mediated by the Sec insertion sequence-binding protein 2 (SBP2). Although SBP2 is considered a rate-limiting factor mediating Sec incorporation, there has been little evidence so far linking SBP2 dysfunction to widespread selenoprotein-related disease. OBJECTIVE: The objective of the study was to report the discovery of novel truncation mutations in the SBP2 gene (R120X/R770X) in a female adolescent and the clinical consequences of the combined deficiency of selenoproteins. SUBJECTS AND METHODS: A 12-yr-old girl who presented with a syndrome of abnormal thyroid hormone metabolism, delayed bone maturation, congenital myopathy, and impaired mental and motor coordination development and her family were studied. The coding region of the SBP2 gene was analyzed by sequencing, and gel shift assays were performed to address the in vitro binding properties of the mutant SBP2 protein. RESULTS: Serum levels of selenium and glutathione peroxidase in the proband were reduced, and selenoprotein P levels were undetectable. DNA sequencing of the SBP2 gene revealed a compound heterozygous mutation (R120X/R770X). The R120X mutation disrupted all functional motifs and the R770X inhibited the binding of SBP2 to Sec insertion sequence elements. Interestingly, selenium supplementation normalized serum selenium and glutathione peroxidase but not selenoprotein P levels and did not restore thyroid hormone metabolism dysfunction. CONCLUSIONS: This distinctive phenotype can only be explained by the combined deficiency of functionally important selenoproteins and pinpoints the clinical relevance of selenoproteins and selenium economy in human development.

Allele-specific PCR assay to genotype SNP rs7903146 in TCF7L2 gene for rapid screening of diabetes susceptibility / Ensaio de PCR alelo-específico para genotipar o SNP rs7903146 no gene TCF7L2 para rápida triagem de suscetibilidade ao diabetes

OBJECTIVE: The aim of the present study is to validate a rapid and simple allele-specific PCR that genotypes TCF7/L2 rs7903146 (C/T) polymorphism with standard PCR instruments. METHODS: Two forward primers with variations in their 3' nucleotides were designed in such a way that each was specific for one of the two variants. They were combined with a common reverse primer into two PCR reactions. Specific amplification indicates the presence of the allele. One hundred and four DNA samples were genotyped by this method. To evaluate the assay, the polymorphism spanning region of 63 DNA samples representing the three possible genotypes was sequenced. RESULTS: The rs7903146 allele assignments derived from the allele-specific PCR were in complete agreement with sequencing. CONCLUSIONS: The assay described here is a suitable strategy for the TCF7/L2 rs7903146 (C/T) genotyping also allowing rapid and reliable identification.

OBJETIVO: O objetivo deste estudo foi validar um método de PCR alelo-específico, rápido e simples, para genotipagem do polimorfismo rs7903146 (C/T) no gene TCF7/L2 utilizando equipamentos convencionais. MÉTODOS: Dois primers forward com variações nos seus nucleotídeos 3' foram desenhados de forma que cada um fosse específico para uma das variantes. Eles foram combinados com um primer reverso comum em duas reações de PCR. A amplificação de tamanho específico indica a presença do alelo. Cento e quatro amostras de DNA foram genotipadas por esse método. Para validar o ensaio, uma amostragem representativa dos três possíveis genótipos (63 amostras) teve a região contendo o polimorfismo seqüenciada. RESULTADOS: A genotipagem do polimorfismo rs7903146 derivada da PCR alelo-específica estava em completa concordância com o sequenciamento. CONCLUSÕES: O ensaio aqui descrito é uma estratégia adequada para a genotipagem do polimorfismo rs7903146 (C/T) do gene TCF7/L2 e permite identificação alélica rápida e precisa.

Hepatitis C is less aggressive in hemodialysis patients than in nonuremic patients.

BACKGROUND AND OBJECTIVES: The severity of liver disease among hepatitis C patients on hemodialysis is controversial. The aim of this study was to compare the clinical, biochemical, and liver histologic characteristics of hepatitis C virus (HCV) in hemodialysis patients and in those with normal renal function. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: A case-control study was carried out with 36 HCV patients on hemodialysis and 37 HCV patients with normal renal function matched for gender, age at infection, and estimated time of infection. RESULTS: HCV patients on hemodialysis had lower levels of alanine aminotransferase and lower viral load. Hepatic fibrosis was significantly higher in the patients with normal renal function (73%) than in hemodialysis patients (47.2%, P < 0.025); the same was observed for inflammatory activity (control group 59.5% versus hemodialysis patients 27.7%, P = 0.003). In addition, the risk of tissue inflammation was four times lower in hemodialysis patients (odds ratio = 0.23, P < 0.004), and severe inflammatory activity on biopsy was the only independent risk factor for fibrosis (P < 0.001). CONCLUSIONS: The lower biochemical and inflammatory activities observed in hemodialysis patients suggest that hemodialysis and uremia may have a protective role against progression of the disease caused by HCV.

Allele-specific PCR assay to genotype SNP rs7903146 in TCF7L2 gene for rapid screening of diabetes susceptibility.

