Assessing false paternity risk in simulated motherless cases from more than 20 000 real exclusion trios.

BACKGROUND: When the mother's DNA profile is not available for paternity testing, there is a smaller probability that a locus will exclude an alleged father. This study aims to evaluate the risk of potential false paternity inclusions in motherless cases. STUDY DESIGN AND METHODS: More than 20 000 duos were generated by removing the maternal genotypes from exclusion trios. After recalculating paternity in these duos, any found inclusions would be false. RESULTS: The use of an appropriate number of loci, mutation model, and mutation rates to analyze motherless paternity cases was robust against false inclusions. A single potential false inclusion was observed in a case wherein kinship plays a role. This result highlights the importance of testing the mother when available and of obtaining information on family circumstances for the proper handling of cases involving related individuals. CONCLUSION: The guidelines we used here were sufficient to avoid false inclusions in a data set of more than 20 000 motherless cases.

Polymorphism in the vitamin D receptor gene is associated with maternal vitamin D concentration and neonatal outcomes: A Brazilian cohort study.

OBJECTIVES: This study evaluated the associations between single-nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) gene, maternal vitamin D concentration, and gestational outcomes. METHODS: The cohort consisted of 270 pregnant women who received prenatal services at basic public healthcare centers in the city of Santo Antônio de Jesus, Bahia, Brazil. For statistical analysis, multiple linear regression was used. RESULTS: A mean of 72.62 (SD = 31.51) nmol/L for 25-hydroxyvitamin D (25(OH)D) concentrations was found. The mean birth weight was 3.340 g (SD = 0.545 g), and the mean duration of gestation was 38.66 (SD = 1.83) weeks. Pregnant women who were homozygous for the low-frequency allele GG of SNP TaqI had a higher concentration of vitamin D during gestation (ß = 14.09 nmol/L; 95% CI = 0.85, 27.34) than the higher frequency homozygotes AA (ß = 3.33 nmol/L; 95% CI = -4.37, 11.05). The children of heterozygous women for the ApaI SNP (GA) were born with a lower weight (ß = -131.99 g, 95% CI = -258.50, -5.47, P = .04). The heterozygote genotype of the SNP TaqI (CA) decreased the risk of short duration of gestation (ß = 0.54 weeks, 95% CI = 0.09, 0.99, P = .01), and the homozygote for the lower frequency allele in the SNP ApaI (CC) showed a negative effect, decreasing the duration of gestation (ß = -0.69 weeks, 95% CI = -1.35, -0.26, P = .04). CONCLUSIONS: The VDR gene is an important genetic predictor of a higher concentration of vitamin D during gestation, low birth weight, and decreasing duration of gestation.

Presence of infection and analysis of HPV subtypes in girls younger than 9 years old attended at a referral service in Espírito Santo, Brazil.

Human papillomavirus (HPV) is found in adults and adolescents and is associated with genital warts and cervical cancer. However, it has been detected in girls younger than 10 years old. Currently, there are no prevention methods for this age group, since it is not considered a risk group. The aim of this study was to evaluate the presence of infection and HPV subtype in girls under 9 years old attended at a referral service in the State of Espírito Santo, Brazil. Forty-three girls younger than 9 years old had gynecological brush samples collected from vulval and perineal/anal regions. Viral detection and subtyping were done using polymerase chain reaction, restriction fragment length polymorphism and DNA sequencing. Statistics was performed using Action Stat 3.1. The mean age of girls was 6.1 years. Sexual activity and abuse were not reported by 95.3%. Family stories showed viral infection in 9.3% of mothers, 4.7% of fathers and 9.3% of caretakers. None of these were related with the children infection. In the only case of mother's gestational HPV infection, the daughter tested negative. Genital warts and infection were observed in 7% and 13.9% of the patients, respectively. Viral subtypes detected were 6, 11, 38, and 42. These results demonstrate the presence of HPV infection in girls under 9 years of age. Prevalence studies are needed in order to evaluate a possible alteration in age of vaccination policy.

Analysis of 12 X-STRs loci in a population from southeastern Brazil.

Short tandem repeat (STR) markers on the X chromosome have a high potential for solving complex kinship analysis and individual identification cases. To achieve such purposes, allele and haplotype frequencies for the specific population are necessary. Nonetheless, such frequencies are not always available. Therefore, we obtained haplotypes from 520 unrelated males from four different geographic regions of Espírito Santo - Brazil, using the Investigator Argus X-12 kit. Forensic parameters for linked groups of four X-STR loci are reported. Genetic distance analyzes suggest that ES population is genetically closer to the Italian population and farther from the Mexican one, among the populations analyzed in this study.

Forensic Applications of Markers Present on the X Chromosome.

Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.

Seasonality, molecular epidemiology, and virulence of Respiratory Syncytial Virus (RSV): A perspective into the Brazilian Influenza Surveillance Program.