OBJECTIVE: The aim of the present study is to validate a rapid and simple allele-specific PCR that genotypes TCF7/L2 rs7903146 (C/T) polymorphism with standard PCR instruments. METHODS: Two forward primers with variations in their 3' nucleotides were designed in such a way that each was specific for one of the two variants. They were combined with a common reverse primer into two PCR reactions. Specific amplification indicates the presence of the allele. One hundred and four DNA samples were genotyped by this method. To evaluate the assay, the polymorphism spanning region of 63 DNA samples representing the three possible genotypes was sequenced. RESULTS: The rs7903146 allele assignments derived from the allele-specific PCR were in complete agreement with sequencing. CONCLUSIONS: The assay described here is a suitable strategy for the TCF7/L2 rs7903146 (C/T) genotyping also allowing rapid and reliable identification.

Thyroid hormone response element organization dictates the composition of active receptor.

Thyroid hormone (triiodothyronine, T(3)) is known to activate transcription by binding heterodimers of thyroid hormone receptors (TRs) and retinoid X receptors (RXRs). RXR-TRs bind to T(3) response elements (TREs) composed of direct repeats of the sequence AGGTCA spaced by four nucleotides (DR-4). In other TREs, however, the half-sites can be arranged as inverted palindromes and palindromes (Pal). Here we show that TR homodimers and monomers activate transcription from representative TREs with alternate half-site placements. TR beta activates transcription more efficiently than TR alpha at an inverted palindrome (F2), and this correlates with preferential TR beta homodimer formation at F2 in vitro. Furthermore, reconstruction of TR transcription complexes in yeast indicates that TR beta homodimers are active at F2, whereas RXR-TRs are active at DR-4 and Pal. Finally, analysis of TR beta mutations that block homodimer and/or heterodimer formation reveal TRE-selective requirements for these surfaces in mammalian cells, which suggest that TR beta homodimers are active at F2, RXR-TRs at DR-4, and TR monomers at Pal. TR beta requires higher levels of hormone for activation at F2 than other TREs, and this differential effect is abolished by a dimer surface mutation suggesting that it is related to composition of the TR.TRE complex. We propose that interactions of particular TR oligomers with different elements play unappreciated roles in TRE-selective actions of liganded TRs in vivo.

[Molecular mechanism of thyroid hormone action]. / Mecanismo molecular da ação do hormônio tireoideano.

Thyroid hormones (TH) are involved in normal differentiation, growth, and metabolism in several tissues of all vertebrates. Their actions are mediated by the TH receptors (TRs), members of the nuclear hormone receptor superfamily. These receptors are transcription factors that bind to DNA on specific sequences, the TR response element (TREs), in promoters of target genes. Two genes encode TRs, alpha e beta, located in chromosomes 17 and 3, respectively. These isoforms show different functions and exhibit a tissue specific expression. TRs function as monomers, homodimers or heterodimers with retinoid X receptor (RXR) and modulate transcription activity (repression or activation) by interacting with co-repressor and co-activators, which associate with TR in the absence or presence of T3, respectively. Understanding the molecular mechanism of TR action and the definition of its crystallographic structure will provide new insights into transcription mechanisms and will facilitate the design of new drugs with greater therapeutic value.

Mecanismo molecular da ação do hormônio tireoideano / Molecular mechanism of thyroid hormone action

Os hormônios tireoideanos (HTs) são necessários para a diferenciação, crescimento e metabolismo de diversos tecidos de vertebrados. Seus efeitos são mediados pelos receptores do hormônio tireoideano (TRs), membros da superfamília dos receptores nucleares. Estes receptores são fatores de transcrição modulares que se ligam em seqüências específicas do DNA denominadas elementos responsivos ao TR, que são encontrados nos promotores dos genes regulados pelo HT. Os TRs são codificados por dois genes distintos, alfae beta, localizados nos cromossomos 17 e 3, respectivamente. Estas isoformas apresentam diferentes funções e sua expressão é específica para cada tecido. O TR se liga ao DNA como monômero, homodímero ou heterodímero com o receptor de retinóide X (RXR). Além disso, o TR modula a atividade transcricional (repressão ou ativação) através da interação com correpressores e co-ativadores, na ausência e na presença do T3, respectivamente. A compreensão do mecanismo molecular da ação do receptor do hormônio tireoideano e a definição de sua estrutura cristalográfica contribuirão para a aquisição de novos conceitos envolvidos na transcrição e nos distúrbios hormonais presentes nas doenças endócrinas, assim como facilitará o desenho de novas drogas, agonistas ou antagonistas, com grande valor terapêutico.

Structure-function relationships in nucleosomal arrays containing linker histone H5.

To study the structural and functional changes accompanying the integration of histone H5 into the nucleosome structure, linear DNA species have been employed with a terminal promoter for bacteriophage T7 RNA polymerase followed by tandem repeats of a 207-bp nucleosome positioning sequence. The oligonucleosomes assembled from 12-repeat DNA and saturating amounts of core histone octamer plus histone H5 are compacted, in the presence of 1 mM free magnesium ions, to the level of the 30-nm fiber. Under these ionic conditions the efficiency in RNA synthesis and the size distribution of RNA chains obtained with this template are the same as those corresponding to the template without H5, indicating that the 30-nm fiber stabilized by H5 does not impair RNA elongation. Therefore, under our experimental conditions, incorporation of one molecule of histone H5 per nucleosome does not affect elongation of RNA even when a folded structure is produced. However, elongation is inhibited by binding of an excess of H5.