BACKGROUND: Respiratory Syncytial Virus (RSV) is the main cause of pediatric morbidity and mortality. The complex evolution of RSV creates a need for worldwide surveillance, which may assist in the understanding of multiple viral aspects. OBJECTIVES: This study aimed to investigate RSV features under the Brazilian Influenza Surveillance Program, evaluating the role of viral load and genetic diversity in disease severity and the influence of climatic factors in viral seasonality. METHODOLOGY: We have investigated the prevalence of RSV in children up to 3 years of age with severe acute respiratory infection (SARI) in the state of Espirito Santo (ES), Brazil, from 2016 to 2018. RT-qPCR allowed for viral detection and viral load quantification, to evaluate association with clinical features and mapping of local viral seasonality. Gene G sequencing and phylogenetic reconstruction demonstrated local genetic diversity. RESULTS: Of 632 evaluated cases, 56% were caused by RSV, with both subtypes A and B co-circulating throughout the years. A discrete inverse association between average temperature and viral circulation was observed. No correlation between viral load and disease severity was observed, but children infected with RSV-A presented a higher clinical severity score (CSS), stayed longer in the hospital, and required intensive care, and ventilatory support more frequently than those infected by RSV-B. Regarding RSV diversity, some local genetic groups were observed within the main genotypes circulation RSV-A ON1 and RSV-B BA, with strains showing modifications in the G gene amino acid chain. CONCLUSION: Local RSV studies using the Brazilian Influenza Surveillance Program are relevant as they can bring useful information to the global RSV surveillance. Understanding seasonality, virulence, and genetic diversity can aid in the development and suitability of antiviral drugs, vaccines, and assist in the administration of prophylactic strategies.

Effects of glyphosate exposure on human health: Insights from epidemiological and in vitro studies.

Glyphosate (GLY) is a broad-spectrum, post-emergent, non-selective and synthetic universal herbicide, whose commercial formulations are referred to as glyphosate-based-herbicides (GBHs). These chemicals and their metabolites can be found in soil, air, water, as well as groundwater and food products. This review summarizes to summarize current in vitro and epidemiological studies investigating the effects of GLY exposure on human health. Recent human cell studies have reported several GLY and GBH toxicological effects and have contributed to a better understanding of the deleterious consequences associated with their exposure. However, these detrimental effects are dependent on the cell type, chemical composition, as well as magnitude and time of exposure, among other factors. Moreover, the deleterious effects of GLY exposure on human health were observed in epidemiological studies; however, most of these studies have not determined the GLY dosage to confirm a direct effect. While GLY toxicity is clear in human cells, epidemiological studies investigating individuals exposed to different levels of GLY have reported contradictory data. Therefore, based on currently available in vitro and epidemiological data, it is not possible to confirm the complete safety of GLY use, which will require additional comprehensive studies in animal models and humans.

Induction of KLF4 in basal keratinocytes blocks the proliferation-differentiation switch and initiates squamous epithelial dysplasia.

KLF4/GKLF normally functions in differentiating epithelial cells, but also acts as a transforming oncogene in vitro. To examine the role of this zinc finger protein in skin, we expressed the wild-type human allele from inducible and constitutive promoters. When induced in basal keratinocytes, KLF4 rapidly abolished the distinctive properties of basal and parabasal epithelial cells. KLF4 caused a transitory apoptotic response and the skin progressed through phases of hyperplasia and dysplasia. By 6 weeks, lesions exhibited nuclear KLF4 and other morphologic and molecular similarities to squamous cell carcinoma in situ. p53 determined the patch size sufficient to establish lesions, as induction in a mosaic pattern produced skin lesions only when p53 was deficient. Compared with p53 wild-type animals, p53 hemizygous animals had early onset of lesions and a pronounced fibrovascular response that included outgrowth of subcutaneous sarcoma. A KLF4-estrogen receptor fusion protein showed tamoxifen-dependent nuclear localization and conditional transformation in vitro. The results suggest that KLF4 can function in the nucleus to induce squamous epithelial dysplasia, and indicate roles for p53 and epithelial-mesenchymal signaling in these early neoplastic lesions.

Comparative gene expression profile analysis of GLI and c-MYC in an epithelial model of malignant transformation.

Transcription factor oncogenes such as GLI and c-MYC are central to the pathogenesis of human tumors. GLI encodes a zinc finger protein that is activated by Sonic Hedgehog signaling. Mutations in this pathway induce GLI expression in basal cell carcinoma, and expression of GLI in mice is sufficient to induce these skin tumors. We used microarrays to identify transcripts regulated by GLI or c-MYC after retroviral transduction and short-term culture of epithelial RK3E cells. Although each of these oncogenes induces malignant transformation of RK3E, two distinct sets of genes were identified. Of approximately 17,500 transcripts represented on the microarrays, GLI up-regulated the expression of 158 and repressed the expression of 52. In contrast, transcripts regulated by c-MYC were mainly repressed (424 of 682 regulated transcripts). Transcripts induced by the GLI transgene are likewise expressed in association with endogenous GLI in Ptch-deficient murine fibroblasts or in human skin tumors, but are not up-regulated in RK3E cells transformed by c-MYC, KLF4, or HRAS1. Unlike these other oncogenes, GLI induced the expression of mesenchymal cell markers including Snail, a zinc finger protein implicated in epithelial-mesenchymal transition in development and during tumor progression. A novel GLI-estrogen receptor fusion protein rapidly induced Snail mRNA expression in a manner like Ptch, a known direct transcriptional target gene. Induction of Snail expression and epithelial-mesenchymal transition by GLI may account for certain histopathological features of basal cell carcinoma, such as the absence of a well-defined, intraepithelial precursor lesion. In addition, consistent expression of the newly identified GLI-induced transcripts within GLI-expressing tumors in vivo indicates that oncogene-specific transcriptional profiles may be useful diagnostic tools for analysis of human tumors.

Relative validation of a food frequency questionnaire to assess dietary fatty acid intake / Validación relativa de un cuestionario de frecuencia de alimentos para evaluar la ingesta dietaria de ácido graso

OBJECTIVES: This study aimed to develop and validate a Food Frequency Questionnaire (FFQ) for assessing consumption of fatty acids among pregnant women. METHODS: Two lists of foods were created according to percent contribution of each nutrient estimated by three 24-hour recalls: a long and short version FFQ to estimate long-chain polyunsaturated fatty acids (LCPUFAs). Student paired t-test and Pearson correlation coefficients were used to verify the differences in mean consumption of nutrients from the FFQ and 24-hour recall. The concordance between the consumption values of the two methods was assessed using the Bland-Altman method and quartiles concordance. RESULTS: For the FFQ - long version, correlation values ranged from 0.33 (<0.05) to 0.62 (<0.01) for docosahexaenoic acid (DHA) and linoleic acid (LA), respectively. Eicosapentaenoic acid (EPA) and docosapentaenoic acid (DPA) were not correlated. Exact concordance ranged from 49.0% (energy) to 22.4% (EPA), and discordance ranged from 14.3% (DPA) to 2.0% (Saturated). The FFQ - short version had high correlations for LCPUFAs. Exact concordance ranged from 36.7% (n-3 LCPUFA) to 16.3% (DHA); and discordance from 12.2% (DPA) to 2.0% (arachidonic acid). Bland-Altman analysis showed good concordance for both versions. CONCLUSION: This nutrient-specific FFQ is a valid instrument to be used to estimate the level of consumption of fatty acids among pregnant women.

OBJETIVO: Este estudio tuvo como objetivo desarrollar y validar un cuestionario de frecuencia de consumo de alimentos para evaluar el consumo de ácidos grasos en gestantes. MÉTODOS: Dos listas de alimentos fueron creadas de acuerdo con la contribución porcentual de cada nutriente estimado por 3 recordatorios de 24 horas: CFC - versión larga y CFC - versión corta para estimar ácidos grasos poliinsaturados de cadena larga (AGPICL). La prueba de t pareada de Student y el coeficiente de correlación de Pearson se utilizaron para verificar las diferencias entre el consumo medio de nutrientes de del CFC y el recordatorio de 24 horas. La concordancia entre los valores de consumo de los dos métodos se evaluó mediante el método de Bland-Altman y la concordancia de cuartiles. RESULTADOS: En CFC - versión larga, los valores de correlación oscilaron entre 0.33 (<0.05) y 0.62 (<0.01) para ácido docosahexaenoico (DHA) y ácido linoleico (LA), respectivamente. Ácido eicosapentaenoico (EPA) y ácido docosapentaenoico (DPA) no presentaron correlación. La concordancia exacta varió de 49,0% (energía) a 22,4% (EPA), y la discordancia varió de 14,3% (DPA) a 2,0% (saturado). CFC: la versión corta mostró los mejores valores de correlaciones para los AGPICL. La concordancia exacta varió de 36,7 (n-3 LCPUFA) a 16,3% (DHA); y discordancia de 12,2% (DPA) a 2,0% (ácido araquidónico). El análisis de Bland-Altman mostró una buena concordancia para ambas versiones. CONCLUSIÓN: Este método CFC específico de nutrientes es un instrumento válido que se utiliza para estimar el nivel de consumo de ácidos grasos en mujeres gestantes.

Fitting the Balding-Nichols model to forensic databases.

Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how they result from inappropriate implementation of the Balding-Nichols model in the context of database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.

New CODIS core loci allele frequencies for 96,400 Brazilian individuals.

We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

Noninvasive genetic sampling of endangered muriqui (Primates, Atelidae): efficiency of fecal DNA extraction

The muriqui (Brachyteles) is one of the most endangered primates in the world, however little is known about the viability of the remaining populations. We evaluated the technique of extracting DNA from wild muriqui feces for PCR applications. In order to determine the effect of the DNA in subsequent amplifications, we analyzed five different extracts. The importance of the recommended BSA and the HotStarTaq DNA polymerase was tested. The minimal conditions to successfully amplify highly degraded fecal DNA were determined, showing that the recommended reagents are not required. We envision that this method may be useful in further conservation management studies.